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Thursday, 2 April 2020

Probiotics for the prevention of Upper Respiratory Tract infections - a back-of-the-envelope Bradford Hill analysis

“With most people, disbelief in a thing is founded on a blind belief in something else" 
      G. C. Lichtenberg

The Cochrane Collaboration found low-quality evidence that probiotics prevent UTRIs, and moderate-quality evidence that probiotics reduce antibiotic prescriptions for UTRI.
Because the antibiotic finding is most robust (aside from bearing the higher-quality GRADE score, it's also not a self-reported outcome), we'll take this as our baseline and see if it is strengthened or weakened by a Bradford Hill analysis.

1) Strength of association: for antibiotic use, RR 0.65 (0.45 to 0.94), n=1184.[1]
The true association is subject to type 2 confounding by two factors - by intention-to-treat analysis, and potentially by the random consumption of yogurt and other fermented foods supplying similar effects.

2) Consistency of association: the association is consistent, with similar (but slightly larger) effect sizes for all other measures of URTI. The association is reasonably consistent between different trials (there is no major contradiction). The association is strongly consistent with the effects of probiotics on vaccination immunity (RCTs using independently measured serum makers so more robust than the UTRI trials). The association is consistent with results for sambucus (effect size 1.717)
 (see 9, "analogy").[1,2,3,4]

3) Specificity: Probiotics have had no consistent association with several other outcomes predicted for them. Probiotic treatment of mothers during pregnancy only results in better immunity after vaccine for mother, not infant, consistent with dendrite cell pathway for effect.[2]

4) Temporality: Implicit in trial design

5) Biological gradient: dose-reponse is seldom tested in probiotic experiments perhaps because of assumption that a living organism can replicate, however a dose-response for duration of treatment is seen in the vaccine studies.[3] The analogous effect of echinacae purpurea in zebrafish is strongly dose-dependent.[5]

6) Plausibility: effect of probiotic on immune tone is well-studied, insofar as the immune system is currently understood the effect is plausible. Increased innate immunity around infection improves the acquired immune response. "A significant property of these bacteria is their ability to mimic natural infections, while intrinsically possessing mucosal adjuvant properties".[6] Dendrite cell presentation provides plausible pathway.[7]

7) Coherence - laboratory and field work are strongly coherent, animal experiments support human, herbs with similar immune effects to probiotics in experiments tend to have similar associations with URTIs in RCTs.[4]

8) Experiment - the association is experimental, the mechanism holds across a wide range of experiment types, including those with lowest risk of confounding or placebo effect.

9) Analogy - herbal effects are analogous, as when plant polysaccharides mimic bacterial lipopolysaccharides. Vaccine adjuncts are also analogous. Probiotics and herbal antivirals are researched as adjuvants.

Bradford Hill analysis allows us to see an association within its complete scientific context, to test whether it is causal.
It was originally designed to test the low-quality evidence that arises from purely observational, non-interventional studies, but is also useful to test the results of experiments where one considers these inadequate by themselves.

Here's what I think is the parsimonious way to explain the association: In the vaccine research, probiotics double the odds of lasting immunity after vaccination. Many infections are "repeats" of infections we have had before but lost immunity to. If probiotics prevent "repeat" infections by maintaining antibody responses, this can account for the effect, even without a direct effect on immunity to any new pathogen (although this is also plausible).
Immunologists are currently worried that many exposed to COVID-19 have not had a sufficient or lasting antibody response and are at risk of re-infection. The less re-infectious COVID-19 is, the sooner we can safely end our current economic restrictions, which will also take a toll on human life if maintained indefinitely.

1] Cochrane Database of Systematic Reviews. Q Hao, RB Dong, T Wu.
Probiotics for preventing acute upper respiratory tract infections

2] Zimmermann P, Curtis N. The influence of probiotics on vaccine responses - A systematic review.
Vaccine. 2018 Jan 4;36(2):207-213. doi: 10.1016/j.vaccine.2017.08.069. Epub 2017 Sep 18.

3] Lei WT, Shih PC, Liu SJ, Lin CY, Yeh TL. Effect of Probiotics and Prebiotics on Immune Response to Influenza Vaccination in Adults: A Systematic Review and Meta-Analysis of Randomized Controlled Trials. Nutrients. 2017;9(11):1175. Published 2017 Oct 27. doi:10.3390/nu9111175

4] Hawkins J, Baker C, Cherry L, Dunne E. Black elderberry (Sambucus nigra) supplementation effectively treats upper respiratory symptoms: A meta-analysis of randomized, controlled clinical trials. Complement Ther Med. 2019 Feb;42:361-365. doi: 10.1016/j.ctim.2018.12.004. Epub 2018 Dec 18.

5] Guz L, Puk K, Walczak N, Oniszczuk T, Oniszczuk A.
Effect of dietary supplementation with Echinacea purpurea on vaccine efficacy against infection with Flavobacterium columnare in zebrafish (Danio rerio). Pol J Vet Sci. 2014;17(4):583-6.

6] Benef Microbes. 2020 Mar 27:1-14. doi: 10.3920/BM2019.0121. [Epub ahead of print]
Immune modulatory capacity of probiotic lactic acid bacteria and applications in vaccine development.
Mojgani N, Shahali Y, Dadar M.

7] Gallo PM, Gallucci S. The dendritic cell response to classic, emerging, and homeostatic danger signals. Implications for autoimmunity. Front Immunol. 2013;4:138. Published 2013 Jun 10. doi:10.3389/fimmu.2013.00138

Wednesday, 25 March 2020

You can't Boost your Immunity? or, Debunking the COVID-19 Skeptics.

Kate's elderberry concoction, photograph by Hayley Theyers

Is there anything as useless as the professional Skeptic community in a health  crisis? Some people are paid to be roadblocks, others are educated professionals going well outside their lanes after the witches they despise for getting in their lanes at other times, others are just the sort of people who get an existential thrill from negating what they don't understand, or journalists with a "tough" reputation to uphold and a grab-bag of empty rhetoric.
In the history of science no-one has been wrong more often than the skeptic. What we usually call scepticism in the scientific method is just BEING CAREFUL.
"The first principle is that you must not fool yourself and you are the easiest person to fool." Richard P. Feynman
This is nothing like rushing into print with a negative opinion and a few pejoratives on a subject you haven't studied until now so you're either linking to the first blog that agrees with you on an emotional level, instead of looking at the literature, or you're scanning the literature quickly for reasons to dismiss it.

It's far more useful to point to what we DO know. And the first thing to be said, quite clearly, is that you CAN boost your immune system. See the evidence below. And a fast-acting, broad-spectrum immune response is how we get on top of new pathogens.

Straight up, it needs to be stated that COVID-19 is a new virus, with some specific features. Not everything that applies to previous colds, flus, or pneumonial diseases may apply.  So all older evidence needs to be evaluated carefully. But it's not completely new, this isn't smallpox in the New World, it's a nasty variation on the cold viruses we've seen before and the healthiest immune systems can usually react appropriately, as we see when we consider the high rate of mild cases and the low symptom load in the very young. The pattern so far is characteristic of other pandemics; people with no or light symptoms seem to have had a strong initial immune response and are producing antibodies to COVID-19. Here is a COVID-19 immunological case study of a mild infection, which concludes:
“our study indicates that robust multi-factorial immune responses can be elicited to the newly emerged virus SARS-CoV-2 and, similar to the avian H7N9 disease, early adaptive immune responses might correlate with better clinical outcomes.“

In humans, we can test whether a compound (or organism) improves the recognition of new pathogens by giving it with a vaccine.
Consistently, acetaminophen (tylenol, paracetamol) suppresses this function in infants.
Effects are dose- and drug-dependent - low-dose aspirin doesn't impair immunity in elderly given flu vaccine, ibuprofen doesn't impair it compared with paracetamol in infants.
Probiotics enhance it.

We know that probiotics enhance the immune response in vaccinated infants, but we can't take those infants and then expose them to the disease to learn how significant this is - herd immunity means that the risk is low in a vaccinated population even for people whose vaccines didn't work. We can however do this in animals.
Here's an experiment where zebrafish were vaccinated against a bacterial pathogen, Flavobacterium columnare, then bathed in said pathogen, with varying amounts of echinacea purpurea in their diets.
It's a tough test with, you might think, little possibility of a placebo effect.
The first point is that this vaccine doesn't really work. Only 5% of vaccinated fish are surviving exposure to Flavobacterium columnare. But add the echinacea to their feed, and we see survival climb dose-dependently. 5g echinacea per Kg is the same as none - 5% survival. 10g/Kg = 6%. 20g/Kg = 30%. 30g/Kg = 36%.
That link is down at sci-hub, so here is a similar study by the same team - without the vaccine.

You're not going to get ethics approval to try this in humans, so make of this what you can. Firstly, why echinacea? The active ingredient is a polysaccharide, and it likely activates a variety of TLR and NOD receptors much as pathogen lipopolysaccharides do.
Similarly with probiotic cell wall lysates. A company I worked for tested a lysate from a lactobacillus rhamnosus strain many years ago and found it had ligand activity at TLRs 2,4,7,9, and NOD2, which latter is a gamma-interferon pathway.
This is going to enhance the response to a pathogen, which relies on you recognising quickly that it IS a pathogen via PAMPs and DAMPs (q.v.), a signal which compounds with such activity are amplifying.
This is well-known in human vaccine research - such compounds are called adjuvants and play a poorly-understood role in establishing immunodominance (the identification and proliferation of the "right" antibody-producing (B, Th2) immune cell).

Another commonly used herbal supplement, andrographis, has similar adjuvant effects given with vaccines in animal experiments

Elderberry has AFAIK not been tested as an adjuvant but has direct antiviral effects in mice exposed to human influenza A.

So what is the human evidence? Elderberry (sambucus) is effective for seasonal URT infections in a meta-analysis. The studies only add up to n=180, but the effect is large and consistent (you don't need a high-powered study when something has a decent effect - we're not counting crumbs here, there's a loaf on the table).

This is likely due to cytokine effects, and some people might ask "what about cytokine storm?"

Cytokines early in infection are the immune system's alert response. If viral levels are controlled early, there is a lower risk of cytokine storm.
The analogy here is the phase one insulin response, which, if inadequate to manage glucose levels, may be followed by an exaggerated and hyperinsulinaemic phase 2 response.
There is some question as to whether COVID-19 mortality is really due to cytokine storm, as in SARS or swine flu, or due to a direct effect of the virus on the lung, where cells producing pulmonary surfactant (Type II alveolar epithelial cells) are damaged by the virus and reduce normal lung function.

Andrographis is effective for reducing cough.
It has an opposite effect on TNF-alpha from sambucus, so if you are worried that sambucus is too inflammatory use a combined supplement, in my experience these are effective enough for easing the misery and shortening the course of the usual cold and flu.

An AI-type analysis of data found that andrographis suppressed ACE2 expression most; sambucus and the TCM staple astragalus (another adjuvant) were also on the list.

Now, you may not want ACE2 suppressed if you are in extremis. It is a normal feature of lung function, and vitamin D supplementation (25 ug/Kg) increases ACE2 expression but prevents LPS-induced lung injury in this Wistar rat example.
The jury is very much still out on ACE inhibitors (which may increase ACE2 expression) and risk.

However - if you use these medicines, the idea is to use them around exposure, or PRN for symptoms, as advised. If they work, the disease will be less serious, if they don't and you do experience pneumonia you're not going to be taking them in the ICU.
Never keep taking something that makes you feel worse.

Interestingly, echinacea, which is a star in the animal studies, has only weak effects in human trials.
Yet these studies were just as small and had the same potential for bias as the elderberry and andrographis trials. That quite distinct effects or strength of effect appears consistently when different compounds are tested answers the specificity test of a Bradford Hill analysis of the "immune boosting" question. In fact every Bradford Hill criteria is being well-met, whatever the limitations of the human research.

The weak effects of echinacea may be due to its relative fragility and variation as an extract, inadequate dosage, or to the timing of its use as a prophylactic. I use these extracts only when I am either obviously exposed, "coming down with something", or actually sick. My opinion, not necessarily what the science says and just the voice of experience, is that echinacea and elderberry, if good extracts in adequate doses, both work if taken soon enough (elderberry was very effective taken within 24 hours in the swine flu but had no effect when given more than 48 hours after symptoms started). Perhaps echinacea is better for colds and sambucus for flus, but even if that were true COVID-19 is not necessarily playing by all rules. I also use Sanderson's Viramax, a mixed supplement of sambucus, andrographis, echinacea and olive leaf extract when I'm sick for PRN symptom relief, on the basis of past satisfaction with its effects. There is some evidence for olive leaf extract, but the active ingredient seems to be found in extra virgin olive oil.

Apart from herbs and probiotics, what else is there evidence for?

Malnutrition impairs antibody production, obviously, so eat a sensible diet that includes minimally processed animal products, including meat, if you're skeptical about supplements.

Apart from that, it's well worth supplementing selenium (by Brazil nuts or supplements). A pre-2019 coronavirus encoded for 60 selenocysteine residues per core protein. This is a common viral adaptation and protects the stability of the viral genome (a good thing) while depressing host immunity (a bad thing).
Wuhan, Northern Italy, the UK and NZ are all low-selenium areas where deficiency is common. Check the data for your region or county, which is usually available online.

The jury's still out on supplementary vitamin C, and I seemed to stop responding to it when my metabolic health improved, but it's cheap and can't hurt.
Update: high dose vitamin C is being used in New York hospitals.
It's the end of winter in the Northern hemisphere so I'd be supplementing vitamin D3 if I lived there.

Inorganic zinc lozenges (especially zinc acetate) seem to have a role to play here, but may be a lot of trouble to maintain for the duration. It might be worth it depending on your level of risk, as the effect is strong enough.

The spread and virulence of viral infections is in large part a numbers game. Needlestick exposures to HCV had a higher clearance rate than exposures to contaminated blood transfusions. Every line of defense matters, and every proven or even just most-likely barrier to the pathogen establishing dominance over the immune system can be worth investment.

Tuesday, 10 March 2020

The Official COVID-19 protocol from Shanghai, China, in English

This detailed protocol, which appeared online last week on an official Chinese Govt website, includes high-dose Vitamin C within the SOC drug recommendations. So far, when this has been pointed out to anyone in the "evidence-based medicine" community who has been busy online dismissing nutrient protocols for viral illnesses, they have pretended not to notice. Nor does there seem to be any reporting  or discussion in the western mainstream media.
What about prophylaxis? The blood concentrations of vitamin C from IV use are higher than we can get from oral dosing.
I think, if you read the Cochrane reviews of vitamin C for the common cold or pneumonia, there is a clinically significant advantage in high-risk subcategories (people stressed by cold or rigorous exercise for cold, seriously ill elderly for pneumonia). There is heterogeneity in exposure methods, some of which will replicate natural coronavirus exposure better than others. And the general advantages - reduced symptoms and duration - are reductions in COVID-19 transmission factors that could have a meaningful impact at a population level. Read them closely, don't just look for the first limitation that you think might allow you to dismiss a whole body of evidence.
"Nevertheless, given the consistent effect of vitamin C on the duration and severity of colds in the regular supplementation studies, and the low cost and safety, it may be worthwhile for common cold patients to test on an individual basis whether therapeutic vitamin C is beneficial for them."

If you disagree that EBM, for a lot of proponents, stands for emotionally biased medicine, consider this: New Zealand has had to ration acetaminophen (Panadol, Tylenol) prescriptions due to a run on pharmacy stocks.
There is no human RCT of the safety of acetaminophen in pneumonia (we know vitamin C is safe from the Cochrane review), but antipyretics, including acetaminophen, cause a 37% increased risk of mortality in animal models.
Yet there is no EBM push online to warn about this and to mock the people buying or prescribing antipyretics.
EBM - it ought to be essential, it's lovely in theory, yet it seems to be toxic at the level of science communication.

I can't tell you what to do, but here's what I'm doing, besides all the washing and contact common sense stuff - I'm making sure I'm replete in selenium, zinc, retinol, and vitamin D. I'm taking 500mg vitamin C a day. If I start to get ill, I'll take a standardised elderberry extract and a standardised andrographis extract. I may increase the dose of vitamin C.

The Shanghai Protocol, from

[Editor's note] 

On March 1st, the Chinese Journal of Infectious Diseases, which was hosted by the Shanghai Medical Association, pre-published the "Expert Consensus on Comprehensive Treatment of Coronavirus in Shanghai 2019" ( .htm), which has attracted widespread attention in the industry. Shanghai TV also reported on the news last night. This consensus was reached by 30 experts representing the strongest medical force in the treatment of new-type coronavirus pneumonia in Shanghai. Through the research and summary of more than 300 clinical patients, and fully drawing on the treatment experience of colleagues at home and abroad, the "Shanghai Plan" was finally formed. At the end of the article, the list of 30 subject experts (18 writing experts and 12 consulting experts) from various medical institutions in Shanghai is attached.

Corona virus disease 2019 (COVID-19) was first reported on December 31, 2019 in Wuhan, Hubei Province. COVID-19, as a respiratory infectious disease, has been included in the Class B infectious diseases stipulated in the Law of the People's Republic of China on the Prevention and Control of Infectious Diseases and managed as a Class A infectious disease.

With the deepening of understanding of the disease, COVID-19 has accumulated a certain amount of experience in the prevention and control of COVID-19. The Shanghai New Coronary Virus Disease Clinical Treatment Expert Group follows the National New Coronary Virus Pneumonia Diagnosis and Treatment Program and fully draws on the treatment experience of colleagues at home and abroad to improve the success rate of clinical treatment and reduce the mortality rate of patients, prevent the progress of the disease, and gradually reduce the disease The proportion of patients with severe disease improves their clinical prognosis. Based on the continuous optimization and refinement of the treatment plan, expert consensus has been formed on the relevant clinical diagnosis and treatment.

I. Etiology and epidemiological characteristics

2019 novel coronavirus (2019-nCoV) is a new coronavirus belonging to the genus β. On February 11, 2020, the International Committee on Taxonomy of Viruses (ICTV) named the virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Patients with COVID-19 and asymptomatic infection can transmit 2019-nCoV. Respiratory droplet transmission is the main route of transmission and can also be transmitted through contact. There is also the risk of aerosol transmission in confined enclosed spaces. COVID-19 patients can detect 2019-nCoV in stool, urine, and blood; some patients can still test positive for fecal pathogenic nucleic acid after the pathogenic nucleic acid test of respiratory specimens is negative. The crowd is generally susceptible. Children, infants, and young children also develop disease, but the condition is relatively mild.

Clinical characteristics and diagnosis

(A) clinical characteristics

The incubation period is 1 to 14 d, mostly 3 to 7 d, with an average of 6.4 d. Main symptoms are fever, fatigue, and dry cough. May be accompanied by runny nose, sore throat, chest tightness, vomiting and diarrhea. Some patients have mild symptoms, and a few patients have no symptoms or pneumonia.

The elderly and those suffering from basic diseases such as diabetes, hypertension, coronary atherosclerotic heart disease, and extreme obesity tend to develop severe illness after infection. Some patients develop symptoms such as dyspnea within 1 week after the onset of the disease. In severe cases, they can progress to acute respiratory distress syndrome (ARDS) and multiple organ dysfunction. The time to progression to severe illness was approximately 8.5 days. It is worth noting that in the course of severe and critically ill patients, there may be moderate to low fever, even without obvious fever. Most patients have a good prognosis, and deaths are more common in the elderly and those with chronic underlying disease.

The early CT examination showed multiple small patches or ground glass shadows, and the internal texture of the CT scans was thickened in the form of grid cables, which was obvious in the outer lung zone. A few days later, the lesions increased and the scope expanded, showing extensive lungs, multiple ground glass shadows, or infiltrating lesions, some of which showed consolidation of the lungs, often with bronchial inflation signs, and pleural effusions were rare. A small number of patients progressed rapidly, with imaging changes reaching a peak on days 7 to 10 of the course. Typical "white lung" performance is rare. After entering the recovery period, the lesions are reduced, the scope is narrowed, the exudative lesions are absorbed, part of the fiber cable shadow appears, and some patients' lesions can be completely absorbed.

In the early stage of the disease, the total number of white blood cells in the peripheral blood was normal or decreased, and the lymphocyte count was reduced. Some patients may have abnormal liver function, and the levels of lactate dehydrogenase, muscle enzyme, and myoglobin may increase; troponin levels may be increased. Most patients had elevated CRP and ESR levels and normal procalcitonin levels. In severe cases, D-dimer levels are elevated, other coagulation indicators are abnormal, lactic acid levels are elevated, peripheral blood lymphocytes and CD4 + T lymphocytes are progressively reduced, and electrolyte disorders and acid-base imbalances are caused by metabolic alkalosis See more. Elevated levels of inflammatory cytokines (such as IL-6, IL-8, etc.) may occur during the disease progression stage.

(Two) diagnostic criteria

1. Suspected case: Combined with the following epidemiological history and clinical manifestations. Suspected cases were diagnosed as having any one of epidemiological history and meeting any two of the clinical manifestations, or having no clear epidemiological history but meeting three of the clinical manifestations. ① Epidemiological history: travel history or residence history of Wuhan City and surrounding areas, or other communities with case reports within 14 days before the onset; history of contact with 2019-nCoV infection (positive nucleic acid test) within 14 days before the onset ; Patients with fever or respiratory symptoms from Wuhan and surrounding areas or from communities with case reports within 14 days before the onset of the disease; cluster onset. ② Clinical manifestations: fever and / or respiratory symptoms; with the above-mentioned imaging features of the new coronavirus pneumonia; the total number of white blood cells is normal or decreased in the early stage of onset, and the lymphocyte count is reduced.

2. Confirmed cases: Those with one of the following etiology evidence are diagnosed as confirmed cases. ① Real-time fluorescent reverse transcription PCR detected 2019-nCoV nucleic acid positive. ② Viral gene sequencing revealed high homology with the known 2019-nCoV. ③ Except for nasopharyngeal swabs, take sputum as much as possible. Patients undergoing tracheal intubation can collect lower respiratory tract secretions and send viral nucleic acid test positive.

(Three) differential diagnosis

It is mainly distinguished from other known viral pneumonias such as influenza virus, parainfluenza virus, adenovirus, respiratory syncytial virus, rhinovirus, human metapneumovirus, severe acute respiratory syndrome (SARS) coronavirus, etc. , Different from Mycoplasma pneumoniae, Chlamydia pneumonia and bacterial pneumonia. In addition, it must be distinguished from non-infectious diseases such as pulmonary interstitial lesions and organizing pneumonia caused by connective tissue diseases such as vasculitis and dermatomyositis.

(Four) clinical classification

1. Mild: The clinical symptoms are slight, and no pneumonia manifestations on imaging examination.

2. Ordinary type: fever, respiratory tract symptoms, etc. Pneumonia manifestations on imaging examination.

Early warning of severe cases of common patients should be strengthened. Based on current clinical studies, elderly (aged> 65 years) with underlying diseases, CD4 + T lymphocyte count <250 2="" 3="" and="" blood="" days="" found="" il-6="" imaging="" increased="" lesions="" levels="" lung="" on="" progress="" significant="" significantly="" to="" were="">50 %, lactic dehydrogenase (LDH)> 2 times the upper limit of normal value, blood lactic acid ≥ 3 mmol / L, metabolic alkalosis, etc. are all early warning indicators of severe disease.

3. Heavy: Any one of the following. ① Shortness of breath, respiratory rate ≥ 30 times / min; ② In resting state, arterial oxygen saturation (SaO2) ≤ 93%; ③ arterial partial pressure of oxygen, PaO2) / fraction of inspired oxygen (FiO2) ≤ 300 mmHg (1 mmHg = 0.133 kPa). At high altitudes (above 1 000 m), PaO2 / FiO2 should be corrected according to the following formula: PaO2 / FiO2 × [Atmospheric Pressure (mmHg) / 760].

Pulmonary imaging examination showed that the lesions progressed significantly within 24 to 48 hours, and those with more than 50% of the lesions were managed as severe.

4. Dangerous: A person who meets any of the following conditions can be judged as critical. ① Respiratory failure occurs and requires mechanical ventilation; ② Shock occurs; ③ Combined with other organ failure, ICU monitoring and treatment is required.

(5) Clinical monitoring

The patient's clinical manifestations, vital signs, fluid volume, gastrointestinal function and mental state are monitored daily.

All patients were dynamically monitored for terminal blood oxygen saturation. For critically ill and critically ill patients, timely blood gas analysis is performed according to the changes in the condition; blood routine, electrolytes, CRP, procalcitonin, LDH, blood coagulation function indicators, blood lactic acid, etc. are tested at least once every 2 days; liver function, kidney function , ESR, IL-6, IL-8, lymphocyte subsets, at least once every 3 days; chest imaging examination, usually every 2 days. For patients with ARDS, routine ultrasound examination of the heart and lungs at the bedside is recommended to observe extravascular lung water and cardiac parameters. For monitoring of extracorporeal membrane oxygenation (ECMO) patients, refer to the implementation section of ECMO.

Treatment plan

(A) antiviral treatment

You can try hydroxychloroquine sulfate or chloroquine phosphate, or Abidol for oral administration, interferon nebulization and inhalation, interferon κ is preferred, and interferon α recommended by the national scheme can also be applied. It is not recommended to use 3 or more antivirals at the same time. The viral nucleic acid should be stopped in time after it becomes negative. The efficacy of all antiviral drugs remains to be evaluated in further clinical studies.

For patients with severe and critical viral nucleic acid positives, recovery patients can be tested for recovery plasma. For detailed operation and management of adverse reactions, please refer to the "Clinical Treatment Program for Recovery of New Coronary Pneumonia Patients During Recovery Period" (trial version 1). Infusion within 14 days of the onset may be more effective. If the viral nucleic acid is continuously detected at the later stage of the disease, the recovery period of plasma treatment can also be tried.

(Two) treatment of light and ordinary patients

Supportive treatment needs to be strengthened to ensure sufficient heat; pay attention to water and electrolyte balance to maintain internal environment stability; closely monitor patient vital signs and finger oxygen saturation. Give effective oxygen therapy in time. Antibacterials and glucocorticoids are not used in principle. The patient's condition needs to be closely monitored. If the disease progresses significantly and there is a risk of turning into severe, it is recommended to take comprehensive measures to prevent the disease from progressing to severe. Low-dose short-course glucocorticoids can be used with caution (see the application section of glucocorticoids for specific protocols) ). Heparin anticoagulation and high-dose vitamin C are recommended. Low-molecular-weight heparin 1 to 2 per day, continued until the patient's D-dimer level returned to normal. Once fibrinogen degradation product (FDP) ≥10 µg / mL and / or D-dimer ≥5 μg / mL, switch to unfractionated heparin. Vitamin C is administered at a dose of 50 to 100 mg / kg per day, and the continuous use time is aimed at a significant improvement in the oxygenation index. If lung lesions progress, it is recommended to apply a large-dose broad-spectrum protease inhibitor, ulinastatin, at 600 to 1 million units / day until the pulmonary imaging examination improves. In the event of a "cytokine storm", intermittent short veno-venuous hemofiltration (ISVVH) is recommended.

(III) Organ function supportive treatment for severe and critically ill patients

1. Protection and maintenance of circulatory function: implement the principle of early active controlled fluid replacement. It is recommended to evaluate the effective volume and initiate fluid therapy as soon as possible after admission. Severe patients can choose intravenous or transcolonic fluid resuscitation depending on the conditions. The preferred supplement is lactated Ringer's solution. Regarding vasoactive drugs, noradrenaline and dopamine are recommended to maintain vascular tone and increase cardiac output. For patients with shock, norepinephrine is the first choice. It is recommended to start low-dose vasoactive drugs at the same time as fluid resuscitation to maintain circulation stability and avoid excessive fluid infusion. Cardioprotective drugs are recommended for severe and critically ill patients, and sedative drugs that inhibit the heart are avoided as much as possible. For patients with sinus bradycardia, isoprenaline can be used. For patients with sinus rhythm, a heart rate of <50 80="" about="" and="" at="" beats="" dopamine="" font="" heart="" hemodynamic="" instability="" intravenous="" is="" isoproterenol="" low-dose="" maintain="" min.="" min="" of="" or="" pumping="" rate="" recommended="" the="" to="">

2. Reduce pulmonary interstitial inflammation: 2019-nCoV leads to severe pulmonary interstitial lesions that can cause pulmonary function deterioration. It is recommended to use a large dose of a broad-spectrum protease inhibitor ulinastatin.

3. Protection of renal function: Reasonable anticoagulant therapy and appropriate fluid therapy are recommended as soon as possible. See chapter "Cytokine storm" for prevention, protection and maintenance of circulatory function.

4. Protection of intestinal function: Prebiotics can be used to improve the intestinal microecology of patients. Use raw rhubarb (15-20 g plus 150 ml warm boiling water) or Dachengqi decoction for oral administration or enema.

5. Nutritional support: parenteral nutrition is preferred, via nasal feeding or via jejunum. The whole protein nutrient preparation is preferred, and the energy is 25 to 35 kcal / kg (1 kcal = 4.184 kJ) per day.

6. Prevention and treatment of cytokine storm: It is recommended to use large doses of vitamin C and unfractionated heparin. Large doses of vitamin C are injected intravenously at a dose of 100 to 200 mg / kg per day. The duration of continuous use is to significantly improve the oxygenation index. It is recommended to use large doses. Dose of the broad-spectrum protease inhibitor ulinastatin, given 1.6 million units, once every 8 h, under mechanical ventilation, when the oxygenation index> 300 mmHg can be reduced to 1 million units / d. Anticoagulation The treatment protects endothelial cells and reduces the release of cytokines. When FDP ≥ 10 µg / mL and / or D-dimer ≥ 5 μg / mL, anticoagulation is given to unfractionated heparin (3 to 15 IU / kg per hour). Heparin is used for the first time. The patient's coagulation function and platelets must be re-examined 4 h later. ISVVH is used for 6 to 10 h every day.

7. Sedation and artificial hibernation: Patients undergoing mechanical ventilation or receiving ECMO need to be sedated on the basis of analgesia. For patients with severe man-machine confrontation during the establishment of an artificial airway, short-term application of low-dose muscle relaxants is recommended. Hibernation therapy is recommended for severe patients with oxygenation index < 200 mmHg. Artificial hibernation therapy can reduce the body's metabolism and oxygen consumption, and at the same time dilate the pulmonary blood vessels to significantly improve oxygenation. It is recommended to use continuous intravenous bolus medication, and the patient's blood pressure should be closely monitored. Use opioids and dexmedetomidine with caution. Because severely ill patients often have elevated IL-6 levels and easily cause abdominal distension, opioids should be avoided; 2019-nCoV can still inhibit sinus node function and cause sinus bradycardia, so it should be used with caution on Inhibitory sedatives. In order to prevent the occurrence and exacerbation of lung infections, and to avoid prolonged excessive sedation, try to withdraw muscle relaxants as soon as possible. It is recommended to monitor the depth of sedation closely.

8. Oxygen therapy and respiratory support: ① nasal cannula or mask oxygen therapy, SaO2 ≤93% under resting air condition, or SaO2 < 90% after activity, or oxygenation index (PaO2 / FiO2) 200-300 mmHg; With or without respiratory distress; continuous oxygen therapy is recommended. ② High-flow nasal cannula oxygen therapy (HFNC), receiving nasal cannula or mask oxygen therapy for 1-2 hours, oxygenation fails to meet treatment requirements, and respiratory distress does not improve; or hypoxemia during treatment And / or exacerbation of respiratory distress; or an oxygenation index of 150 to 200 mmHg; HFNC is recommended. ③ Noninvasive positive pressure ventilation (NPPV), receiving 1 to 2 h of HFNC oxygenation does not achieve the treatment effect, and there is no improvement in respiratory distress; or hypoxemia and / or exacerbation of respiratory distress during treatment; or When the oxygenation index is 150 ~ 200 mmHg; NPPV can be selected. ④ Invasive mechanical ventilation, HFNC or NPPV treatment does not meet the treatment requirements for 1 to 2 hours of oxygenation, and respiratory distress does not improve; or hypoxemia and / or exacerbation of respiratory distress during treatment; or oxygenation index <150 a="" are="" as="" be="" body="" considered.="" core="" font="" ideal="" invasive="" kg="" mass="" ml="" mmhg="" preferred.="" protective="" should="" small="" strategies="" the="" tidal="" ventilation="" volume="" with="">

9. Implementation of ECMO: Those who meet one of the following conditions may consider implementing ECMO. ① PaO2 / FiO2 < 50 mmHg for more than 1 h; ② PaO2 / FiO2 < 80 mmHg for more than 2 h; ③ Arterial blood pH < 7.25 with PaCO2 > 60 mmHg for more than 6 h. ECMO mode is preferred for intravenous-venous ECMO.

(4) Special problems and treatment in treatment

1. Application of glucocorticoids: Use glucocorticoids with caution. Imaging showed significant progress in pneumonia. Patients with SaO2 ≤ 93% or shortness of breath (respiratory frequency ≥ 30 breaths / min) or oxygenation index ≤ 300 mmHg in the state of no oxygen inhalation. Glucocorticoids can be added at the risk of intubation. Patients are advised to withdraw promptly from glucocorticoid use when intubation or ECMO support can maintain effective blood oxygen concentrations. For non-severe patients using methylprednisolone, the recommended dose is controlled at 20 to 40 mg / d, severe patients are controlled at 40 to 80 mg / d, and the course of treatment is generally 3 to 6 days. Can be increased or decreased according to the body weight.

2. Use of immunoregulatory drugs: Subcutaneous injection of thymosin 2 to 3 times per week has certain effects on improving patients' immune function, preventing the disease from becoming worse, and shortening the time of detoxification. Due to the lack of specific antibodies, high-dose intravenous immunoglobulin therapy is currently not supported. However, some patients have low levels of lymphocytes and the risk of co-infection with other viruses. Human immunoglobulin can be infused intravenously at 10 g / d for 3 to 5 days.

3. Accurate diagnosis and treatment of combined bacterial and fungal infections: clinical microbiological monitoring of all severe and critically ill patients. The sputum and urine of the patients are kept daily for culture, and the patients with high fever should be cultured in time. All patients with suspected sepsis who have indwelling vascular catheters should be sent for peripheral venous blood culture and catheter blood culture at the same time. All patients with suspected sepsis may consider collecting peripheral blood for molecular diagnostic tests for etiology, including PCR-based molecular biology testing and next-generation sequencing.

Elevated procalcitonin levels have implications for the diagnosis of sepsis / septic shock. When patients with new type of coronavirus pneumonia get worse, there is an increase in the level of CRP, which is not specific for the diagnosis of sepsis caused by bacterial and fungal infections.

Critically ill patients with open airways are often prone to bacterial and fungal infections at a later stage. If sepsis occurs, empirical anti-infective treatment should be given as soon as possible. For patients with septic shock, empirical antibacterial drugs can be used in combination before obtaining an etiological diagnosis, while covering the most common Enterobacteriaceae, Staphylococcus and Enterococcus infections. Patients with infection after hospitalization can choose β-lactamase inhibitor complex. If the treatment effect is not good, or the patient has severe septic shock, it can be replaced with carbapenem drugs. If considering enterococci and staphylococcal infections, glycopeptide drugs (vancomycin) can be added for empirical treatment. Daptomycin can be used for bloodstream infections, and linezolid can be used for lung infections. Attention should be paid to catheter-related infections in critically ill patients, and treatment should be empirically covered with methicillin-resistant staphylococci. Glycopeptide drugs (vancomycin) can be used for empirical treatment. Candida infection is also more common in critically ill patients. Candida should be covered empirically when necessary. Echinocin drugs can be added. With the length of hospitalization of critically ill patients, drug-resistant infections have gradually increased. At this time, the use of antibacterial drugs must be adjusted according to drug sensitivity tests.

4. Nosocomial infection prevention and control: ① In accordance with the Basic System for Infection Prevention and Control of Medical Institutions (Trial) of the National Health and Health Commission in 2019, actively implement evidence-based infection prevention and control clustering intervention strategies to effectively prevent ventilator-related pneumonia and intravascular Multidrug-resistant bacteria and fungal infections such as catheter-related bloodstream infections, catheter-related urinary tract infections, carbapenem-resistant gram-negative bacilli. ② Strictly follow the National Health and Health Commission's "Technical Guide for the Prevention and Control of New Coronavirus Infection in Medical Institutions (First Edition)", "Guidelines for the Use of Common Medical Protective Products in the Prevention and Control of Pneumonitis Due to New Coronavirus (Trial)" During the epidemic period, the technical guidelines for protection of medical personnel (trial implementation), strengthened process management, correctly selected and used personal protective equipment such as masks, gowns, protective clothing, eye masks, protective masks, gloves, and strict implementation of various disinfection and isolation measures Minimize the risk of nosocomial infections and prevent 2019-nCoV infections in hospitals by medical staff.

5. Treatment of infants and young children: Only mild symptomatic oral treatment is needed for mild children. In addition to symptomatic oral administration for children with common type, treatment with syndrome differentiation can be considered. If combined with bacterial infection, antibacterial drugs can be added. Severely ill children are mainly symptomatic and supportive treatment. Ribavirin injection was given antiviral therapy empirically at 15 mg / kg (2 times / day). The course of treatment did not exceed 5 days.

(V) Treatment plan of integrated traditional Chinese and western medicine

The combination of traditional Chinese and western medicine for the treatment of new coronavirus pneumonia can improve the synergistic effect. For adult patients, the condition can be improved through TCM syndrome differentiation. For light patients, those with a syndrome of wind-heat type are given the traditional Chinese medicine Yinqiaosan plus and minus treatment; those with gastrointestinal symptoms and those with damp-wetting and yang-type syndrome are given the addition and subtraction of Zhipu Xialing Decoction and Sanren Decoction. For ordinary patients, those with syndromes of hot and evil stagnation of lungs can be treated with Chinese medicine Ma Xing Shi Gan Decoction; those with syndromes of dampness and stagnation of lungs can be treated with traditional Chinese medicine Da Yuan Yin, Gan Lu Fang Dan, etc., which can be controlled to some extent Progression of the disease, reducing the occurrence of common to severe; for anorexia, nausea, bloating, fatigue, anxiety and insomnia, the addition and subtraction of Chinese medicine Xiao Chai Hu Tang can significantly improve symptoms. For severe patients, if the fever persists, or even the high fever, bloating, and dry stools are closed, and those who are heat-tolerant and the lungs are closed, give the Chinese medicine Dachengqi Decoction enema to relieve fever or reduce fever, or use Chinese medicine. The treatment of Baihu Decoction, Shengjiang San and Xuanbai Chengqi Decoction were added and subtracted to cut off the condition and reduce the occurrence of heavy to critical illness. Children with light patients, when the disease belongs to the defender, can be added or subtracted from Yinqiaosan or Xiangsusan. Ordinary children, those with damp heat and closed lungs, are given Ma Xing Shi Gan Decoction and Sanren Decoction; those with moderate scorching dampness and heat such as bloating and vomiting with abdominal distension can be added or subtracted without changing Jinzhengqi San. For severe patients with epidemic and closed lung (currently rare in the country), please refer to adult Xuanbai Chengqi Decoction and Manna Disinfection Danjiao; if the poison is hot, the gas can't pass, and the medicines are not good, the Rhubarb Decoction is given to enema for emergency.

(6) Discharge standards

Patients who meet the following conditions at the same time can be considered for discharge: ①The body temperature returns to normal > 3 d; ②Respiratory symptoms are significantly improved; ③ Imaging examination of the lungs shows that the acute exudative lesions are significantly improved; At least 1 d); ⑤ After the nucleic acid test of the respiratory specimen is negative, the fecal pathogen nucleic acid test is also negative; ⑥ The total disease course exceeds 2 weeks.

(VII) Health management of discharged patients

1. For discharged patients, close follow-up is still required. Follow-up is recommended from 2 weeks and 4 weeks after discharge to the designated follow-up clinic.

2. When the patient is discharged from the hospital, the place of residence and address in the city should be specified.

3. Patients should rest at home for 2 weeks after leaving the hospital, avoid activities in public places, and must wear masks when going out.

4. According to the patient's address (including hotel or hotel), the relevant district health and health committee will organize the corresponding medical institution to do a good job of health management. Professionals will visit the patient's temperature twice a day for 2 weeks, ask their health status, and carry out related health education.

5. If fever and / or respiratory symptoms recur, the corresponding medical institution shall report to the District Health and Health Commission and the District Centers for Disease Control and Prevention in a timely manner, and assist in sending them to the designated medical institution in the area for treatment.

6. After receiving the report, the District Health and Health Committee and the District Centers for Disease Control and Prevention report to the superior department in a timely manner.

Thursday, 22 August 2019

Gene-diet interactions and the risk of colorectal cancer

There's nothing like a bit of cognitive dissonance to get the brain working if you steel yourself against the instinct to invoke protective stupidity. It's much like Marx's internal stresses of capitalism (or communism for that matter), awareness of contradictions may be the birth-pangs of the next state of existence/awareness, or it may just be the subconscious motivation for repression and consequent dysfunction (it's uncanny how Marxist and Freudian terminologies overlap here, but I digress).

When you join the keto cult, first you have to overcome cognitive dissonance just to entertain the idea that eating high fat can do you some good, and try it. God knows that's hard enough, well done everyone. But that's the beta effect (short term results); what about the alpha effects, i.e. longevity and disease resistance? We know risk markers improve, and why do we have risk markers? Because doctors prefer to diagnose diseases from blood tests, and not your stories about what you had for dinner. Your lipids, BP. HbA1c are measured with considerably more accuracy that saturated fat ever was in any FFQ, so if you have to trust epidemiology trust biomarker epidemiology, and get with the lipid triad and LMHR news over at

And as for saturated fat and cardiovascular disease in epidemiology, read em and weep saturophobes - latest, biggest meta-analysis the other month, very good methodology, and SFA is beginning to look just a little bit protective.[1]

Cancer though - doesn't that have a biodiversity that's harder to predict than a metabolic disease? Well, most of the common cancers, including colorectal cancer, have a very strong, Bradford Hill strong, association with hyperinsulinaemia (and/or the IGF1/IGFBP3 axis), and we've taken care of that. But still - you read papers where processed meat (way too heterogenous a set of stuff to combine as if it were homogenous, but nutrition epidemiology is what it is, a very blurry snapshot that you need to squint at hard to see anything at all really) is mildly associated with CRC but unprocessed meat isn't, or vice versa, or only in one sex, or in the other, etc etc etc and wonder if there still could be anything in it.
If nothing else, it's good for refuting accusations of orthorexia,

One tool I've found recently that seems to let you look a bit more closely at the murk is the epidemiology of gene-diet interactions. It still doesn't tell you if residual confounding is at play, but it does let you see the spread of association in a population and can help to validate plausible mechanisms, another Bradford Hill criteria. One thing that impresses me is that it's rather full of null results. Dietary patterns are baloney, so they have no interaction with any genes associated with BMI in this Chinese-Singaporean population, (study pulled at random, fairly typical so far of this sort of question). Interestingly there's an interaction with cholesterol, which seems like the opposite of what's happened in the West, maybe just the diets of the wealthy in Singapore, but there it is.[2]

So anyway, to the subject in hand - I looked up gene-diet interactions for CRC and it turns out processed meat (I know, I know) is the only one in this large pooled case-control study.
Genome-Wide Diet-Gene Interaction Analyses for Risk of Colorectal Cancer.[3]

 Our results provide strong evidence for a gene-diet interaction and colorectal cancer risk between a genetic variant (rs4143094) on chromosome 10p14 near the gene GATA3 and processed meat consumption (p = 8.7E-09).

Now, this gene has nothing to do with nitrate metabolism as far as I can see - it seems to be a cell proliferation gene. So we could still be seeing residual confounding, because there's no absolute way to adjust for the huge effect of hyperinsulinaemia on this cancer and processed meat is what you have on a pizza or in a sandwich. And the people who clean up chemical spills for you are unlikely to be vegan and/or rich, so processed meat is kind of their thing. But still.

The study wasn't designed to implicate carbs, by the way (but the fibre results will be interesting)

In this large combined analysis using GECCO from 10 case-control and nested cohort studies comprising 9,287 colorectal cancer cases and 9,120 controls, we build upon these previous reports [13], [14] to examine over 2.7 million common polymorphisms for multiplicative interactions with selected dietary factors (red meat, processed meat, fiber, fruit and vegetables) and risk of colorectal cancer.

Of the 7 studies listed here, the association goes the other way in 2 - NHS and HPFS. This helps to validate it according to my bias, which is that NHS and HPFS are the last place to look if you want results that correspond to reality.
If, on the other hand, you love Harvard epidemiology, then eat more bacon (I know, I know).

There are 3 significant loci and they all have positive interactions. Nothing good.

And here's the spread. This stuff interests me:

Stratified by genotype, the risk for colorectal cancer associated with each increasing quartile of processed meat was increased in individuals with the rs4143094-TG and -TT genotypes (OR = 1.20, 95% CI = 1.13–1.26 and OR = 1.39, 95% CI = 1.22–1.59, respectively) and null in individuals with the rs4143096-GG genotype (OR = 1.03, 95% CI = 0.98–1.07, Table 2). Results are very similar for minimal and multivariable adjusted ORs.

Only 6% of these populations had TT, most people had GG. So all the risk is in one corner. (you could get tested for this these days, but who knows what other genetic factors also influence it at the personal level).

What about red meat etc?

With the other dietary factors evaluated, no interactions using the conventional case-control logistic regression analysis reached the genome-wide significance threshold.

So I dug down into the supplementary data and found this amazing table.

 If you have the most significant interactive allele for red meat, you get a 10% higher cancer risk if you don't eat enough. If you have one of the other 2, you get an 11% increased risk from too much.
And look at fibre - it's pretty much the same.
This helps to explain the Polyp Prevention Trial, doesn't it?[4]
I've long suspected that something like this goes on - that null or near-null results can disguise a mild 2-tailed effect - a little extra harm in one corner of the population and a similar-sized protective effect in another.
If any of this is real - insulin is, as always, the elephant in the room, as are the true carcinogens, which you'll find in the storeroom. But surely it has a bit more validity than the naked FFQ epidemiology it's based on?

Anyway, this seems like a useful reality check, and there are others - does the epidemiology of bowel movements support the motility part of the fibre hypothesis? Not really.[5] Does the epidemiology of aspirin (a drug that notoriously leaches blood into the gut, even when vegans take it) support the heme iron hypothesis? Not really.[6] Maybe this seems like nonsense to some, but if people want to draw drastic conclusions from FFQ epidemiology, they need to get outside the box more.

Oh, and why do people want to draw drastic conclusions from FFQ epidemiology anyway?
Adam Curtis has the best take on how this happened here.

[1] Zhu Y, Bo Y, Liu Y. Dietary total fat, fatty acids intake, and risk of cardiovascular disease: a dose-response meta-analysis of cohort studies. Lipids Health Dis. 2019;18(1):91. Published 2019 Apr 6. doi:10.1186/s12944-019-1035-2

[2] Chang X, Dorajoo R, Sun Y, et al. Gene-diet interaction effects on BMI levels in the Singapore Chinese population. Nutr J. 2018;17(1):31. Published 2018 Feb 24. doi:10.1186/s12937-018-0340-3

[3] Figueiredo JC, Hsu L, Hutter CM, et al. Genome-wide diet-gene interaction analyses for risk of colorectal cancer. PLoS Genet. 2014;10(4):e1004228. Published 2014 Apr 17. doi:10.1371/journal.pgen.1004228

Schatzkin A, Lanza E, Corle D, Lance P, Iber F, Caan B, Shike M, Weissfeld J, Burt R, Cooper MR, Kikendall JW, Cahill J. Polyp Prevention Trial Study Group.

Lack of effect of a low-fat, high-fiber diet on the recurrence of colorectal adenomas. N Engl J Med. 2000 Apr 20;342(16):1149-55.

[5] Kojima M, Wakai K, Tokudome S, et al. Bowel movement frequency and risk of colorectal cancer in a large cohort study of Japanese men and women. Br J Cancer. 2004;90(7):1397–1401. doi:10.1038/sj.bjc.6601735

[6] Qiao Y, Yang T, Gan Y, et al. Associations between aspirin use and the risk of cancers: a meta-analysis of observational studies. BMC Cancer. 2018;18(1):288. Published 2018 Mar 13. doi:10.1186/s12885-018-4156-5

Saturday, 23 February 2019

Why the High-Fat Hep C Diet? Rationale and n=1 results.

[pinned post hence the unusual date]

I originally started this blog to publicise the hypothesis that a diet low in carbohydrate and linoleic acid, but high in saturated fat and long-chain PUFA, will inhibit HCV replication.

The blog header with the pig above is the abstract for this hypothesis.

I first worked this out in 2010 after reading Dr Atkins New Diet Revolution while studying HCV replication. The lipid patterns in low-carb dieters - low TG and VLDL, high HDL, normal or high LDL - are those associated with lower viral load and improved response to treatment in HCV cases.
The mechanics of HCV replication and infection support this link.

HCV inhibits PPAR-a, a ketogenic diet reverses this inhibition

I wrote a fairly comprehensive version of the hypothesis in 2012:

Recently I was sent a link to an article that cited this paper: and the hepatic lipid pathway as a potential treatment target. Bassendine MF, Sheridan DA , Felmlee DJ, et al. Journal of Hepatology 2011 vol. 55 j 1428–1440

This review compiles a great deal of supporting evidence regarding the interaction between HCV and lipids, and between lipids and HCV. The only thing missing is the role of carbohydrate. It mentions multiple lipid synthetic pathways as targets for indirect-acting antiviral drugs (IDAA), pathways which are also well documented as targets of low carbohydrate ketogenic diets, or of saturated fat in the diet (in the case of the LDL-receptor complex).

From 2012:
A little n=1 experimental data; 4 years ago (2008) my viral load was 400,000 units, now after 2 years of low carb dieting and intermittent mild ketosis (2012) it is 26,000.

Later in 2012:
Total Cholesterol:  6.7  H     
Triglyceride:          0.8         
HDL:                     1.63              (63.57)
LDL (calc.)            4.7   H    
Chol/HDL ratio:     4.1          

HCV viral load on this day (21st May 2012): 60,690 IU/mL (4.78 log)

Lipid panel from 07 Feb 2012, during ketogenic diet phase (non-fasting)

Total Cholesterol: 8.9   HH  (347.1)
Triglyceride:         1.3          (115.7)
HDL:                    1.65         (64.35)
LDL (calc):           6.7    H    (261.3)
Chol/HDL ratio:     5.4   H

HCV viral load on this day: 25,704 IU/mL (4.41 log)

From 2014:
On a personal note, I have started an 8-week trial of Sofosbuvir and GS-5816 (Vulcan). It is day 11 and it seems tolerable so far.
A pre-trial blood test on 22nd October was normal except for these counts:
AST 74
ALT 174

and viral load was 600,419 (log 5.78), counts consistent with the tests I've had done this last year.

But the day the trial started, 18th November, before my first dose, things were different:
AST 21

ALT 32
Viral load 27,167 (log 4.43)

The low viral load is easy to explain; I get a consistent 1 log drop (to 14,000-60,000*) when I try to eat very low carb (50g/day or lower) and an elevation to 400-600,000 when my carbohydrate intake is over 50g/day. When I ate very high carb (but took antioxidant supps) it was as high as it was on 22nd October. So for me the tipping point seems to be where ketosis begins, and other variations don't have much effect; it's an on/off switch, not a dial (and the name of that switch is PPAR-alpha).
[edit: though the very low scores are at ketogenic, or nearly so, carb intakes, the exact increase in carbohydrate needed to cause a significant increase in viral load seemed to vary]
(I do however, according to CAPSCAN elastography, have zero excess fat in my liver, which is an effect of low carb in general, as well as avoiding vegetable seed oils).

My belief is that my viral load was much higher than any of these counts previous to 2003. This was the year I started taking antioxidant supplements, eating a bit better (in a normal, confused "healthy eating" pattern), and using herbal antivirals like silybin. Prior to that I was seriously ill, and I believe that my viral load would have reflected my extra autoimmune symptoms, signs of liver failure, and elevated enzymes. Unfortunately in those days one didn't get a PCR unless one was considering donating one's body to interferon, which I was not.

* I don't seem to have a record of the date of the 14,000 VL reading, but will include it when I find it.

A very low carbohydrate ketogenic diet, without enough PUFA to lower LDL artificially, had a significant inhibitory effect on HCV viraemia in my case.
Effective DAA drugs for HCV infection are now available. There is a ~98% SVR rate at present. These drugs are expensive, they sometimes have side effects (though much less so than interferon + ribavirin), and interferon + ribavirin is still being used.
If my results are more generally applicable, VLCKD diet offers an adjunct therapy for patients with a high viral load, steatosis that relates to diet and lifestyle as well as HCV infection, or a need to postpone treatment. In people who oppose or cannot complete or afford treatment, it offers a way to manage the disease, and in particular to reverse the autoimmune syndromes caused by immune complexes when viraemia is excessive.

Tuesday, 19 February 2019

Two important new papers on climate change.

Whad'ya mean, this has to last me a year?

People in the LCHF community can be resistant to considering climate change and greenhouse gas levels because this argument can be used to shift the goalposts in a clumsy, overt fashion in order to sidestep the evidence on health and keep everyone eating nutrient-poor diets.
Our critics even use these manufactured opportunities to resuscitate their zombie saturated fat and TMAO hypotheses, knowing that most of the audience for ecological debates has no clue how intellectually bankrupt and scientifically desperate these arguments are and have been for some time.
So people can be forgiven for both hiding their heads in the sand and distrusting all "consensus" authority - in our specific area of health, consensus authority has been damagingly wrong for many people's entire
 lifetimes. And ironically some of this wrongness, the saturated fat question, has contributed to global warming - we'll discuss how later.

However, I for one believe in keeping a close eye on existential threats, and whether you see climate change as a threat to your access to a diet that will keep you healthy, or merely as a threat to the future of human existence on this planet, I think you should too.
Don't listen to headlines, certainly don't listen to the dodgy and ideologically skewed EAT-Lancet commision, but do listen out for the people doing the hard work; the people working out how we should most accurately measure the things that the usual suspects want us to think were measured most accurately back when the results were more favourable to them.
And try to understand the systems involved.

There are essentially two - the usual cycling of carbon through plants and animals back into the atmosphere, which has shaped our climate through most of our history, with fluctuations due to  deforestation and reforestation that mattered (as we shall see) yet did not wipe out life on Earth.
And then there is the geological cycle - carbon from Earth's hothouse youth slowly trapped under the crust as fossil hydrocarbons, which make excellent fuel.
The system of free trade and free travel that fossil fuels allow has replaced warfare since WW2 for most of the world's countries; but it is a potlatch peace, dependent on wasteful gestures, firstly the making and transportation of shit that will either be thrown away, or that in most cases could be made closer to home with lower energy costs, in order to keep wages at a level consistent with a desire for peace, and secondly the transportation of people who will stay in herds or on their phones at the world's beauty spots, only visited for the bragging rights, and for something to do instead of making war against the people who live there.

In the ecological cycle, plants sequester CO2 as they grow, though the soil around them, if very fertile, will release methane (CH4) - recently noted with alarm in the Amazon rainforest, as well as in rice paddies.
CO2 in plants is released by forest or grass fires, and by the metabolism of animals that eat them, which also sequester some of the carbon in their bodies during their lives, mainly in stored fat and protein. When plants and animals rot to return nutrients to the soil this can also release methane, as can the fermentation of plants in the gut by bacteria - the bacteria in the foregut of ruminants are great at processing inedible (to us) fibre to energy substrates, so are high producers of methane (which escapes in burps, not farts).

Our first paper looks at the contribution of methane to the warming effect. CH4 is much more warming than CO2. This is why we hear that 51% of NZ's GHG come from agriculture, when the proportionate amount of CH4 released by ruminants compared to fossil fuel CO2 in NZ each year is much smaller than this - because GHG emissions have, till now, been calculated on the warming effect of each gas. However CO2 lasts for hundreds of years; CH4 has a half-life of only 10 years before turning to CO2. Thus, if we are looking at a 10-year GHG emissions target, half the CH4 should be counted as CO2, and the further out we get, the smaller the difference between CH4 and CO2 gets.
The full model is more complex than this, but the gist of it is the mathematical demonstration that GHG as methane is being badly overestimated whenever the calculation is for a long term impact.

Climate mitigation: An improved emission metric 

A new approach allows the temperature forcing of CO2 and short-lived climate pollutants (SLCPs) to be examined under a common cumulative framework. While anthropogenic warming is largely determined by cumulative emissions of CO2, SLCPs—including soot, other aerosols and methane—also play a role. Quantifying their impact on global temperature is, however, distorted by existing methodologies using conventional Global Warming Potentials (GWP) to convert SLCPs to "CO2-equivalent" emissions. A team of international scientists led by Myles Allen at the University of Oxford provide a solution. A modified form of GWP—GWP*, which relates cumulative CO2 emissions with contemporary SLCP emissions—is shown to better represent the future climate forcing of both long- and short-term pollutants. Use of GWP* could improve climate policy design, benefiting mitigation strategies to achieve the Paris Agreement targets.
Dr Michelle Cain explains the meaning of this paper in this twitter thread and this short YouTube video.

You can't get fossil fuels off the hook. The billionaire owners of EAT-Lancet make their money from a hotel chain. No doubt the hotels are eco-friendly and serve vegan meals. But you can't fill hotels without jet aircraft and cars and cruise ships. Without unnecessary travel, that is - because people with sounder reasons to travel tend to stay with family or friends. A successful hotel chain today is a prime symptom of the fossil fuel binge-for-gold mentality that is breaking the planet.

Our second paper looks at the effects of reforestation on the climate after 56 million mesolithic farming peoples died following the colonisation of the New World.[2] It supplies the evidence for an earlier claim that when their disused cropland was overtaken by forest regrowth, the additional retention of CO2 carbon involved in the creation of standing forests caused the Little Ice Age. Animal numbers are not mentioned in the paper but it is extremely unlikely that ruminant numbers in the Americas declined as a result of the tragic deaths, mainly through introduced diseases, 
of much of the human population that hunted them. Any additional methane release during forest regrowth also did not stop the Ice Age.

Again, this paper revises the estimates used in GHG calculations - the retention of carbon in forests was missed before - again a case of early GHG formulas missing the all-important effect of time scaling.

Now, let's do some modelling of our own. It's silly, I admit, but no sillier than anything EAT-Lancet have proposed. We have an obesity epidemic; a 2012 estimate of the extra food needed to maintain that extra weight was, that biomass due to obesity was 3.5 million tonnes, the equivalent of 56 million people of average body mass (1.2% of human biomass globally).[3] In other words, if the obesity epidemic could be entirely reversed, the food savings would be roughly equivalent to the annual food consumption of Australia and Canada combined (minus that of little New Zealand).
The reduction in biomass would also be exactly the same as the population drop that caused the Little Ice Age.

In our model all the weight lost is lost because of a reduction in wheat, corn, rice and sugar consumption, and their cropland is replaced by permanent forest (not forestry). Of course farming today is more intensive, and thus causes more harm to biodiversity, soil health, and marine health, so the total hectarage saved will be less - but we can compensate for that if we also tell people they can eat the fat from the animals they eat instead of soy oil or palm oil. This will reduce demand for the two human foods that most drive deforestation. If palm and soy plantations collapse as a result and the Indonesian and Brazilian rainforest takes back the land, so much the better.
Of course, the Adam Curtis voiceover should be telling you about now, "but it was a fantasy". But it was a fantasy that demonstrates how misguided public health experts and their inability to correct error on the saturated fat question have helped to change the climate. We can afford to eat meat, we just can't afford to keep eating lean meat and avoiding the fat-and-cholesterol rich parts of the animal. We can't afford to keep cooking exclusively with vegetable oil (and then often throwing it away). Keep on crowbarring that rubbish advice into climate change statements and no-one but vegans will ever believe you.


[1] Myles R. Allen, Keith P. Shine, Jan S. Fuglestvedt, Richard J. Millar, Michelle Cain, David J. Frame & Adrian H. Macey. A solution to the misrepresentations of CO2-equivalent emissions of short-lived climate pollutants under ambitious mitigation. NPJ Climate and Atmospheric Science volume 1, Article number: 16 (2018).

[2] Alexander Kocha, Chris Brierley, Mark M.Maslina, Simon L.Lewis. Earth system impacts of the European arrival and Great Dying in the Americas after 1492. Quaternary Science Reviews
Volume 207, 1 March 2019, Pages 13-36.

[3] Walpole SC, Prieto-Merino D, Edwards P, Cleland J, Stevens G, Roberts I. The weight of nations: an estimation of adult human biomass. BMC Public Health. 2012;12:439. Published 2012 Jun 18. doi:10.1186/1471-2458-12-439

Wednesday, 16 January 2019

Don't Drink (oil) and Fry (in the sun) - the link between polyunsaturated vegetable oil and skin cancer

It was good to see this well-researched burst of sunscreen scepticism doing the rounds this (southern) summer - Is Sunscreen the New Margarine? *
I was particularly struck by the unintentionally ironic title, because margarine's role in this story goes well beyond that of a handy analogy for a misguided public health initiative.

When I first read the Nanji and French research - countless rat experiments, consistent with what human epidemiology there was - showing that high PUFA oils potentiated the progression of alcoholic liver disease, were indeed essential fats if one wanted to develop this condition, I replaced the rice bran oil I had been conned into using with beef fat. One of the first things I noticed, being a clumsy cook, was that my skin stopped blistering when I burned myself. At the worst I might get a short-lived patch of dead skin, but I've had about 2 blisters in the 7 years since then and neither became painful. Then gradually I noticed I wasn't getting burnt in the sun as easily. I wasn't big on the sun in those days, but as I got more exposure to sun and less exposure to linoleic acid my resistance grew. I try to limit exposure, using clothes and shelter, to what seems reasonable, having no desire to turn nut-brown and wrinkled in my dotage, but occasionally I've been caught out for far longer than I intended, and no harm has ensued. In part this has been due to a policy of tanning early and often so that the protective pigment is in full effect once the summer reaches its peak, but dietary choice is a critical factor, as we shall see.

The first experiment I came across showing the photosentising effect of linoleic acid was this one (in hairless mice - obviously you can't use a hairy animal) [1];

However, dietary ALA inhibited the increase in erythema score after UVB irradiation compared with LA. The peroxidizability index of the skin total lipids was significantly higher, but UVB-induced prostaglandin E2 (PGE2) production was significantly lower in the group fed an ALA-rich diet compared with the group fed an LA-rich diet. 

There's a lot of this stuff recently, showing that omega-3 fats, and especially the long-chain fish oil ones, are protective - but also that their irradiation puts more strain on the antioxidant defense system, depleting vitamin C and glutathione. The Linus Pauling Institute website has an excellent summary of this research, including human trials, but if you think like me you want to know, is saturated fat protective too? I mean there are people out there exposed to very high UV levels eating not-especially-oily fish and coconut or ghee for generations - are they OK?

The Linus Pauling Institute doesn't tell us, nor does it really warn us about omega-6. The modern idea is just to increase our intake of flaxseed oil and salmon and antioxidant vitamins and minerals. Sounds expensive, for one thing, and I'm not sure our obsession with fish will prove to be sustainable if we're not allowed to eat anything else.

To answer this question we need to go back to the 1990's, when researchers were mostly looking at omega 6 fats and using saturated fats as controls.

We find:

When polyunsaturated fat intake had been increased, tumorigenesis had been exacerbated and a remarkable persistence of immunosuppression remained measurable. There was no difference apparent in the CHS responsiveness in mice fed 20% sunflower oil or saturated fat in the absence of UV irradiation, indicating that the persistent immunosuppression was likely to have been induced by the carcinogenic irradiation regime.[2]

Diet 1 is 20% hydrogenated cottonseed oil, diet 5 is 20% sunflower oil

Now 20% sunflower oil is exactly the kind of exposure you'd get if you replaced other fats with oil in a low fat diet, as the experts want you to. It's an amount of LA that the epidemiologists at Harvard Chan have no problem with, using as they do data collection methods unreliable enough to produce false negatives as well as false positives, and not controlling for UV exposure anyway. Note that the control here - hydrogenated cottonseed oil - is 69.25% trans fat, the rest all SFA.

Here's another, where there are two controls - 12% menhaden oil (basically fish oil) and 0.75% corn oil.[3]
The most interesting finding is that while menhaden oil is protective, crossing over to 12% menhaden oil from 12% corn oil is not; it's about the worst thing you can do; crossing over from 12% corn oil to 0.75% corn oil seems safer.

In summary, we have shown that (1) high dietary level of an omega-6 FA source (corn oil) enhances photocarcinogenic expression, both with respect to tumor latent period and multiplicity; (2) that this lipid-induced exacerbation of cancer expression occurs at the post-UV initiation, or promotion, stage of carcinogenesis; (3) modification of diet to low lipid level (corn oil), after UV-initiation, negates the enhancement of cancer expression exhibited by high level of corn oil; (4) high level of dietary menhaden oil containing omega-3 FA, when compared to an equivalent level of corn oil, inhibits photocarcinogenic expression; and (5) menhaden oil mediated inhibition of UV-carcinogenesis appears to occur during the initiation stage and by a mechanism dissimilar to that exerted by low levels of corn oil.

These data suggest a complexity of dietary lipid effects upon cancer expression that perhaps has not been widely appreciated.

But here's my favourite - finally someone uses butter and ghee as controls.[4]

They're measuring ear swelling in response to a hapten test, which I assume is some sort of irritant. Low swelling means the immune system is suppressed, and this predicts that the risk of cancers is increased, just as it did in the other experiments. Note this took 4 weeks of a 20% fat diet - the protective effect of butter wasn't obvious after only 2 weeks, but the harmful effect of sunflower oil was.

Now, how do we know that this applies to human populations or has anything to do with the high rates of melanoma (the most fatal skin cancer) in New Zealand or Australia?
There is a natural experiment we can look at. NZ, unlike Australia, is not a land of extreme natural sunlight - it's the "land of the long white cloud", so that travel to the tropics greatly increases UV exposure. (However, we do have greater UV variability at our lower latitude, described by NIWA's Richard Mackenzie here.) Kiwis didn't travel much in the past, especially to the tropics, with one important exception; around 140,000 men (mostly) served overseas in WW2, around 10% of the population, and most of them served in places like Greece, Crete, Egypt, Libya, Italy and the Solomon Islands. Wearing shorts and short-sleeved shirts - US naval officials in the Solomons were appalled by the lack of protection the NZ sailor's uniform gave against flash burns - with only a Tommy helmet for shade (too hot and heavy to wear all the time). Sunburn on arrival in the combat zone is mentioned in memoirs - in the Armed Forces you stay where you're told and work where you're told, shelter or not.

Soldiers of the 2nd NZEF20th Battalion, C Company marching in Baggush, Egypt, September 1941.
The NZ diet, and British Army rations, at this time were very low in omega 6. In NZ, margarine wasn't even legalised until 1972. We cooked with butter, hydrogenated coconut oil, and beef and lamb dripping - even chicken and pork were unusual foods until the 70's. Some time during that decade the use of oil (mostly soy and corn oil at first) took off and was entrenched by the 1980's.
Now if exposure to the excess UV rays of the tropics, rather than the combination of UV and oil, caused skin cancer we'd expect to see an age-specific curve in skin cancer mortality in NZ that rose after the war (starting in the mid-1950's would match the usual cancer latency) then dropped as that generation began to die off from all causes, and a generation raised on "slip slop slap" UV protection took over.
Instead we see this:

And if you check different age groups in this part of the Mortality Trends website, you find the same pattern (most obvious where there is highest mortality), despite the different rates of overseas service in each age group, and the dying off of each generation - mortality from skin cancer climbs rapidly from the 1970's, when the NZ nutritional transition to high-PUFA oils began, and has not declined at all as the Greatest Generation dies off and the lesser slip, slop, slap-happy generations take its place (melanoma mortality in NZ has remained stable from 2001 to the present, I can't find earlier stats specific for melanoma but of course it is the most lethal skin cancer). This data is a better fit for diet than it is for UV exposure. (Of course there's the ozone hole, dating from the 70's, but "The ozone hole does not have a large effect on the concentration of ozone over New Zealand. However, when the ozone hole breaks up in spring, it can send ‘plumes’ of ozone-depleted air over New Zealand." The relative unimportance of this is mentioned on page 6 of Mackenzie's paper.)
Which is not to say that UV exposure has unlimited safety, of course this is not the case, but that heart-healthy vegetable oil and margarine advice has made even limited exposure more dangerous than it needs to be. Much the same phenomenon we see with alcohol and liver disease (and, who knows, alcohol and the risk of other cancers).

Anyway, if you plan to go out in the sun for long enough to raise some vitamin D and nitric oxide, or drink enough alcohol to get drunk, or especially both, skip anything cooked in or made with a vegetable oil other than coconut or, within reason, olive oil (this includes mayonnaise), [Edit: olive oil is rich in the terpenoid antioxidant squalene, perfectly configured to quench singlet oxygen radicals released by UV exposure, likely to offset risk from its moderate 10-12% linoleic acid content], eat some butter or cheese or full-fat yoghurt, some fatty fish, chocolate, tomatoes and all the other antioxidant-rich foods with some evidence as UV-protective (caffeine seems to help too). Also keep insulin low - that means no refined carbs, intermittent fasting, low carb diet if necessary. Insulin and IGF-1 are important in skin repair and insulin resistance due to excessive insulin response to diet creates all sorts of skin problems, as well as underwriting most of those non-communicable diseases we hear so much about. (it's not easy to get insulin tested here but the TG/HDL ratio after a 12-14 hr fast is a decent proxy for the 2-hour insulin response).

[EDIT 11/02/19 - analysis of NHS/HPFS data has confirmed an association between omega 6 PUFA and skin cancers, up to 1.23 (1.08, 1.41) for squamous cell carcinoma. Of course this is an unreliable FFQ data set, but the finding runs contrary to the direction we'd expect conscientiousness bias to take in this population. It's not obvious what the range of omega 6 was, this information may be in supplementary tables I can't access.
Park MK, Li WQ, Qureshi AA, Cho, E. Fat intake and risk of skin cancer in u.s. adults. Cancer Epidemiol Biomarkers Prev. 2018 Jul;27(7):776-782. doi: 10.1158/1055-9965.EPI-17-0762. Epub 2018 Apr 10.]

* IMO the vitamin D supplement scepticism in this article is premature - vit D3 works if you use it for the right reason and take enough of it. It's just as good as sunlight for fixing my minor but annoying psoriasis, but I need 10,000 iu a day till it goes away. This only takes 6 days every month or two now - I used to need to take that amount all winter.


1] Takemura N, Takahashi K, Tanaka H, Ihara Y, Ikemoto A, Fujii Y, Okuyama H. Dietary, but not topical, alpha-linolenic acid suppresses UVB-induced skin injury in hairless mice when compared with linoleic acids. Photochem Photobiol. 2002 Dec;76(6):657-63. link

2] Reeve VE, Bosnic M, Boehm-Wilcox C. Dependence of photocarcinogenesis and photoimmunosuppression in the hairless mouse on dietary polyunsaturated fat. Cancer Lett. 1996 Nov 29;108(2):271-9. Full-text link

3] Homer S. Black  John I. Thornby  Janette Gerguis  Wanda Lenger. INFLUENCE OF DIETARY OMEGA‐6, ‐3 FATTY ACID SOURCES ON THE INITIATION AND PROMOTION STAGES OF PHOTOCARCINOGENESIS. Photochemistry and Photobiology Vol. 56, No. 2, pp. 195-199, 1992.

4] Cope RB, Bosnic M, Boehm-Wilcox C, Mohr D, Reeve VE. Dietary butter protects against ultraviolet radiation-induced suppression of contact hypersensitivity in Skh:HR-1 hairless mice. J Nutr. 1996 Mar;126(3):681-92. free full-text