COVID Resources

NY Times Case Count Map,

Vermont Interactive

See a whole section on Omicron and J&J below.

I found this great blog for following Covid: Your Local Epidemiologist. Her main goal is: “… to “translate” the ever-evolving public health science so that people will be well-equipped to make evidence-based decisions, rather than decisions based in fear.”

I began reading it primarily to learn about Omicron, starting on Nov. 26, but some older posts also stood out as quite helpful.

This pandemic is getting old, but the current Omicron variant suggests a return to the level of care that we took in the early days of the pandemic. Remember gathering outdoors, walking, biking, or skiing, staying six feet apart and making sure no-one was down wind? It is far more contagious, the incubation period is only a few days, and even with an mRNA series and booster, the efficacy is only 70% vs. 94%+ against other variants.

In her Jan. 6, 2022 post she reminds that a “layered approach [to prevention] (vaccine, mask, ventilation, testing) is crucial” and references a great chart on mask effectiveness. The surgical mask is not nearly as protective as I had thought/hoped. Go N95 if possible.

We may be feeling we will all eventually become infected, but there are many reasons to still strive to avoid exposure, namely organ damage and long Covid. Guidance from the state and national governments is not always sufficient. Your own research as it applies to your situation is important.

For example, the CDC reduced isolation and quarantine periods to too short a timeframe, especially for the unvaccinated: They took a lot of flack for this and have modified.

This page explains a sensible antigen testing approach before a gathering:
Adapt the dates. Notice that part of the preparation is taking less risk during the few days or weeks before the gathering.

“There’s now enough data to estimate the reproductive number (i.e. contagiousness) in the United States. And it’s not looking good: R(t)=3. With this high level of transmissibility, cases are doubling every ~3-4 days, so Omicron will easily be the dominant variant in coming weeks. … Even though the number of infections will substantially increase, we will largely stay out of the hospital.”

Omicron Update Dec. 22: “JJ people need 2 mRNA shots for full neutralizing antibody protection instead of just one.”

This page notes antigen tests remain valid for Omicron: However, in her Jan. 5 post, Antigen Tests and Omicron, throat swabbing as is done in the UK is highlighted as important to detecting Omicron during the infectious period because it inhabits the bronchial area more so than the nose. See the Jan. 19 post also.

Go get your vaccine, especially with Omicron: “… while antibodies that are generated are highly specific, B-cells can adapt to any variant and create new specific antibodies.” Boosters are important.

How vaccines reduce long COVID: In a small study, the rate of long COVID19 among vaccinated was 0.5%. “Vaccines minimize the time the virus is in the body and reduce the number of infectious particles. So, the less virus, the less likelihood of damaging organs, and the less likelihood of long COVID.”

While the above argument is sensible, here is a counter argument. “… vaccination does not protect against Long Covid, … Long Covid symptoms become more likely over time:”

COVID19’s impact on the brain: “Those with COVID19 had significant loss of gray matter, … regardless of disease severity.”

“The decisions we make (like not wearing a mask or not getting a vaccine) directly impact those around us. And not just those around at the time. SARS-CoV-2 can linger in the room for more than 16 hours. … We have to stop transmission until we can build our immunity wall. Masks reduce transmission. Vaccines reduce transmission. And we have the tool, in ample supply, to build a protective wall for our most vulnerable. … The vaccine couldn’t save Colin Powell, but we could have. His death is a reminder of how serious this pandemic is and that we need to [do] everything in our power to protect the 5.5 million immunocompromised around us.”

We came together as a country to eliminate Rubella through 1) community vaccination instead of 2) just vaccinating women and girls in their child-bearing years. Option 2 did not work sufficiently in other countries.

How many breakthrough cases are there? July 16, 2021

Long COVID among breakthrough cases?: In one study on the Alpha variant “… 1 in 5 breakthrough cases reported long COVID19, regardless of severity of disease.”

More detail about Long Covid (same link as counter-argument above).

From Kaiser Health News 3/4/21: Coronavirus Deranges the Immune System in Complex and Deadly Ways. Rather old now; there may be some updates in other research. Makes the case for not getting infected. Even a mild Covid infection can have long-term ramifications.

Even before Omicron, Sep 19, 2021, it was being suggested that J&J shots get mRNA boosters.

Off topic, with the prominence of abortion in the news this year, this epidemiologist weighs in with some good data highlighting that most abortions are being performed early, and changes in laws will not reduce the number substantially.

A friend  led me to this essay by an unvaccinated American living in South Africa who has done MUCH research, questions policy and logic, and makes good arguments on many Covid topics. A long read but provides for good contemplation.

SARS-CoV-2 vaccine protection and deaths among US veterans during 2021 highlights the topic of waning effectiveness in a large sample.


I found bulk packages of rapid (antigen) tests at a company that supplies offices. Rapid tests in bulk quantity:

Good write-up about each type of test:

Care sheet:

Testing at home is now reimbursable. Find similar info for your state.

Antigen test method adjustment during Omicron: Take a throat swab as well as nasal. There is a link to a British video showing how to do the throat and nasal swab, from 2:10 – 3:00, you can ignore the rest. This is standard in the UK but the US has not adopted.

Another resource saying to do a throat swab: “drink a glass of water, not eat or drink for 30 minutes, swab your throat, and then swab your nose with the same test stick.”

Here are a couple articles rejecting the idea of throat swabbing until approved:

My own opinion, if Omicron replicates in the throat, shouldn’t our guidance be updated? Or at least tell people that rapid testing is not a good precaution against Omicron?

Another post from Jan. 19, Antigen Tests: Real World Data, discusses rapid tests as a way of determining when it’s safe to go back into society, but doesn’t sufficiently address using it as a preventive tool, nor does it back up her Jan. 5 posts about throat swabbing.

I am personally disappointed that more attention hasn’t been given to how to prevent spread. Now in April 2022, all the attention is on getting back to life. I think there is some hope that the immunity developed from infection will make up for the lack of community immunity due to insufficient vaccination numbers.


The Dec. 30, 2021 NY Times reports J&J shot with J&J booster provides great protection against severe illness once infected with Omicron.

For those striving to prevent becoming infected: The following excerpts that I hastily copied from Twitter note that some studies have shown that J&J alone is not sufficient protection against infection by Omicron.

See CDC links below for updates on boosters.

See discussion and links above for test swabbing for Omicron.
Findings are good for Pfizerites and Modernans but sobering for JnJers, even after boosting have lower neutralizing antibodies against Delta and Omicron vs 3x Pfizer
Make sure you get 3 shots, at most 1 J&J, and space them 2-6 months apart”

One issue is that rules don’t allow for that 3rd dose, officially. But seems people are finding a way, as there’s broad acceptance that rules limiting vaccines do not account for all need cases.

2x JJ has low protection from infection, and once infected, vaccinated are as contagious as nonvaccinated. 2mo after the second shot would be a safe time to get a RNA boost. Not medical advice, just conveying study results.

Another clear result is that J&J is inferior in all states.

“But the most concerning thing is this: J&J+booster doesn’t work as well against new variants compared to Moderna+booster or Pfizer+booster.

“JnJers need a RNA vax dose at some point to prime a wide memory B cell (antibody factories) population, and then need to be boosted to get the broad antibody response to protect against Delta and Omicron.
JnJers who got boosted by Moderna or Pfizer have that RNA dose already. They would benefit greatly from another shot any time after 1 month (based on other studies, 3 months is probably ideal for max response). This “another” shot can be RNA (guaranteed) or could be J&J (below)
Essentially J&J is not a good way to start a vaccine series when we are faced with variants against which a broad antibody response is useful. Instead a J&J primary vaccine should be considered similar to a natural infection: not enough vs variants.
“JnJers who haven’t gotten a RNA booster should be told to get one 2 months after their last J&J, and then another booster 6 months later. They can benefit from the wider B cell repertoire. If they are in a vulnerable population, they absolutely will need it.

“Basically you need a RNA vaccine at some time to prime a wide B cell population for antibodies against variants. J&J does not substitute. If you don’t do it earlier, you’ll just have to do it later. I hope for the health of JnJers that @CDCgov and @CDCDirector will consider it.
So in a sense JJ+RNA booster gets to where 2xRNA was to begin with (pic1 below). But it is worse than 3xRNA for variants, esp Omicron (pic2 below). And with decay we expect some loss of protection to Delta in the upcoming months.
Another way to explain the data is that 3 immunizations are needed for broad nAbs.
Since 1xJJ is similar to infection by WT strain (ref below), then we expect that after a second RNA boost (i.e. JJ+RNA+RNA) then nAb levels may be like 3xRNA. So this is even more reason to advocate for a 2nd boost.

From Balazs Lab
“I want to stress that all of this work has been done with pseudovirus which is a model of coronavirus, but there are plenty of caveats in measurements like ours. Keep in mind that the virus has plenty of other immune responses to contend with (like T cells or NK cells).


12/17/21: J&J, Sinopharm, Sputnik V COVID-19 shots less effective against Omicron -study | Reuters

Another really good blog: The Omicron situation – by Noah Smith – Noahpinion. Look for the Omicron posts among his many topics.

An article highlighting the difficulties of making and enforcing policy among groups with varying beliefs: Students Are Walking Out Over COVID


It’s a Terrible Idea to Deny Medical Care to Unvaccinated People,” The Atlantic, 1/20/22. Although I would not suggest denying medical care to the unvaccinated, I do find it appalling that partisanship has not only caused us to lose possible control of the pandemic, but also to drive up the human costs and medical costs. We could possibly have reached herd immunity on Biden’s original timeline. That could have resulted in a more normal 2021-2022 winter. Think of the toll on our taxes and health insurance.


Update related to getting a booster with J&J primary/booster:

Appendix A with Feb. 2022 updates explained: