Category Archives: reproduction number

COVID UPDATE FROM Institute of Functional Medicine

I just viewed an excellent video presentation from the Institute of Functional Medicine providing very useful data on COVID, particularly focusing on the Omicron variants. You can watch it here:

COVID-19 Functional Medicine Resources – The Institute for …

https://info.ifm.org/covid-19

I will summarize the information. But first a few disclaimers.

  1. I have not vetted all of these notes but none disagree with any reports or studies I have read
  2. I have read many but not all of the studies that support these statements
  3. I viewed the video with frequent pauses and replays to facilitate accurate note taking. If you view the video and find any errors please make a comment.
  4. I had a mild case of breakthrough COVID last week and seem to have some brain-fog, feeling like the morning after working most of the night on-call in the operating room.
  5. Many general observations on varied topics related to COVID-19

Omicron Timeline:

11/11/21 Omicron first appears,

1/15/22 Omicron is 99.5% of US cases

1/26/22 B.2 variant appears in US and Europe

2/5/22 B.2 variant 3.6% of US cases

Omicron presents with about 50 mutations, 15 on the RBD (receptor binding domain) with increased affinity for the ACE 2 receptor

Omicron has a cluster of mutations at the S1S2 Furin Cleavage Site. Furin is an enzyme that cleaves the virus to allow for entry into human cells, present in large amounts in the brain, lung and GI tract (thus omicron affecting these organs perhaps more and possibly increasing the risk in people with comorbidities “associated with Furin”.)

Some Omicron mutations are associated with a degree of immune escape, evading anti-bodies and T cells.

B2 may not be picked up by some tests (not discussed in detail)

Compared to B1, B2 is 2.5 times more transmissible in non-VAX folks.

But Vaccine effectiveness against B2 appears to be at least as good or possibly better than effectiveness against B1. (Strange but stated)

Omicron has on average a 3 day latency between infection and symptoms. It appears to replicate “70X more quickly” compared to delta with 3.5 times greater household transmission. Fortunately lung involvement is 10 times lower compared to the original “Wuhan virus”.

Prior infection with delta DOES NOT SEEM TO PROTECT AGAINST OMICRON.

Hospitalization rate with omicron 38/1000 infections vs 101/1000 infections with delta.

In hospital mortality 29% with delta vs 3% with Omicron BUT because of a dramatic increase in transmission with Omicron, daily death rate in US has been 2200 to 2900 per day during the surge, more than delta. (Greater number of infections outweighs the lower mortality rate)

 preprint study published last month looked at data from about 52,000 people infected with the omicron variant, and about 17,000 infected with delta, in southern California. Compared with patients who had the delta variant, omicron patients had a 53% reduced risk of hospitalization, a 74% reduced risk of ICU admission and a 91% reduced risk of death. The study has not yet been peer-reviewed.

Duration of infection averages 10 days. Estimates for being contagious after onset of symptoms:

5 days 1/3, 7 days 16%, 10 days 5%, therefor some practitioners are recommending isolation for 14 days after onset of symptoms.

PCR can remain positive for months after infection because of non-infectious remnants of viral RNA.

Negative antigen test after isolation is reassuring but does not guarantee patient is not contagious. The home antigen tests were not designed or studied for predicting degree of contagion, only for diagnosis.

LONG COVID can be as high as 30% of all cases, as high as 10% after mild cases.

Vaccination reduces risk of LONG COVID by about 50%.

A study published in GUT demonstrates altered GI microbiome 6 months after infection. The gut microbiome is extremely important for immune function.

One year following COVID infection (previous variants) there is a 60-70% increased risk of heart attack, stroke and congestive heart failure.

In the UK 25% of worker absenteeism is due to LONG COVID.

Infection rates: UNVAX 1000/100,000, VAX 600/100,000, VAX+BOOSTER 300/100,000

A Swiss study showed 98% reduction in death with VAX plus booster.

2/15/22 published study from IOWA showed that 90 minutes of exercise on the day of vaccination increased antibody levels measured 4 weeks after vaccination. Similar data are available for influenza vaccination. I reviewed data on various non COVID vaccine effectiveness relative to sleep and exercise in 2 talks given last year. This result is not surprising.

Individuals with infection from prior variants, but not vaccinated, show no effective neutralizing antibody activity against omicron. (Very worrisome, I will try to vet this one)

Omicron has 4.5 times higher re-infection rate compared to delta.

Omicron infection appears to decrease risk of infection with delta, but prior infection with delta (without vaccination) does not appear to protect against omicron.

Prior infection (before omicron) PLUS vaccination provides 76% protection against omicron infection which is about the same protection of VAX + booster, and this appears to include protection against B2 variant.

T cell immunity after infection (pre omicron) and after vaccination appears to persist and T cell activity increases with time after infection and after vaccination.

Novavax has applied for EUA with the FDA. This is a vaccine made with S-protein particles plus adjuvant (no mRNA).

“The Novavax COVID-19 vaccine, codenamed NVX-CoV2373, is a subunit COVID-19 vaccine candidate developed by Novavax and the Coalition for Epidemic Preparedness Innovations (CEPI), brand name Covovax.”

“Results from a Phase 3 clinical trial enrolling 29,960 adult volunteers in the United States and Mexico show that the investigational vaccine known as NVX-CoV2373 demonstrated 90.4% efficacy in preventing symptomatic COVID-19 disease. The candidate showed 100% protection against moderate and severe disease. In people at high risk of developing complications from COVID-19 (people 65 years or older and people under age 65 with certain comorbidities or with likely regular exposure to COVID-19), the vaccine showed 91.0% efficacy in preventing symptomatic COVID-19 disease.”

Read more on en.wikipedia.org

The US Army is in phase I clinical trial with a multi-valent “ferritin nanoparticle multi-faced” vaccine. This “soccer ball shaped” vaccine has 24 “faces” with multiple variant antigens. Each “face” carries a different antigen.

US Army developing vaccine to fight ‘array’ of COVID variants

“The Spike Ferritin Nanoparticle platform is designed to protect against an array of SARS-CoV-2 variants and SARS-origin variants but was not tested on the Omicron variant,” Walter Reed officials said.

J&J vaccine issues:

The J&J vaccine is associated with a risk of thrombosis-thrombocytopenia (blood clots and decreased platelets). Risk: 1:100,000 doses in women age 30-50. CDC recommends against J&J vaccine unless there is a contra-indication to mRNA vaccine. 15% of these cases are fatal.

A full discussion of therapeutics (drugs) against COVID can be read at IFM.org/COVID

PAXLOVID is an oral combination of two anti-viral medications reserved for adults (age >= 18) with increased risk, given within day 3-5 of symptom onset. It decreases risk of hospitalization and death by about 70% in low-risk and 89% in high risk groups. There are many contra-indications to use including specific medications and supplements (such as Saint John’s Wort). Availability is a problem.

A recent study published in NEJM used IV Remdesivir (daily for 3 days) for early out- patient treatment in high risk patients, reduced risk of hospitalization/death by 87%. This would represent an off-label use of the drug based on a well controlled study.

Home antigen tests on average become positive 3 days after first positive PCR (nasal swab), 2 days after a positive saliva PCR.

The BiaxNOW home antigen test is 73% sensitive (27% false negative rate)

Pregnancy-COVID and vaccination:

A study of 40,000 pregnant women found no increase in pre-term birth, small for gestational age, or any other complication following vaccination during pregnancy.

But COVID infection in unvaccinated women during pregnancy is associated with increased risk for pre-term birth, still born, low birth weight, cesarean section, decreased fetal growth, maternal intubation and death.

Maternal Vaccination produces anti-Covid antibodies found in fetal cord blood at birth.

Intra-uterine demise with COVID is associated with massive placental insufficiency.

There is no data to support decreased female or male fertility following vaccination.

A study of menstrual regularity following vaccination showed < 1 day change in cycle length post vaccination, not clinically significant. Post vaccination regularity equivalent to expected variation in menstrual cycles.

Two months following COVID infection there is a decrease in male but not female fertility rate.

Multiple studies have demonstrated association between low Vitamin D status and risk for severe-critical disease and death. Association does not equal causation but there is biologic plausibility (Vitamin D is a major immune regulator) and consistently increased risk associated with low levels. A recent study demonstrated 14 times greater risk for severe-critical disease in hospitalized patients with levels <20 compared to patients with levels >40. I will update my previous discussion of Vitamin D and COVID in a future post. Spoiler alert: An intervention study with high dose Vitamin D done in Spain demonstrated improved clinical outcome.

Risk factors for poor outcome in descending order:

  1. Age > 65
  2. immuno-compromised state
  3. lung disease
  4. liver disease
  5. kidney disease
  6. neurologic disorders
  7. diabetes
  8. cardiac disease

Patients with severe disease had >= 1 risk factor

78% of patients who died had >= 4 risk factors.

“Nearly two years into the pandemic, unvaccinated Americans are still making up the majority of COVID deaths.”

“Data from the Centers for Disease Control and Prevention shows that during the first week of December — when the omicron variant began taking hold — unvaccinated people were dying at a rate of 9 per 100,000.”

“By comparison, fully vaccinated people were dying at a rate of 0.4 per 100,000, meaning unvaccinated people were 20 times more likely to die of the virus”

In the context of the COVID 19 pandemic I will close with the usual summary.

  1. Avoid alcohol consumption (alcohol wreaks havoc with your immunity)
  2. Get plenty of sleep (without adequate sleep your immune system does not work well )
  3. Follow good sleep habits
  4. Exercise, especially out of doors in a green space, supports the immune system
  5. Get some sunshine and make sure you have adequate Vitamin D levels. Supplement with Vitamin D3 to get your levels above 30 ng/ml, >40ng/ml arguably better.
  6. Eat an anti-inflammatory diet rich in micronutrients.
  7. Practice stress reduction like meditation and yoga which improves the immune system
  8. Eliminate sugar-added foods and beverages from your diet. These increase inflammation, cause metabolic dysfunction, and suppress immunity.
  9. Eliminate refined-inflammatory “vegetable oils” from your diet, instead eat healthy fat.
  10. Clean up your home environment and minimize your family’s exposure to environmental toxins by following recommendations at EWG.org with regards to household products, personal care products, and organic foods. (https://www.ewg.org/)
  11. Drink water filtered through a high quality system that eliminates most environmental toxins.
  12. If you are eligible for vaccination, consider protecting yourself and your neighbor with a few jabs. Age > 50 and/or risk factors means clear benefit from a booster.

THIS WEBSITE PROVIDES INFORMATION FOR EDUCATIONAL PURPOSES ONLY. CONSULT YOUR HEALTH CARE PROVIDER FOR MEDICAL ADVICE.

Eat clean, drink filtered water, love, laugh, exercise outdoors in a greenspace, get some morning sunlight, block the blue light before bed, engage in meaningful work, find a sense of purpose, spend time with those you love, AND sleep well tonight.

Doctor Bob

UK variant, Ro and herd immunity

The new SARS-CoV-2 variant first appearing in southern England has a transmission advantage of 0.4 to 0.7 points higher in reproduction number, also known as R0, compared to the initial strain, British researchers found.

From the study itself:

There is a consensus among all analyses that the VOC has a substantial
transmission advantage, with the estimated difference in reproduction numbers between VOC and non-VOC ranging between 0.4 and 0.7, and the ratio of reproduction numbers varying between 1.4 and 1.8.

The researchers published their findings on the school’s website. VOC means “variant of concern”.

In other words, this new variant has an Ro which is 1.4 to 1.8 times higher than the previously circulating predominant strain.

CDC has concluded that based on genetic studies (discussed in a previous post) and reactivity to antibodies found in the blood of vaccinated individuals it appears unlikely to impact COVID-19 vaccine effectiveness. This conclusion has been reached by multiple immunologists who did those studies. (See https://practical-evolutionary-health.com/2020/12/31/new-uk-sars-cov-2-variant-we-see-no-evidence-that-the-reported-mutations-would-substantially-increase-reinfection-risk-or-decrease-vaccine-efficacy/)

So what is the reproduction number? Ro is the average number of individuals infected by one person. A Ro of 2 means that every infected person on average infects 2 other people.

When a critical proportion of a population becomes immune, called the herd immunity threshold (HIT), the disease no longer spreads exponentially in the population. The disease reaches an endemic steady state. It neither grows nor declines exponentially.

From Wikipedia:

This threshold can be calculated from the effective reproduction number Re, which is obtained by taking the product of the basic reproduction numberR0, the average number of new infections caused by each case in an entirely susceptible population that is homogeneous, or well-mixed, meaning each individual can come into contact with every other susceptible individual in the population,[and S, the proportion of the population who are susceptible to infection, and setting this product to be equal to 1:

Ro X S = 1

S can be rewritten as (1 − p), where p is the proportion of the population that is immune so that p + S equals one. Then, the equation can be rearranged to place p by itself as follows:

Ro x (1-p) = 1, 1-p = 1/Ro, so {\displaystyle p_{c}=1-{\frac {1}{R_{0}}}.}

When the effective reproduction number Re of a contagious disease is reduced to and sustained below 1 new individual per infection, the number of cases occurring in the population gradually decreases until the disease has been eliminated.

An assumption in these calculations is that populations are homogeneous, or well-mixed, meaning that every individual comes into contact with every other individual, when in reality populations are better described as social networks as individuals tend to cluster together, remaining in relatively close contact with a limited number of other individuals. In these networks, transmission only occurs between those who are geographically or physically close to one another. The shape and size of a network is likely to alter a disease’s HIT, making incidence either more or less common

But transmission is not just affected by the characteristics of the virus, it is also affected by the behavior of the population in which the virus is observed. So it is complicated. As stated by the authors of the transmission study.

We note that these estimates of transmission advantage apply to a period
where high levels of social distancing were in place in England; extrapolation to other
transmission contexts therefore requires caution.

So if social distancing is relaxed, fewer people wear masks, more people congregate, then this variant could have a much higher Ro.

Ro for measles is 12-18 rendering HIT at 92-95%

Ro for SARS CoV-1 (2002-2004 pandemic) was estimated at 2-5 rendering HIT 50-80%

Ro for SARS CoV-2 (COVID-19) has been estimated at 2.5-4 giving and HIT of 60-75%.

This is not the first variant to demonstrate increased transmission. A new variant emerged in February of 2020 called D614G which had a higher Ro compared to the previously circulating predominant strain. Such strains with higher transmission rates eventually become the predominant strain circulating in a population.

So just as more people suffer from pandemic fatigue and drop their guard we have a more easily transmitted virus. Now is not the time to loosen up on precautions.

In the context of the COVID 19 pandemic I will close with the usual summary.

  1. Avoid alcohol consumption (alcohol wreaks havoc with your immunity)
  2. Get plenty of sleep (without adequate sleep your immune system does not work well )
  3. Follow good sleep habits
  4. Exercise, especially out of doors in a green space, supports the immune system
  5. Get some sunshine and make sure you have adequate Vitamin D levels.
  6. Eat an anti-inflammatory diet rich in micronutrients.
  7. Practice stress reduction like meditation and yoga which improves the immune system
  8. Eliminate sugar-added foods and beverages from your diet. These increase inflammation, cause metabolic dysfunction, and suppress immunity.
  9. Eliminate refined-inflammatory “vegetable oils” from your diet, instead eat healthy fat.
  10. Clean up your home environment and minimize your family’s exposure to environmental toxins by following recommendations at EWG.org with regards to household products, personal care products, and organic foods. (https://www.ewg.org/)

THIS WEBSITE PROVIDES INFORMATION FOR EDUCATIONAL PURPOSES ONLY. CONSULT YOUR HEALTH CARE PROVIDER FOR MEDICAL ADVICE.

Eat clean, drink filtered water, love, laugh, exercise outdoors in a greenspace, get some morning sunlight, block the blue light before bed, engage in meaningful work, find a sense of purpose, spend time with those you love, AND sleep well tonight.

Doctor Bob