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March 16, 2022

To Mask or Not to Mask - The Here

OUR SURGE IS HERE!  Last night the Covid Stats in NYS, NYC, and Manhattan jumped to 3.7%, 3.8%, and 4.7%!!   

Over the last several months the Omicron Variant BA.1 cases dropped very rapidly, and then case numbers plateaued at 1.0 to 1.5% for 12 days in NY.  The last variant data was published on Mar 5th, which is at least 1 week after the samples were collected.  At the time our Region 2 (NY, NJ, Puerto Rica and the Virgin Islands) had 17.3% Omicron BA.2 and 83.7% BA.1.  The transmissibility of BA.2 is 1.5X greater than BA.1, and BA.1 was the most transmissible variant to date.  Right now cases are increasing in Britain, Germany, Italy, France, Switzerland and the Netherlands, and the percent of the BA.2 variant is increasing each week. Throughout the pandemic the UK was a bell weather for the next variant to spread in the US. It is feared that the next 4-6 weeks here we will see the surge in BA.2 cases. 

Over a year ago one of my Covid-19 posts was about the use of wastewater testing to detect early Covid case increases in geographic areas.   At that time the Univ. of Arizona was collecting and testing waste water from individual dormitories on campus, and an increase in the virus in the waste water was the first sign that the Covid cases had spread to students in that dorm. Shedding of the virus in the waste water system from infected people occurs even before they have symptoms.  There is now a well developed wastewater testing system in 37 states for monitoring the presence of the virus.  In CDC news from today, they reported a "bump in the virus" in the wastewater in 1/3rd of American cities - and the northeast had the most notable change.  Read Below 


After such a rapid fall in Omicron cases why should there now be a rise in cases?  There are 3 possible reasons:  Omicron BA.2 is more transmissible, it is spreading because all of the mandates have been lifted and people want to return to a normal life, and there is waning immunity.  45% of Americans were infected with Omicron BA.1 and they will be protected from BA.2.  The highest infection rate will be in the unvaccinated, and so far the infections and the hospitalizations are going up at the same time in Europe instead of with the usual lag of two weeks - which no one can figure out,  ICU cases are not going up - so the infections may not be more severe. There re are still 1200 Covid deaths in the US per day, before a surge.  The vaccine efficacy is about 77% - the same for BA.1 and BA.2  The UK rate of fully vaccinated people is 86% (US 67%) and boosted 67% (US 50%) which might mean UK has less severe cases because of their level of vaccination.  

March 12, 2022

Will There Be Another Surge?

"Two years into the official pandemic, Covid-19 remains an emergency" writes Dr. Jeremy Faust. 

On March 11, 2020 the WHO declared the SARS-CoV-2 a pandemic.  By April 22, there were 2200 more daily deaths than the average number of deaths per day in the US.  Since then there have been over 1 million "excess deaths" in the US in the last 2 years - defined as the reported number of deaths compared to the expected number of deaths in a given period.

Dr. Faust wrote this week that we are still in an epidemiologic emergency.  He goes on to say that it depends on what metric you want to use.  He believes that the strongest and most reliable indicator for the US is "excess mortality."  Now that rapid home tests are being done in record numbers, the number of cases, or percent of the virus in a given area, can no longer be an accurate measure of the circulating virus.  In January 2022 the US death rates were nearly 130% of normal in adults 65+.  February and March data are not available yet.  Two days ago there were 1559 Covid deaths in the US.  Why does it matter if we declare the emergency over?   If the emergency is declared over there will not be continuing insurance coverage for millions of Americans on Medicaid, and telehealth services to millions of seniors on Medicare will end. The Executive Branch will also have less flexibility in fighting Covid-19.  On the 2 year anniversary of the pandemic, cases and deaths are falling, but we need to see the number of excess deaths drop as well.  See Below  


I follow the NY State, City, and Manhattan Covid case numbers and although the %infections fell very rapidly, they are now hovering at 1.4%, 1.1%, and 1.5% respectively - and seem to have plateaued.  Many experts believe that the rise of the Omicron BA.2 variant will cause a long slow tail to the surge numbers.  BA.2 is still increasing weekly and in the variant sequencing report released this week the variant has climbed to 17.7% in our region (US Region 2).  It is more transmissible than Omicron BA.1, but probably not more severe.  It is detected by current tests, and vaccines.  We want the pandemic to be over so badly that I hope we didn't "open" too rapidly.  We will soon know. 

March 9, 2022

Rapid Antigen Tests and RT.PCR - Collected At Home

It is time to request more free covid rapid antigen tests from the gov't this week.  I just reviewed a study pre-print comparing the Rapid Antigen Tests (3 manufacturers) and RT.PCR tests to compare the sensitivity of the results when their isolated sequenced virus was either the delta variant or the omicron variant.  The study was conducted by NIH, FDA, and the UMass Chan Medical School. All of the subjects were part of a very large "at home testing program" and there were >5000 participants enrolled in the study between Oct 18, 2021 and Jan 24, 2022.  All of the subjects collected 2 nasal samples every other day for 15 days - nasal swab collections were separated by at least 15 minutes.  RT-PCR tests were all sent to and performed by the same lab.  The "at Home tests" were read by the subjects and the information submitted to the study coordinators. 

153 subjects developed +RT-PCR tests (61 delta, 92 omicron) during the study and 24% of subjects had a +rapid antigen test on the same day.  There were then increases in the number of + antigen tests over the next days demonstrating that the test picks up Covid-19 cases as the amount of the virus increases and the period of infectivity begins.  There was no significant difference between the data for delta vs omicron virus samples which was one of the important questions about the variants tested in this study. See Below 


There are a number of rapid at home antigen tests that are approved by the FDA.  In this study the 3 manufacturers for the tests were BD Veritor At Home Covid-19 Test, Quidel Quick View At Home OTC Covid-19 Test, and Abbott BinaxNOW Covid-19 Antigen Self Test.  It is important to make sure that the tests have not expired when you start to use them, and to follow the instructions carefully. My 10 year old grandson collected my nose samples and added the swab to the container - under the supervision of his MD uncle.  I was one of many he did that morning when our family was together and I was impressed.  If you have symptoms and the test is negative, repeat it in 1-2 days when the amount of virus might have increased.  And if you are doing the test to make sure you are NOT infected, perform the test immediately before going out, especially to visit susceptible people. The tests can rapidly become positive - testing in the morning for an evening party may be too long before the event.  

March 5, 2022

Wild type, alpha, beta, delta, omicron. What's Next?


The White House, with a group of outside experts, developed a National Covid-19 Preparedness Plan which can serve as a roadmap going forward.  It has 4 sections and I thought it might be a good time to look at  section 2 - "To Prepare For New Variants."  The Omicron BA.2 variant is increasing in the US, with the percent of infections doubling every week in our region. The percent of the infections was 12.4% in the last report for our region on Feb 26. But as in other countries, the total number of infections are not increasing as the BA-2 variant increases, which is good news.  In order to stay ahead of new variants going forward, the plan will "monitor variants, adapt our tools swiftly to combat a new variant, and deploy emergency resources to help communities." 

The administration has enhanced the collection and analysis of data, expanding electronic case reporting to all 50 states and DC.  The US has also established a world-class sequencing operation - studying 90,000 virus isolates/week.  When a new isolate is discovered, there is now a network of researchers to analyze transmission, severity, and immune escape from vaccines, tests, and drugs.  As part of this plan the government can also use new FDA processes to expedite the regulatory review of the variant while maintaining strict longstanding practices to ensure the efficacy and safety of the products.   


Early in the pandemic the US relied on variant information from other countries who had already ramped up genetic sequencing of emerging variants in their country.  We relied heavily on the information from the UK and S. Africa.  Genomic sequencing, in which the RNA structure of the virus in each virus sample, is a laborious process and since the coronaviruses are mutating a little faster than expected, these systems are now able to detect as little as 0.1% of a new variant in patient samples.  As part of this plan a permanent section was established at HHS/NIH to ensure "accelerated development, production, and delivery of Covid-19 vaccines and treatments."   This information was taken from <>


March 2, 2022

New CDC Covid-19 Guidelines

The CDC published new Covid Pandemic health guidelines last week and they are based on a combination of 3 metrics in order to calculate the Covid-19 community level.  

The 3 metrics used for the calculation are the number of Covid cases, the number of hospitalizations, and the number of hospital beds being used.  Once the names of your state and county are entered into the CDC online program, the level of infection in your county is determined as low, medium, or high.  Then based on your community level, guidelines for protection are listed.  Fill in your state and county at this link.   The calculation is based on:

1.) Number of new admissions per 100,000 population in past 7 days

2.) Percent of staffed inpatient beds occupied by Covid-19 patients

3.) Total number of cases per 100,000 population in the past 7 days

If your county is LOW (green), the prevention steps are:  Stay up to date with Covid vaccines which means 2 doses plus a booster.  Get tested if you have symptoms.

If your county is MEDIUM (yellow), the prevention steps are: If you are at high risk for severe illness, talk to your healthcare provider about whether you need to wear a mask and take other precautions, stay up to date with Covid-19 vaccines (2 doses plus a booster), get tested if you have symptoms.

If your county level is HIGH (orange), the prevention steps are:  Wear a mask indoors in public, Stay up to date with Covid-19 vaccines, Get tested if you have symptoms.  Additional precautions may be needed for people at high risk for severe illness.

People MAY wear a mask at any time, but people with symptoms, a positive test, or exposure to someone with Covid-19 SHOULD wear a mask.   See Below 


The CDC has an expanded version of this information at the following link - including information for immunocompromised people. 

In an article I read they estimate that 70% of the US is currently in the green or yellow category.