COVID-19

SARS-CoV-2 Update

It’s time for our next 14-day moving average determinations and projections for infections and deaths from SARS-CoV-2 for the United States and my thoughts on vaccines and mutant viruses. We use the WORLDOMETERS aggregators data set to make any projections since it includes data from the Department of Veterans Affairs, the U.S. Military, federal prisons and the Navajo Nation.

In the United States, SARS-CoV-2 deaths have decreased for the sixth time in a 14-day period. There were 28 fewer deaths per day than in the last 14-day period. In the last 14 days, the number of infections has decreased by 17,700 infections per day.  Our infections per day is still extremely high, probably secondary to SARS-CoV-2 mutants, to include the B.1.1.7 (UK isolate), a New York isolate B.1.526, the CAL.20C isolate, the South African isolate and the Brazilian isolates and the new Indian isolate. I would predict that the opening of schools, places of worship, bars, restaurants, indoor dining and travel all will contribute to further spread of multiple SARS-CoV-2 mutants and rising numbers  in infections, hospitalizations and deaths in the coming months. Increased traveling as well as upgoing Memorial Day weekend, summer vacations and the July 4th holiday will all cause further increases. Vaccinations, increased mask usage and social distancing, which are a part of the Biden SARS-CoV-2 plan (day 108 of plan) will be necessary to stop spread of mutants and cause  further reductions in infections, hospitalizations and deaths in the future. On 5/07/21, 49,491 new infections occurred in the United States. There were also 770 deaths. The number of hospitalized patients is decreasing, but 9,140  patients are still seriously or critically ill. The number of critically ill patients has decreased by 692 in the last 14 days, while 9,836 new deaths occurred. The number of critically ill patients is decreasing for the second 14 day period but a large number of patients are still dying each day. 

As of 5/07/21, we have had 594,911 deaths and 33,418,826 SARS-CoV-2 infections in the United States. We have had 683,122 new infections in the last 14 days. We are adding an average of 341,561 infections every 7 days. Each million infections usually results in 10,000 to 20,000 deaths. On 5/07/21, twenty-two states have had greater than 500,000 total infections, and 32 states have had greater than 5,000 total deaths. Eight states (Geogia, illinois, New Jersey, Pennsylvania,Florida, Texas, New York and California) have had greater than 20,000 deaths. Four states (Florida, Texas, New York and California) have had greater than 35,000 deaths.

For comparison, on 11/20/20 in the United States, 3.70% of the population had a documented SARS-CoV-2 infection. California was ranked 41st in infection percentage at 2.77%. In North Dakota 9.18% of the population was infected (ranked #1), and in South Dakota 8.03% of the population was infected (ranked #2).

As of 5/07/21, in the United States, 10.04% of the population has had a documented SARS-CoV-2 infection. In the last 5 months nearly 6% of our country became infected with SARS-CoV-2. 

As of 5/07/21, California was still ranked 35th in infection percentage at 9.50%. In North Dakota 14.21% of the population was infected (ranked #1), while Rhode Island was at 14.11% (ranked #2) and South Dakota was at 13.93% of the population infected (ranked #3). Thirty states have greater than 10% of their population infected. Only one state has less than 3.5% of their population infected: Hawaii (2.30%). Fourteen states still have greater than 1,000 new infections per day with Florida leading again on 5/7/21 with 4,175 infections.

New Mutants

A new mutant SARS-CoV-2 virus (lineage B.1.1.7), first seen in the UK in September 2020, has now been found in multiple other countries. There are 3,170 reported cases in the USA as of 3/11/21, 8337 cases as of 3/25/21 and 20,915 cases as of 4/10/21 in the US. This isolate has now been found in 50 states and the District of Columbia. This isolate is more infectious than other previously circulating B2 lineage isolates. There are two deletions and six other mutations in its spike protein. One mutation involves a change of one amino acid, an asparagine at position 501 in the receptor binding motif with a tyrosine. This enhances binding (affinity) to the ACE-2 receptor and may alone be responsible for the increased infectivity of this isolate. A study published March 10 in the British Medical Journal (BMJ) found that the risk of death increased by 64% in patients infected with the B.1.1.7 variant compared to all other isolates. Due to air and other travel, this isolate will become the dominant isolate worldwide. 

On 4/10/21, the CDC stopped providing data to the public on the number of reported cases of all variants of SARS-CoV-2, both nationally and by state. This data used to be available at https://www.cdc.gov/coronavirus/2019-ncov/transmission/variant-cases.html. The CDC claims that the data is available in its COVID-19 Data Tracker, but only percentages, not actual case numbers, are available, and the data ends on April 10, 2021.   

Luckily, GISAID is still reporting variant data. The United States has had more isolations of B.1.1.7 in the last four weeks (15,909) than any other country in the world, to include the United Kingdom. There have been a total of 85,324 cases of B.1.1.7 identified in the US to date. (See chart below.)

At 197 cases, the United States has the fourth highest number of isolations of B.1.351 (the South African variant) in the last four weeks and a total of 1,161 isolations. 

And the United States has now surpassed Brazil for the most isolations of P.1 in the world, with 5,355 overall and 1,955 in the past four weeks. 

As for B.1.617, the variant recently identified in India, only India and the United Kingdom have more isolated cases than in the United States, which has 334 total cases, 197 of which were identified in the last four weeks. This also means that we had 137 known cases of this variant in the US more than a month ago, despite the fact that American news media and the CDC have only recently begun educating the public about this variant. 

A disturbing report out of the UK has found a second mutation in B.1.1.7. This mutation, which occurs in the loop sequence has also been found in the South African (B.1.351) and Brazilian (P.1) variants. (The loop sequence is in the receptor binding motif in the receptor binding domain of the S1 sequence of the spike protein.) This mutation involves a change of one amino acid of the spike protein, number 484, from glutamic acid to lysine. This point mutation allows the virus to bind better to the ACE2 receptor, which increases infectivity. People who are exposed to one of these variants (versus the old B2 isolate) are more likely to be infected and are more likely to transmit the virus to others. 

In our last three updates we summarized a research letter published in Clinical Infectious Diseases about a patient in the UK who was first infected in April with a B2 isolate and experienced only mild symptoms but was infected with the new B.1.1.7 variant in December and became critically ill. The patient described in this research letter was not protected by a natural infection with a B2 lineage SARS-CoV-2 isolate in April 2020 from having a potentially lethal second infection with a B.1.1.7 lineage variant in December 2020, suggesting that folks who have had a past SARS-CoV-2 infection should not expect to have any immunity to new variants such as B.1.1.7. All of the currently available vaccines were developed with spike protein from B2 lineages. Moderna, Pfizer, and AstraZeneca/Oxford are currently remaking their spike protein vaccines to address the mutations in the South African variant of SARS-CoV-2 because the AstraZeneca/Oxford vaccine did not work in a small trial in South Africa, where most of the patients had the South African mutant (B.1.351). 

A California Mutant

A fourth mutant isolate of SARS-CoV-2, B.1.429 + B.1.427 (CAL.20C), is the predominant mutation identified in California. This isolate does not have any of the mutations mentioned above, but contains five mutations, three of which are in the spike protein, but not in the receptor binding motif. This mutant may be partially responsible for the massive increase in infections in California, to include infections of people who had already recovered from a SARS-CoV-2 infection earlier. In California to date, we have had 3,756,393 infections and 62,220 total deaths. California is averaging 58 deaths per day in the last 14 days, which is a 22 deaths per day decrease from the preceding 14 day period. Currently, 9.50% of the population in California is infected. Nationally, we rank 35th in the percentage of people in the state infected. To my knowledge, only one privately held company is currently modifying their vaccine to cover the B.1.429 + B.1.427 mutant. 

New Indian Mutant B.1.617 Arrives in California

Stanford University announced three weeks ago that they have identified five infections with the Maharashtra India VOC 32421 (new variant designation B.1.617) in the San Francisco Bay Area. Two additional isolates were PCR positive and pending sequencing. This isolate is a double-mutant responsible for greater than 40% of the infections in India.  In the last 14 day update India had had 2,080,793 new infections in the  7 days prior which was a 58% change in the number of infections from the preceding 7 days (1,318,900 infections). Indian had reported the three highest numbers of new infections per day at 349,165 on 3/24/21, 345,147 on 2/23/21, and 332,503 new infections on 4/22/21. India is the only country to report over a million infections in three days. The previous one day record was 302,000 infections in the United States. In India 13,876 new SARS-CoV-2 deaths had occurred in the last seven days compared to 7,206 deaths in  the preceding seven days. This was a 93% increase in the death rate in the last seven days. 

The data from India the last 14 days ending on 5/07/21 is even more disturbing. India has had 5,284,155 infections in the last 14 days with an average of 377,440 infections per day or 1,132,320 infections every three days. During this 14 day period India reported 48,716 deaths or 3,480 deaths per day. On May 7, 2021 India reported 401,326 new infections and 4,194 new deaths. On 5/7/21 the total deaths due to SARS-CoV-2 infections in India now stands at 238,265. India with a population of 1,390,456,911 has had only 1.57% of the country infected. Their hospitals are still running out of oxygen, medications, beds and ventilators. They had only been able to vaccinate approximately 140 million people.Sadly a health disaster is now occurring in the world’s most populous country. I would predict that prior SARS-CoV-2 infection in India or first generation SARS-CoV-2 vaccines will have little effect on this mutant discussed in the next paragraph. 

Many of you may now be familiar with the E484K mutation present in the South African isolate, the Brazilian isolate, the New York isolate (B.1.256), and the new Nigerian/UK double mutant. When vaccine manufacturers make booster vaccines to address these variants, they will only account for the E484K mutation. What sets this Maharashtra India B.1.617 variant apart from the other variants is that it has a different point mutation at amino acid 484 that involves a change of one amino acid of the spike protein, number 484, from glutamic acid to glutamine (E484Q). This point mutation, like E484K, probably allows the virus to bind to the ACE2 receptor and evade neutralizing antibodies directed against the original Wuhan sequence. A vaccine created to address E484K would not address this isolate. 

The second mutation in Maharashtra India VOC B1.617 is L452R, which is one of the same mutations seen in CAL.20C (B.1.429 + B.1.427). This mutation is also not being covered by any vaccine currently being made as a booster. It’s possible that people in California who were infected by the Cal.20C mutant in the last six months might have some cross protective antibodies to B.1.617.

Watching the Data

Over the next few months, we’ll be paying close attention to correlations between the SARS-CoV-2 data, the number of isolates identified in various countries and states, and the non-pharmaceutical interventions (like mask mandates and lockdowns) put in place by state and national governments. Data on infections, deaths, and percent of population infected was compiled from Worldometers. Data for this table for SARS-CoV-2 Isolates Currently Known in Location was compiled from GISAID and the CDC. It’s worth noting that GISAID provided more data than the CDC.

LocationTotal Infections as of 5/07/21New Infections on 5/7/21Total DeathsNew Deaths on 5/07/21% of Pop.InfectedSARS-CoV-2 Isolates Currently Known in LocationNational/ State Mask Mandate?Currently in Lockdown?
World157,526,509836,0313,283,26013,7412.02%B2 lineageB.1.1.7 (UK)B.1.525 (Nigeria/UK)B.1.526 (USA-NYC)B.1.351 (SA)B.1.429 + B.1.427 (USA)*P.1 (Brazil)P.2 (Brazil)A lineage isolateV01.V2 (Tanzania)APTK India VOC 32421Maharashtra India VOC B.1.617 BV-1 (Texas, USA)NoNo
USA33,418,826
(ranked #1)
49,491
(ranked #3)
594,911
(ranked #1)
79010.04%B2 lineageB.1.1.7 (UK)B.1.525 (Nigeria/UK)B.1.526 (USA-NYC)B.1.351 (SA)B.1.429 + B.1.427 (USA)*P.1 (Brazil)P.2 (Brazil)Maharashtra India VOC B.1.617BV-1 (Texas, USA)NoNo
Brazil15,078,360(ranked #3)   78,377(ranked #2) 401,326(ranked #2)2,2177.05%B2 lineageB.1.1.7 (UK)B.1.351 (SA)P.1 (Brazil)P.2 (Brazil)NoNo
India21,886,612(ranked #2)401,326(ranked #1)238,265(ranked #3)4,1941.57%B2 lineageB.1.1.7 (UK)B.1.351 (SA)B.1.429 + B.1.427 (USA)*B.1.525 (Nigeria/UK)APTK India VOC 32421Maharashtra India VOC B.1.617NoNo
United Kingdom4,431,043(ranked #7)2,490127,598156.49%B2 lineageB.1.1.7 (UK)B.1.525 (Nigeria/UK)B.1.351 (SA)B.1.429 + B.1.427 (USA)*P.1 (Brazil)Maharashtra India VOC B.1.617NoNo
California, USA3,756,393(ranked #9 in world)2,16662,220489.50%B2 lineageB.1.1.7 (UK)B.1.351 (SA)B.1.429 + B.1.427 (USA)*P.2 (Brazil)Maharashtra India VOC 32421NoNo
Mexico2,358,831(ranked #15)2,846218,173(ranked #4)1661.81%B2 lineageB.1.1.7 (UK)B.1.429 + B.1.427 (USA)*P.1 (Brazil)NoNo
South Africa1,592,326(ranked #20)1,95654,687672.65%B2 lineageB.1.1.7 (UK)B.1.351 (SA)NoNo
Canada1,273,169(ranked #22)7,84924,529403.54%B2 lineageB.1.1.7 (UK)B.1.525 (Nigeria/UK)B.1.429 + B.1.427 (USA)*P.1 (Brazil)Yes, except Alberta ProvinceNo
Poland2,824,431(ranked #13)6,05369,4451667.46%B2 lineageB.1.1.7 (UK)B.1.525 (Nigeria/UK)B.1.351 (SA)NoNo
Turkey4,998,089(ranked #5)20,10742,4652785.87%B2 lineageB.1.1.7 (UK)B.1.525 (Nigeria/UK)B.1.351 (SA)B.1.429 + B.1.427 (USA)**P.1 (Brazil)NoNo
*Also referred to as CAL.20C

The Road Ahead

We are on Day 108 of the Biden-Harris administration.The President has made the pandemic a first priority and has now ordered enough vaccine to vaccinate everyone who wants a vaccination by July 2021. As of 5/7/21, 149.5 million people have had one dose of any vaccine. 8.6 million have had a single-dose vaccine (J&J). 108.9 million people are fully vaccinated. Therefore, 32 million people still need a second dose of either the Pfizer or the Moderna vaccine. 

As of April 16, all people in the U.S. over the age of 16 are eligible to receive a vaccine. The Biden administration has already exceeded its goal of administering 200 million doses of vaccine in the first 100 days of the administration. Pfizer and Moderna have applied for emergency use authorization to administer their mRNA vaccines to children aged 12-15, and the FDA is expected to authorize the Pfizer vaccine for this age group next week. Testing is ongoing for children in younger age groups and may be approved for ages 2-11 by September 2021. 

Testing, wearing masks, social distancing and washing our hands frequently should no longer be political issues. These are non-pharmaceutical interventions used by most successful countries and some states to protect their citizens and their economies. New Zealand, Taiwan, and Australia are three countries that have done this successfully. In the United States, Hawaii is doing a better job handling the pandemic than many of our states. These interventions and vaccination should keep the pandemic from overwhelming our health care delivery system. New mutations like B.1.429 + B.1.427 (Cal.20C) and the UK, Brazillian, South African, and Indian variants will probably spread rapidly throughout the United States over the next 90 days as several states (including Texas, Florida, Iowa, Mississippi) open up everything and do away with masking and social distancing. We will probably see increased new infections per day in the United States. In the UK, B.1.1.7, has increased the number of infections, hospitalizations and deaths. This and other mutants may do the same thing in the USA.

The Pfizer and Moderna RNA vaccines and the Johnson & Johnson single dose vaccination adenovirus vaccine are all being used to immunize people in the USA. The Oxford-AstraZeneca vaccine and Novavax vaccine may be available in the second or third quarter of 2021. 

The bad news is that all currently available vaccines are based on the Chinese spike protein sequence from December 2019. Mutated isolates, as discussed above, may overtake our ability to produce new vaccines and vaccinate the populace. Like Influenza vaccines, we may have to reformulate vaccines based on active, worldwide surveillance at least every 4 to 6 months. The FDA is currently putting together a guidance document for how to develop booster vaccines for SARS-CoV-2 mutations. A surrogate marker of protection like antibody to the mutated Receptor Binding Domains of SARS-CoV-2 should be considered for vaccine approval. 

I still feel the current approach of companies and governments of making new vaccines against just the South African variant is wrong. In Brazil, where the P.1 isolate is dominant, they’ve had another 849,250 infections and 32,770 deaths in just the last 14 days. In the last 42 days in Brazil 2,762,595 infections have occurred and 115,667 deaths. In South Africa, the total number of infections during the pandemic is 1,592,326 and a total of 54,687 deaths. Brazil had more infections and deaths in one month than South Africa has had for the entire pandemic. It makes no sense to make a vaccine based on just the South African mutant and not make one for the Brazilian P.1 mutant. Even worse is the current situation with the Indian SARS-CoV-2 VOC B.1.617. In the last 14 days India has had 5,284,155 new infections and 48,716 deaths. If India shuts down, among other things the generic drug industry could fail.

The ideal approach to these spreading major mutations on at least five continents would be to make vaccines against each of the mutations. I’d get all of the vaccine companies and contract production companies on a call and “suggest” that two companies at least make and mass produce one of the four mutations. The government would pay the cost and buy at least 200 million doses in advance for each variant at say $40 a dose. The total cost to purchase the vaccine (800 million doses) would only be 32 billion dollars. Give each company a billion dollars each for development costs (another 8 billion dollars). Spend another two billion dollars for syringes and you’ve got enough booster doses to vaccinate 200 million people for all 4 variants. 42 billion dollars would be a small price to pay to catch up with the current mutations. Even if you had to do this every two years, it would be well worth the dollars spent. 

We are not doing adequate numbers of PCR or antigen detection assays in the United States. According to JHU, in January of 2021, we were doing up to 2,307,949 tests per day. In March 2021, the highest number of tests per day was 1,709,210, and in April, the highest number of tests per day was 2,008,319. Currently, we’re doing 1,260,357 tests per day (7-day moving average); that’s 747,962 fewer tests than the April high. 

We still need to perform more virus isolations and perform more DNA sequencing of viruses in each country, state, populous city, and county if we are to rapidly identify new mutations. I’m more hopeful that we will have the facilities, the equipment, and the trained staff needed to perform this work. As a nation we are finally preparing to make more vaccine, new vaccines directed against mutants, and the necessary rapid tests and protective equipment needed by medical staff, first responders, essential workers and especially teachers and students. I’m still hopeful we can work together on our and the world’s infectious disease problems. 

What Our Team Is Reading This Week

COVID-19

SARS-CoV-2 Update

It’s time for our next 14-day moving average determinations and projections for infections and deaths from SARS-CoV-2 for the United States and my thoughts on vaccines and mutant viruses. We use the WORLDOMETERS aggregators data set to make our projections of future total infections and deaths since it includes data from the Department of Veterans Affairs, the U.S. Military, federal prisons and the Navajo Nation.

In the United States, SARS-CoV-2 deaths have decreased for the fourth time in a 14-day period. There were 133 fewer deaths per day than in the last 14-day period. In the last 14 days, the number of infections has increased by 11,210 infections per day. This increase in infections over the last four 14-day periods is secondary to SARS CoV-2 mutants, to include the B.1.1.7 (UK isolate), a New York isolate B.1.526, the CAL.20C isolate, the South African isolate and the Brazilian isolates. I would predict that the opening of schools, places of worship, bars, restaurants, indoor dining and travel all will contribute to further spread of multiple SARS-CoV-2 mutants and rising numbers  in infections, hospitalizations and deaths in the coming months. Increased traveling over Easter and Spring break as well as upgoing Memorial Day weekend, summer vacations and the July 4th holiday will all cause further increases. Vaccinations, increased mask usage and social distancing, which are a part of the Biden 100-day SARS-CoV-2 plan (day 80 of plan) will be necessary to stop spread of mutants and cause  reductions in infections, hospitalizations and deaths in the future. On 4/09/21, 85,638 new infections occurred in the United States. There were also 929 deaths. The number of hospitalized patients is increasing, and only 9,078  patients are critically ill. The number of critically ill patients has increased by 468 in the last 14 days, while 13,006 new deaths occurred. The number of critically ill patients is increasing and a large number of patients are still dying each day. 

As of 4/09/21, we have had 574,840 deaths and 31,802,772 SARS-CoV-2 infections in the United States. We have had 949,742 new infections in the last 14 days. We are adding 474,871 infections every 7 days. Each million infections usually results in at least 20,000 deaths. On 4/9/21, twenty-one states had greater than 500,000 total infections, and 32 states had greater than 5,000 total deaths. 

For comparison, on 11/20/20 in the United States, 3.70% of the population had a documented SARS-CoV-2 infection. California was ranked 41st in infection percentage at 2.77%. In North Dakota 9.18% of the population was infected (ranked #1), and in South Dakota 8.03% of the population was infected (ranked #2).

As of 4/09/21, in the United States, 9.60% of the population has had a documented SARS-CoV-2 infection. In the last 5 months nearly 6% of our country became infected with SARS-CoV-2. 

As of 4/09/21, California was ranked 33rd in infection percentage at 9.34%. In North Dakota 13.71% of the population was infected (ranked #1) and in South Dakota 13.50% of the population was infected (ranked #2). Thirty-five states have greater than 9% of their population infected and 45 states have greater than 6% infected. Only one state has less than 3% of their population infected: Hawaii (2.15%). 

New Mutants

A new mutant SARS-CoV-2 virus (lineage B.1.1.7), first seen in the UK in September, has now been found in multiple other countries. There are 3,170 reported cases in the USA as of 3/11/21. As of 3/25/21 there are 8,337 reported cases in the USA. This isolate has now been found in 50 states and the District of Columbia. This isolate (let’s call it Lineage B.1.1.7 or SARS-CoV-2 UK) is more infectious than other previously circulating B2 lineage isolates. There are two deletions and six other mutations in its spike protein. One mutation involves a change of one amino acid, an asparagine at position 501 in the receptor binding motif with a tyrosine. This enhances binding (affinity) to the ACE-2 receptor and may alone be responsible for the increased infectivity of this isolate. A study published March 10 in the British Medical Journal (BMJ) found that the risk of death increased by 64% in patients infected with the B.1.1.7 variant compared to all other isolates. Due to air and other travel, this isolate will become the dominant isolate worldwide. 

As of 3/11/21 B.1.351, also known as the South African isolate, had 108 reported cases and has occurred in 23 states and the District of Columbia. As of 3/25/21 there are 266 reported cases in 29 states and the District of Columbia. On 3/11/21 the P.1 isolate (Brazil) had 17 reported cases and has been found in 10 states. As of 3/25/21 there were 79 P1 isolates in 11 states. (This data is available at https://www.cdc.gov/coronavirus/2019-ncov/transmission/variant-cases.html)

A disturbing report out of the UK has found a second mutation in B.1.1.7. This mutation, which occurs in the loop sequence has also been found in the South African (B.1.351) and Brazilian (P.1) variants. (The loop sequence is in the receptor binding motif in the receptor binding domain of the S1 sequence of the spike protein.) This mutation involves a change of one amino acid of the spike protein, number 484, from glutamic acid to lysine. This point mutation allows the virus to bind better to the ACE2 receptor, which increases infectivity. People who are exposed to one of these variants (versus the old B2 isolate) are more likely to be infected and are more likely to transmit the virus to others. 

In our last three updates we summarized a research letter published in Clinical Infectious Diseases about a patient in the UK who was first infected in April with a B2 isolate and experienced only mild symptoms but was infected with the new B.1.1.7 variant in December and became critically ill. The patient described in this research letter was not protected by a natural infection with a B2 lineage SARS-CoV-2 isolate in April 2020 from having a potentially lethal second infection with a B.1.1.7 lineage variant in December 2020, suggesting that folks who have had a past SARS-CoV-2 infection should not expect to have any immunity to new variants such as B.1.1.7. All of the currently available vaccines were developed with spike protein from B2 lineages. Moderna, Pfizer, and AstraZeneca/Oxford are currently remaking their spike protein vaccines to address the mutations in the South African variant of SARS-CoV-2 because the AstraZeneca/Oxford vaccine did not work in a small trial in South Africa, where most of the patients had the South African mutant (B.1.351). 

A California Mutant

A fourth mutant isolate of SARS-CoV-2, B.1.429 + B.1.427 (CAL.20C), has been identified in California. This isolate does not have any of the mutations mentioned above, but contains five mutations, three of which are in the spike protein, but not in the receptor binding motif. This mutant may be partially responsible for the massive increase in infections in California, to include infections of people who had already recovered from a SARS-CoV-2 infection earlier. In California to date, we have had 3,618,594 infections and 55,455 total deaths. California is averaging 249 deaths per day in the last 14 days. Currently, 9.15% of the population in California is infected. Nationally, we rank 29th in the percentage of people in the state infected. To my knowledge, only one privately held company is currently modifying their vaccine to cover the B.1.429 + B.1.427 mutant. 

New Mutants Arrive in California

Stanford University announced this week that they have identified five infections with the Maharashtra India VOC 32421 (yet to be named) in the San Francisco Bay Area. Two additional isolates are PCR positive and pending sequencing. This isolate is a double-mutant responsible for up to 40% of the infections in India. 

Many readers may now be familiar with the E484K mutation present in the South African isolate, the Brazilian isolate, the New York isolate (B.1.256), and the new Nigerian/UK double mutant. When vaccine manufacturers make booster vaccines to address these variants, they will only account for the E484K mutation. What sets this VOC from India apart from the other variants is that it has a different point mutation at 484 that involves a change of one amino acid of the spike protein, number 484, from glutamic acid to glutamine (E484Q). This point mutation, like E484K, probably allows the virus to bind to the ACE2 receptor and evade neutralizing antibodies directed against the original Wuhan sequence. A vaccine created to address E484K would not address this isolate. 

The second mutation in Maharashtra India VOC 32421 is L452R, which is one of the same mutations seen in CAL.20C (B.1.429 + B.1.427). This mutation is also not being covered by any vaccine currently being made as a booster. 

In India on 4/9/21, 144,829 new infections and 773 deaths occurred. India now has the third-highest number of infections in the world (13,202,783) and the fourth-highest number of deaths (168,467). India has a population of 1,390,456,911. At the present time, only 0.94% of the country has been infected with SARS-CoV-2. International travel and trade will continue to spread this highly infectious isolate to other parts of the world. This infection has now landed in California, our most-populous state. 

Watching the Data

Over the next few months, we’ll be paying close attention to correlations between the SARS-CoV-2 data, the number of isolates identified in various countries and states, and the non-pharmaceutical interventions (like mask mandates and lockdowns) put in place by state and national governments. Data on infections, deaths, and percent of population infected was compiled from Worldometers. Data for this table for SARS-CoV-2 Isolates Currently Known in Location was compiled from GISAID and the CDC. It’s worth noting that GISAID provided more data than the CDC. 

LocationTotal Infections as of 4/9/21New Infections on 4/9/21Total DeathsNew Deaths on 4/9/21% of Pop.InfectedSARS-CoV-2 Isolates Currently Known in LocationNational/ State Mask Mandate?Currently in Lockdown?
World135,290,124786,147*2,927,75013,3171.73%B2 lineageB.1.1.7 (UK)B.1.525 (Nigeria/UK)B.1.526 (USA-NYC)B.1.351 (SA)B.1.429 + B.1.427 (USA)**P.1 (Brazil)P.2 (Brazil)A lineage isolateV01.V2 (Tanzania)APTK India VOC 32421Maharashtra India VOC 32421NoNo
USA31,802,772
(ranked #1)
85,638
(ranked #3)
574,840
(ranked #1)
9299.56%B2 lineageB.1.1.7 (UK)B.1.525 (Nigeria/UK)B.1.526 (USA-NYC)B.1.351 (SA)B.1.429 + B.1.427 (USA)**P.1 (Brazil)P.2 (Brazil)Maharashtra India VOC 32421NoNo
Brazil13,375,414(ranked #2)   89,090(ranked #2) 348,934(ranked #2)3,6476.25%B2 lineageB.1.1.7 (UK)B.1.351 (SA)P.1 (Brazil)P.2 (Brazil)NoNo
India13,202,783(ranked #3)144,829(ranked #1)168,467(ranked #4)7730.94%B2 lineageB.1.1.7 (UK)B.1.351 (SA)B.1.429 + B.1.427 (USA)**B.1.525 (Nigeria/UK)APTK India VOC 32421Maharashtra India VOC 32421NoNo
United Kingdom4,365,456(ranked #6)3,145127,040606.40%B2 lineageB.1.1.7 (UK)B.1.525 (Nigeria/UK)B.1.351 (SA)B.1.429 + B.1.427 (USA)**P.1 (Brazil)NoNo
California, USA3,694,147(ranked #9)3,60960,2821539.34%B2 lineageB.1.1.7 (UK)B.1.351 (SA)B.1.429 + B.1.427 (USA)**P.2 (Brazil)Maharashtra India VOC 32421NoNo
Mexico2,267,109(ranked #14)5,140206,146(ranked #3)5481.74%B2 lineageB.1.1.7 (UK)B.1.429 + B.1.427 (USA)**P.1 (Brazil)NoNo
South Africa1,556,242(ranked #20)1,26753,226532.50%B2 lineageB.1.1.7 (UK)B.1.351 (SA)NoNo
Canada1,045,278(ranked #23)9,25523,251402.59%B2 lineageB.1.1.7 (UK)B.1.525 (Nigeria/UK)B.1.429 + B.1.427 (USA)**P.1 (Brazil)Yes, except Alberta ProvinceNo
Poland2,528,042(ranked #11)28,52328,5237686.40%B2 lineageB.1.1.7 (UK)B.1.525 (Nigeria/UK)B.1.351 (SA)NoNo
Turkey3,745,657(ranked #7)55,79133,45425314.40%B2 lineageB.1.1.7 (UK)B.1.525 (Nigeria/UK)B.1.351 (SA)B.1.429 + B.1.427 (USA)**P.1 (Brazil)NoNo

*This number is higher than it was 2 weeks ago. It was 630,055. 

**Also referred to as CAL.20C

SARS-CoV-2 and Children

I’m pleased to see that COVID-19 cases and MIS-C (PIMS) cases in children in the US are finally getting national attention. The CDC now tracks total MIS-C cases and deaths in children and young adults up to 20 years old in the United States. As of March 29, CDC reported 3,185 cases of MIS-C that meet the case definition and 33 deaths—that’s 568 new cases and 3 new deaths since the March 1 report. The CDC notes, “As of October 1, the number of cases meeting the case definition for multisystem inflammatory syndrome in children (MIS-C) in the United States surpassed 1,000. As of February 1, this number surpassed 2,000, and exceeded 3,000 as of April 1.” This means it took seven months to reach 1,000 MIS-C cases, only four months to reach additional 1,000 cases, and only two months to add additional 1,185 cases. This suggests to us that B.1.1.7 is causing more MIS-C. 

Schools in the United States have been open throughout the pandemic, with teachers and education support professionals demonstrating their extraordinary ability to adapt in adverse circumstances. Teachers all over the country reinvented their teaching, taking their classrooms online in order to provide safe and remote learning experiences for students. The so-called “reopening” of schools, which more accurately refers to the opening of school buildings, as schools never closed, has been highly politicized, with many governors issuing mandates for in-person instruction, even as case counts, hospitalizations, and deaths in their states rose exponentially. The CDC has maintained that transmission risk in schools is minimal, provided that adequate safety measures are taken; however, we know that many states have not properly enforced universal masking (and some are repealing mask mandates this week), and we know that many school facilities are not equipped with the proper air handling systems. With more school buildings opening, there is a growing body of research that suggests that COVID-19 transmission can and does happen in schools. 

After recommending for months that school buildings be open, in mid-February (a year into the pandemic), The American Academy of Pediatrics, in collaboration with the Children’s Hospital Association, finally began tracking data on COVID-19 in children at the state and national level. Data reporting by states is still voluntary, and every state is different in its willingness to collect and disclose data on infections, hospitalizations, deaths, and testing rates in children. 

As of the APA’s April 1 report, only 11 states provide age distribution for testing. This makes it difficult to hold states accountable for testing each age group in proportion to its population. We’ve seen a trend in states where testing data with age distribution is available that children are tested at lower rates than adults. Hospitalization data by age group is only available in 24 states and New York City, so we only understand the severity of COVID-19 infections in children for about half the country. Age distribution for cases is provided by 49 states, New York City, the District of Columbia, Puerto Rico, and Guam. It’s worth noting that New York State does not provide age data for cases, testing, hospitalizations, and deaths. Two states, Florida and Utah, only report cases in children aged 0-14, so the number of cases, hospitalizations, and deaths in children ages 15-17 is unknown in these states. 

As of April 1, A total of 284 child deaths due to COVID-19 were reported in 43 states (an increase of 16 child deaths since March 18). In the United States, The following states do not report child mortality due to COVID-19: Michigan, Montana, New Mexico, New York, Rhode Island, South Carolina, and West Virginia. Texas only reports age data for 3% of confirmed COVID-19 cases, so state-level data from Texas is extremely limited for assessing the incidence of COVID-19 in children. Even considering this, Texas reported 49 (+2) child deaths. Arizona reported 26 (+2), California 16 (+1), Colorado 12, Georgia 10, Illinois 17 (+1) , Maryland 10, Tennessee 11, and New York City 22 (+1). 

The United Kingdom tracks hospitalizations by age group, and with the increased incidence of B.1.1.7 saw the number of child hospitalizations double from November 2020 to January 2021. This data likely influenced the decision to close school buildings and go into total lockdown there on January 4, 2021. If we truly want to keep children safe, especially as many school buildings open for in-person instruction, we need to collect more complete data in every state on child testing rates, cases, hospitalizations, and deaths.

The Road Ahead

We are just on Day 80 of the Biden-Harris administration.The President has made the pandemic a first priority and has now ordered enough vaccine to vaccinate everyone who wants a vaccination by July 2021. We have been averaging 3 million vaccinations a day for the last seven days after having opened mass vaccination sites in multiple cities and states. To date, 178,837,781 doses of vaccine have been administered. As of 4/9/21, in the U.S., 68,202,458 people are fully vaccinated, which accounts for 20.5% of the population. On April 16, all people in the U.S. over the age of 16 will be eligible to receive a vaccine. The Biden administration is on track to exceed its goal of administering 200 million doses of vaccine in the first 100 days of the administration. Pfizer and Moderna have applied for emergency use authorization to administer their mRNA vaccines to children aged 12-16. Testing is ongoing for children in younger age groups. 

Testing, wearing masks, social distancing and washing our hands frequently should no longer be political issues. These are non-pharmaceutical interventions used by most successful countries and some states to protect their citizens and their economies. New Zealand, Taiwan, and Australia are three countries that have done this successfully. In the United States, Hawaii is doing a better job handling the pandemic than many of our states. These interventions with vaccination should keep the pandemic from overwhelming our health care delivery system. New mutations like B.1.429 + B.1.427 (Cal.20C) and the UK, Brazillian, South African, and Indian variants will probably spread rapidly throughout the United States over the next 90 days as several states (including Texas, Florida, Iowa, Mississippi) open up everything and do away with masking and social distancing. We are seeing an increase of 11,000 new infections per day in the United States, compared to an increase of only 9 new infections per day two weeks ago. In the UK, B.1.1.7, has increased the number of infections, hospitalizations and deaths. This and other mutants may be doing the same thing in the USA.

The Pfizer and Moderna RNA vaccines and the Johnson & Johnson single dose vaccination adenovirus vaccine are all being used to immunize people in the USA. The Oxford-AstraZeneca vaccine and Novavax vaccine should also be available in the second quarter of 2021. 

The bad news is that all currently available vaccines are based on the Chinese spike protein sequence from December 2019. Mutated isolates, as discussed above, may overtake our ability to produce new vaccines and vaccinate the populace. Like Influenza vaccines, we may have to reformulate vaccines based on active, worldwide surveillance at least every 4 to 6 months. The FDA is currently putting together a guidance document for how to develop booster vaccines for SARS-CoV-2 mutations. A surrogate marker of protection like antibody to the mutated Receptor Binding Domains of SARS-CoV-2 should be considered for vaccine approval. 

I still feel the current approach of companies and governments of making new vaccines against just the South African variant is wrong. In Brazil, where the P.1 isolate is dominant, they’ve had 1,050,649 infections and 45,208 deaths in the last 14 days. In South Africa, the total number of infections ever is 1,556,242, and they’ve had 53,226 deaths. Brazil is on track to have more infections and deaths in the next month than South Africa has had for the entire pandemic. It makes no sense to make a vaccine based on the South African mutant and not make one for the Brazilian P.1 mutant. 

The ideal approach to these spreading major mutations on at least five continents would be to make vaccines against each of the mutations. I’d get all of the vaccine companies and contract production companies on a call and “suggest” that two companies at least make and mass produce each of the four mutations. The government would pay the cost and buy at least 200 million doses in advance for each variant at say $40 a dose. The total cost to purchase the vaccine (800 million doses) would only be 32 billion dollars. Give each company a billion dollars each for development costs (another 8 billion dollars). Spend another two billion dollars for syringes and you’ve got enough booster doses to vaccinate 200 million people for all 4 variants. 42 billion dollars would be a small price to pay to catch up with the current mutations. Even if you had to do this every two years, it would be well worth the dollars spent. 

We are not doing adequate numbers of PCR or antigen detection assays in the United States. According to JHU, in January of 2021, we were doing up to 2,307,949 tests per day. In March 2021 so far, the highest number of tests per day has been 1,709,210, so we’re doing nearly 600,000 fewer tests per day. We still need to perform more virus isolations and perform more DNA sequencing of viruses in each country, state, populous city, and county if we are to rapidly identify new mutations. I’m more hopeful that we will have the facilities, the equipment, and the trained staff needed to perform this work. As a nation we are finally preparing to make more vaccine, new vaccines directed against mutants, and the necessary rapid tests and protective equipment needed by medical staff, first responders, essential workers and especially teachers and students. I’m still hopeful we can work together on our and the world’s infectious disease problems. 

What We’re Reading This Week

COVID-19

SARS-CoV-2 (COVID-19) Update

It’s time for our next 14-day moving average determinations and projections for infections and deaths from SARS-CoV-2 for the United States and my thoughts on vaccines and mutant viruses. We use the WORLDOMETERS aggregators data set to make our projections of future total infections and deaths since it includes data from the Department of Veterans Affairs, the U.S. Military, federal prisons and the Navajo Nation.

In the United States, SARS-CoV-2 deaths have decreased for the first time since the last 14-day period. There were 382 fewer deaths per day than in the last 14-day period. In the last 14 days, the number of infections has decreased by 61,644 infections per day. This decrease in infections over the last two 14-day periods may represent increased mask usage and social distancing, which are a part of the Biden 100-day SARS-CoV-2 plan. On 2/12/21, 100,288 new infections occurred in the United States. There were also 2,908 deaths. The number of hospitalized patients is decreasing, and only 19,927 patients are critically ill. The number of critically ill patients has decreased by 4,561 in the last 14 days, while 40,216 new deaths occurred. This suggests that the number of critically ill patients is decreasing because a large number of patients are dying. 

As of 2/12/21, we have had 492,521 deaths and 28,106,704 SARS-CoV-2 infections in the United States. We have had 1,545,917 new infections in the last 14 days. We are adding 772,958 infections every 7 days. Each million infections usually results in at least 20,000 deaths. On 2/12/21, eighteen states have had greater than 500,000 total infections, and 28 states had greater than 5,000 total deaths. 

On 11/20/20 in the United States, 3.70% of the population had a documented SARS-CoV-2 infection. California was ranked 41st in infection percentage at 2.77%. In North Dakota 9.18% of the population was infected (ranked #1), and in South Dakota 8.03% of the population was infected (ranked #2).

As of 2/12/21, in the United States 8.46% of the population has had a documented SARS-CoV-2 infection. California was ranked 25th in infection percentage at 8.74%. In North Dakota 12.92% of the population was infected (ranked #1) and in South Dakota 12.44% of the population was infected (ranked #2). Ten states have greater than 10% of their population infected: North Dakota, South Dakota, Iowa, Nebraska, Arizona, Utah, Tennessee, Oklahoma, Arkansas, and Rhode Island. Only six states have less than 6% of their population infected: New Hampshire (5.51%), Washington (4.33%), Oregon (3.54%), Maine (3.14%), Vermont (2.15%), and Hawaii (1.88%). 

New Mutants

A new mutant SARS-CoV-2 virus (lineage B.1.1.7), first seen in the UK in September, has now been found in multiple other countries. There are 981 reported cases in the US as of 2/11/21. This isolate has now been found in over 37 states. This isolate (let’s call it Lineage B.1.1.7 or SARS-CoV-2 UK) is more infectious than other previously circulating B2 lineage isolates (probably 30 to 40% increased infectivity). There are two deletions and six other mutations in its spike protein. One mutation involves a change of one amino acid, an asparagine at position 501 in the receptor binding motif with a tyrosine. This enhances binding (affinity) to the ACE-2 receptor and may alone be responsible for the increased infectivity of this isolate. Due to air and other travel, this isolate will become the dominant isolate worldwide. 

B.1.351, also known as the South African isolate, has 13 reported cases and has occurred in 5 states: South Carolina, North Carolina, Virginia, Maryland, and California. The P.1 isolate (Brazil) has 3 reported cases and has been found in Minnesota and Oklahoma. (This data is available at https://www.cdc.gov/coronavirus/2019-ncov/transmission/variant-cases.html.)

A new, disturbing report out of the UK has found a second mutation in B.1.1.7. This mutation, which occurs in the loop sequence has also been found in the South African (B.1.351) and Brazilian (P.1) variants. (The loop sequence is in the receptor binding motif in the receptor binding domain of the S1 sequence of the spike protein.) This mutation involves a change of one amino acid of the spike protein, number 484, from glutamic acid to lysine. This point mutation allows the virus to bind better to the ACE2 receptor, which increases infectivity. People who are exposed to one of these variants (verus the old B2 isolate) are more likely to be infected and are more likely to transmit the virus to others. 

In our last update we summarized a research letter published in Clinical Infectious Diseases about a patient in the UK who was first infected in April with a B2 isolate and experienced only mild symptoms but was infected with the new B.1.1.7 variant in December and became critically ill. The patient described in this research letter was not protected by a natural infection with a B2 lineage SARS-CoV-2 isolate in April 2020 from having a potentially lethal second infection with a B.1.1.7 lineage variant in December 2020, suggesting that folks who have had a past SARS-CoV-2 infection should not expect to have any immunity to new variants such as B.1.1.7. All of the currently available vaccines were developed with spike protein from B2 lineages. Moderna, Pfizer, and AstraZeneca/Oxford are currently remaking their spike protein vaccines to address the mutations in the South African variant of SARS-CoV-2 because the AstraZeneca/Oxford vaccine did not work in a small trial in South Africa, where most of the patients had the South African mutant (B.1.351). 

A California Mutant

A fourth mutant isolate (CAL.20C) of SARS-CoV-2 has been identified in California. This isolate does not have any of the mutations mentioned above, but contains five mutations, three of which are in the spike protein, but not in the receptor binding motif. This mutant appears to be responsible for the massive increase in infections in California, to include infections of people who had already recovered from a SARS-CoV-2 infection earlier. In California, we have had 3,457,214 infections, 46,379 total deaths, and 6,533 deaths in the last 14 days. California is averaging 466 deaths per day in the last 14 days. Currently, 8.3% of the population in California is infected. Nationally, we rank 25th in the percentage of people in the state infected. To my knowledge, no company is currently modifying their vaccines to cover the CAL.20C (California) mutant. 

Watching the Data

Over the next few months, we’ll be paying close attention to correlations between the SARS-CoV-2 data, the number of isolates identified in various countries and states, and the non-pharmaceutical interventions (like mask mandates and lockdowns) put in place by state and national governments. 

The Road Ahead

We have a new President and Vice President. The President has made the pandemic a first priority. Testing, wearing masks, social distancing and washing our hands frequently should no longer be political issues. These are non-pharmaceutical interventions used by most successful countries and some states to protect their citizens and their economies. New Zealand, Taiwan, and Australia are three countries that have done this successfully.  In the United States, Vermont and Hawaii are doing a better job handling the pandemic than many of our states. The pandemic problem is overwhelming our health care delivery system in many states.

The Pfizer and Moderna RNA vaccines are both now approved in the USA. The Johnson & Johnson and Novavax vaccines are pending approval. To vaccinate 80% of our population with two doses of vaccine, we will need over 500 million doses of vaccine. The current goal of the Biden administration in the US is to vaccinate one million people each day for 100 days. At this rate, to vaccinate 280 million people it would take 280 days—more than 9 months. The good news is this week, on one day, 2 million vaccinations occurred. If this pace were to continue we could vaccinate everyone who wanted a vaccine in the USA in less than five months.

All current vaccines are based on the Chinese spike protein sequence from December 2019. Mutated isolates, as discussed above, may overtake our ability to produce vaccines and vaccinate the populace. Like Influenza vaccines, we may have to reformulate vaccines based on active, worldwide surveillance every 6 to 8 months. The FDA is currently putting together a guidance document for how to develop booster vaccines for SARS-CoV-2 mutations. We need to perform more virus isolations and perform more DNA sequencing of viruses in each country, state, populous city, and county if we are to rapidly identify new mutations. I’m more hopeful that we will have the facilities, the equipment, and the trained staff needed to perform this work. As a nation we are finally preparing to make more vaccine, new vaccines directed against mutants, and the necessary rapid tests and protective equipment needed by medical staff, first responders, and especially teachers and students. I’m hopeful we can work together on our and the world’s problems.

COVID-19

SARS-CoV-2 (COVID-19) Update

It’s time for our next 14-day moving average determinations and projections for infections and deaths from SARS-CoV-2 for the United States and my thoughts on vaccines and mutant viruses. We use the Worldometer aggregators data set to make our projections of future total infections and deaths since it includes data from the Department of Veterans Affairs, the U.S. Military, federal prisons and the Navajo Nation.

14-day Moving Averages of SARS-CoV-2  Deaths and Infections in USA

1/15/211/01/2112/18/2012/04/2011/21/2011/07/2010/24/2010/10/209/26/209/12/208/28/208/14/207/31/207/17/20
Deaths/day3,163*2,4622,5101,7771,2868917547287878239631,0501,070714
Infections/Day248,131**186,106216,750173,513154,94590,07559,15545,24640,65739,95143,88454,59766,74861,512
*701 more deaths per day than the 14-day period ending in 1/1/21 **62,025 more infections per day than the 14-day period ending in 1/1/21

In the United States, SARS-CoV-2 deaths have increased for the first time since the last 14-day period. There were 701 more deaths per day than in the last 14-day period. In the last 14 days, the number of infections has increased by 62,024 infections per day.  This increase in infections over the last two-week period is due to two major holidays. On 1/15/21, 248,080 new infections occurred in the United States. There were also 3,805 deaths. Over 130,000 people are hospitalized in the USA and 28,937 serious or critically ill patients are in our hospitals as of 1/15/21.

As of 1/15/21, we have had 401,856 deaths and 24,102,429 SARS CoV-2 infections in the United States.  We have had 3,473,834 new infections in the last 14 days. We are adding  over 1.7 million infections every 7 days. Each million infections usually results in at least 20,000 deaths. On 1/15/21, fifteen states have had greater than 500,000 total infections, and 26 states had greater than 5,000 total deaths. 

On 11/20/20 in the United States, 3.70% of the population had a documented SARS-CoV-2 infection. California was ranked 41st in infection percentage at 2.77%. In North Dakota 9.18% of the population was infected (ranked #1), and in South Dakota 8.03% of the population was infected (ranked #2).

As of 1/15/21, in the United States 7.28% of the population has had a documented SARS-CoV-2 infection. California was ranked 26th in infection percentage at 7.40%. In North Dakota 12.54% of the population was infected (ranked #1) and in South Dakota 11.86% of the population was infected (ranked #2). Thirty-six states already have greater than 6% of their population infected (North Dakota, South Dakota, Iowa, Nebraska, Wisconsin, Utah, Montana, Illinois, Idaho, Tennessee, Rhode Island, Minnesota, Wyoming, Kansas, Indiana, Arkansas, Nevada, Alabama, Oklahoma, Mississippi, Arizona, New Mexico, Louisiana, Missouri, Georgia, Alaska, Florida, Texas, Connecticut, North Carolina, Colorado, Massachusetts, Ohio, New Jersey, Delaware and Kentucky). 

A new mutant SARS-CoV-2 virus (lineage B.1.1.7), first seen in the UK in September, has now been found in multiple other countries. In California, two patients in LA county and three patients in San Diego county are infected with this new mutant. Two patients in Colorado and one in Florida have also been identified as of 12/31/20. As of 1/15/21, this new mutant has been found in nine other states (New York, Georgia, Texas, Connecticut, Pennsylvania, Ohio, Utah, Maryland, and Wisconsin. This isolate (let’s call it Lineage B.1.1.7 or SARS-CoV-2 UK) is more infectious than other previously circulating B2 lineage isolates (probably 30 to 40% increased infectivity). There are two deletions and six other mutations in its spike protein. One mutation involves a change of one amino acid, an asparagine at position 501 in the receptor binding motif with a tyrosine. This enhances binding (affinity) to the ACE-2 receptor and may alone be responsible for the increased infectivity of this isolate. Due to air and other travel this isolate should become the dominant isolate worldwide.  

In a research letter pending publication in Clinical Infectious Diseases, a group of NHS doctors describe the case of a patient who was first infected with SARS-CoV-2 in April and became reinfected in December. After the patient’s second infection, Whole Genome Sequencing (WGS) was performed on samples from both instances of infection, and it was determined that the first infection in April was with a B.2 lineage variant and the second infection was with the new B.1.1.7 variant. While the patient, “a 78 year old man with a history of Type 2 Diabetes Mellitus, diabetic nephropathy on haemodialysis, chronic obstructive pulmonary disease (COPD), mixed central and obstructive sleep apnoea, ischaemic heart disease, with no history of immunosuppression” had only had a mild illness (fever being the only symptom) during the first infection, during the second infection, he had much more severe symptoms, including shortness of breath and hypoxia, which led to emergency intubation. He developed “Severe Covid-19 pneumonia complicated by mycocardial infarction with resulting trifascicular block and Atrio-Ventricular (AV) dissociation and pulmonary oedema.” (To read the full research letter, visit https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciab014/6076528 and click PDF.)

The patient described in this research letter was not protected by a natural infection with a B2 lineage SARS-CoV-2 isolate in April 2020 from having a potentially lethal second infection with a B.1.1.7 lineage variant in December 2020, suggesting that folks who have had a past SARS-CoV-2 infection should not expect to have any immunity to new variants such as B.1.1.7. All of the currently available vaccines were developed with spike protein from B2 lineages, so it remains to be seen whether these vaccines will protect against B.1.1.7 infections or the additional isolates discussed below.

A second mutation in the loop sequence has been identified in the South African, Brazilian, and Japanese isolates this week. This mutation will also enhance binding to the ACE-2 receptor and may interfere with binding of monoclonal antibodies to the SARS-CoV-2 receptor binding motif. If this rate of mutations and deletions continues in the spike protein, especially in the receptor binding domain and motif, in my opinion, then vaccine reformulation will be required in 2021.

We have a new President-elect and Vice President-elect, now confirmed by the electoral college and approved in the House and Senate on 1/06/21 despite a riot and invasion of the Capital by President Trump’s supporters. The President-elect has made the pandemic a first priority after Inauguration on January 20, 2021. Testing, wearing masks, social distancing and washing our hands frequently should no longer be political issues. These are non-pharmaceutical interventions used by most successful countries and some states to protect their citizens and their economies. New Zealand, Taiwan, and Australia are three countries that have done this successfully.  In the United States, Maine, Vermont, and Hawaii are doing a better job handling the pandemic than many of our states. The pandemic problem is overwhelming our health care delivery system in many states. Unless things change before Inauguration Day on January 20, 2020 (5 days away) we could, by our predictions, have an additional 1,221,405 SARS-CoV-2 infections and another 15,815 deaths. Our infections per day and deaths per day will continue to increase for at least another 8 to 12 weeks.

The Pfizer and Moderna RNA vaccines are both now approved in the USA. To vaccinate 80% of our population with two doses of vaccine, we will need over 500 million doses of vaccine. Unless we start vaccine shipments to clinics and physicians’ offices, not just hospitals and pharmacies, I doubt most people will be able to receive any vaccine until April 2021.  

All current vaccines are based on the Chinese spike protein sequence from December 2019. Mutated isolates, as discussed above, may overtake our ability to produce vaccines and vaccinate the populace. Like Influenza vaccines, we may have to reformulate vaccines based on active, worldwide surveillance every 8 to 12 months. We need to perform more virus isolations and perform more DNA sequencing of viruses in each country, state, populous city, and county if we are to rapidly identify new mutations. I’m not sure we have the facilities, the equipment, and the trained staff needed to perform this work. I feel we are not prepared (or preparing) to do this and will suffer the consequences if we continue down our current path. “Magical thinking” will not solve these problems, just laborious work by many people. Are we all up to the tasks at hand?