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 second time in a 14-day period. There were 843 fewer deaths per day than in the last 14-day period. In the last 14 days, the number of infections has decreased by 39,769 infections per day. This decrease in infections over the last three 14-day periods may represent increased mask usage and social distancing, which are a part of the Biden 100-day SARS-CoV-2 plan (day 38 of plan). On 2/26/21, 81,942 new infections occurred in the United States. There were also 2,280 deaths. The number of hospitalized patients is decreasing, and only 15,478 patients are critically ill. The number of critically ill patients has decreased by 4,449 in the last 14 days, while 28,426 new deaths occurred. This suggests that the number of critically ill patients is decreasing because a large number of patients are dying. 

As of 2/16/21, we have had 523,116 deaths and 29,138,228 SARS-CoV-2 infections in the United States. We have had 990,465 new infections in the last 14 days. We are adding 495,232 infections every 7 days. Each million infections usually results in at least 20,000 deaths. On 2/26/21, nineteen states have had greater than 500,000 total infections, and 29 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 2/26/21, in the United States 8.76% of the population has had a documented SARS-CoV-2 infection. In the last 3 months 5% of our country became infected with SARS-CoV-2. 

As of 2/26/21, California was ranked 26th in infection percentage at 8.74%. In North Dakota 13.08% of the population was infected (ranked #1) and in South Dakota 12.67% of the population was infected (ranked #2). Twenty-five states have greater than 9% of their population infected and 44 states have greater than 6% infected. Only four states have less than 4% of their population infected: Oregon (3.67%), Maine (3.29%), Vermont (2.39%), and Hawaii (1.93%). 

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 2,102 reported cases in the US as of 2/26/21. This isolate has now been found in 44 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. 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 49 reported cases and has occurred in 15 states and the District of Columbia. The P.1 isolate (Brazil) has 16 reported cases and has been found in five states. (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 two 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 (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 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 3,547,280 infections and 51,377 total deaths. California is averaging 357 deaths per day in the last 14 days. Currently, 8.76% of the population in California is infected. Nationally, we rank 26th 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 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 are just on Day 38 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. 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. These interventions with vaccination should keep the pandemic from overwhelming our health care delivery system. New mutations will probably increase the numbers of infections occurring in the United States over the next 30 days. At least one mutant from the UK, B.1.1.7, has increased the number of infections, hospitalizations and deaths. This mutant may do the same thing in the USA.

The Pfizer and Moderna RNA vaccines are approved in the USA and the Johnson & Johnson single dose vaccination should be approved this weekend. The Oxford-AstraZeneca vaccine and Novavax vaccine should also be available in the second quarter of 2021. To vaccinate 80% of our population with two doses of a 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. The good news is that we are averaging 1.5 million vaccinations a day and have opened mass vaccination sites in multiple cities and states. 

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. 

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. 

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 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 increased for the second time since the last 14-day period. There were 92 more deaths per day than in the last 14-day period. In the last 14 days, the number of infections has decreased by 76,065 infections per day. This decrease in infections over the last two-week period may be because of a peak of infectivity of current circulating B2 lineage isolates. (B2 isolates are those that were most common in the first nine months of the pandemic.) On 1/29/21, 169,033 new infections occurred in the United States. There were also 3,652 deaths. The number of hospitalized patients is decreasing, and only 24,963 patients are critically ill. The number of critically ill patients has decreased by 3,887 in the last 14 days, while 45,575 new deaths occurred. This suggests that the number of critically ill patients is decreasing because a large number of patients are dying. 

As of 1/29/21, we have had 447,459 deaths and 26,512,193 SARS-CoV-2 infections in the United States. We have had 2,408,917 new infections in the last 14 days. We are adding over 1.2 million infections every 7 days. Each million infections usually results in at least 20,000 deaths. On 1/29/21, sixteen 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 1/29/21, in the United States 8.00% of the population has had a documented SARS-CoV-2 infection. California was ranked 24th in infection percentage at 8.30%. In North Dakota 12.7% of the population was infected (ranked #1) and in South Dakota 12.2% of the population was infected (ranked #2). Forty-two 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, South Carolina, Colorado, Massachusetts, Ohio, New York, New Jersey, Delaware, Kentucky, West Virginia, Pennsylvania, California, and Michigan). 

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. This isolate has now been found in over 25 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 should become the dominant isolate worldwide.  

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, 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 mutation also enhances binding to the ACE-2 receptor and interferes with binding of antibodies to the SARS-CoV-2 receptor binding motif. This week, it was announced that in South Carolina, they have two unrelated patients infected with the South African mutant of SARS-CoV-2. Neither patient has traveled outside of South Carolina. According to the Director of the CDC, these represent community acquisition of the South African isolate. In addition, South Carolina announced today that they have identified the UK isolate B.1.1.7 in a patient in their state. Additionally, the state of Minnesota has reported, this week, the first case of the Brazilian mutant in the United States. 

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 3,279,921 infections, 40,206 total deaths, and 6,378 deaths in the last 14 days. California is averaging 456 deaths per day in the last 14 days. Currently, 8.3% of the population in California is infected. Nationally, we rank 24th in the percentage of people in the state infected. 

Pfizer and Moderna announced this week that they would be reformulating their vaccines to cover the mutations in the South African isolate. 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. 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. The current goal in the US is to vaccinate one million people each day for 100 days. At this rate, to vaccinate 280 million people will take 280 days—more than 9 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 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. 

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?

COVID-19, Uncategorized

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. 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.

14-day moving averages of SARS-CoV-2 Deaths and Infections in the USA

11/21/2011/07/2010/24/2010/10/209/26/209/12/208/28/208/14/20
Average deaths per day1,286*8917547287878239631,050
Average infections per day154,945**90,07559,15545,24640,65739,95143,88454,597
*395 more deaths per day than 11/07/20 **64,870 more infections per day than 11/07/20

In the United States, SARS-CoV-2 deaths have increased for the third time in a 14-day period after decreasing in each of five previous 14-day periods. There were 395 more deaths per day in the last 14 days. In the last 14 days, the number of infections has increased by 64,870 infections per day. Deaths per day will continue to increase at least over the next 8 to 10 weeks. On 11/20/20, 204,179 new infections occurred in the United States, another new daily record for infections. There were also 1,999 deaths and 22,789 serious or critically ill patients in our hospitals on 11/20/20.

As of 11/20/20 we have had 260,331 deaths and 12,277,827 SARS CoV-2 infections in the United States. This represents 21.2% of the infections and 18.9% of the deaths in the world from SARS-CoV-2. We have had 2,169,236 new infections in the last 14 days. We are adding one million infections every 7 days. Each million infections usually results in at least 20,000 deaths. On 11/20/20, thirty five states had greater than 100,000 total infections and 29 states had greater than 2,000 total deaths. Only 58 other countries have greater than 100,000 infections and only 51 countries have more than 2,000 deaths.

We have a new President-elect and Vice President-elect that are making the pandemic a first priority after Inauguration on January 20, 2021. Testing, contact tracing, 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 (61 days away) we could by our predictions have an additional 9,451,645 SARS-CoV-2 infections and another 78,446 deaths. If our infections per day and deaths per day continue to increase these numbers will, once again, be underestimations of the problem.

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. 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.

11/07/2010/24/2010/10/209/26/209/12/208/28/208/14/207/31/20
Average Deaths per day*8917547287878239631,0501,070
Average Infections per day**90,07559,15545,24640,65739,95143,88454,59766,748
*137 more deaths per day than 10/24/20 14-day period
**30,920 more infections per day than 10/24/20 14-day period

In the United States, SARS-CoV-2 deaths have increased for the second time in a 14-day period after decreasing in each of five previous 14-day periods. There were 137 more deaths per day in the last 14 days. In the last 14 days, the number of infections per day has increased by 30,920. Deaths per day will continue to increase at least over the next 8 to 12 weeks. On 11/06/20, 132,540 new infections occurred in the United States, another new daily record for infections. There were also 1,248 deaths and 18,303 serious or critically ill patients in our hospitals on 11/06/20.

As of 11/06/20, we have had 242,230 deaths and 10,058,586 SARS-CoV-2 infections in the United States. This represents 20.2% of the infections and 19.4% of the deaths in the world from SARS-CoV-2. On 10/24/20, 29 states in the United States had greater than 100,000 infections and 26 states had greater than 2,000 deaths. On 11/06/20, 32 states have greater than 100,000 infections and 28 states have greater than 2,000 deaths. Only 57 other countries have greater than 100,000 infections, and only 45 countries have more than 2,000 deaths.

As of 10/24/20, in the United States, 2.642% of the population has had a documented SARS-CoV-2 infection. California was ranked 33rd in infection percentage at 2.270%. In North Dakota, 4.716% of the population was infected (ranked #1) and in South Dakota 4.205% of the population was infected (ranked #2). As of 11/06/20, in the United States, 3.038% of the population has had a documented SARS-CoV-2 infection. California was ranked 36th in infection percentage at 2.44%. In North Dakota 6.77% of the population was infected (ranked #1) and in South Dakota 5.95% of the population was infected (ranked #2). On 11/06/20, Texas became the first state to record over a million total infections. They had 9,239 infections and 124 deaths on 11/06/20, bringing their total infections to 1,007,155 and total deaths to 19,154. 3.47% of Texas residents have had an infection. Probably greater than 90% of the people in the USA have not had their first SARS-CoV-2 infection.

We have a new President-elect and Vice President-elect today. Testing, contact tracing, 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, New Hampshire, Hawaii and Oregon are doing a better job handling the pandemic than many of our states. The pandemic problem is about to overwhelm our health care delivery system in many states. Unless things change before Inauguration Day on January 20, 2021 (75 days away) we could, by our predictions, have 6,755,625 new SARS-CoV-2 infections and another 66,825 deaths. If our infections per day and deaths per day continue to increase, these numbers will be underestimations of the problem.

COVID-19

SARS-CoV-2 (COVID-19) Projections

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. 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.

14-day moving averages of SARS-CoV-2 Deaths and Infections

10/10/209/26/209/12/208/28/208/14/20
Average deaths per day728*7878239631,050
Average infections per day45,246**40,65739,95143,88454,597
*59 fewer deaths per day than 9/26/20 **4,589 more infections per day than 9/26/20

In the United States, SARS CoV-2 deaths have decreased in each of the last five previous 14-day periods. There were 59 fewer deaths per day in the last 14 days.  However, in the last 14 days the number of infections has increased by 4,589 infections per day. Deaths per day should increase over the next 2 to 3 weeks.

As of 10/09/20 we have had 218,647 deaths and 7,894,478  SARS CoV-2 infections in the United States. This represents 21.3% of the infections and 20.4% of the deaths in the world from SARS-CoV-2. Twenty-four states in the United States have greater than 100,000 infections, and 26 states have greater than 2,000 deaths. Only 43 other countries have greater than 100,000 infections and only 41 countries have more than 2,000 deaths.

COVID-19

SARS-CoV-2 (COVID-19) Projections

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. 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.

 14-day moving averages of SARS-CoV-2  deaths and infections

9/26/209/12/208/28/208/14/207/31/20
Average Deaths Per Day7878239631,0501,070
Average Infections Per Day40,65739,95143,88454,59766,748
*36 fewer deaths per day than on 9/12/20 **706 more infections per day than 9/12/20

In the United States the SARS-CoV-2 deaths have decreased in each of the last four previous 14-day periods. There were 36 fewer deaths per day in the last 14 days. However, in the last 14 days, the number of infections has increased by 706 infections per day.

As of 9/26/20 we have had 208,440 deaths and 7,244,184 SARS-CoV-2 infections in the United States. This represents 22% of the infections and 21% of the deaths in the world from SARS-CoV-2. Twenty-two states in the United States have greater than 100,000 infections and 26 states have greater than 2,000 deaths. Only 37 other countries have greater than 100,000 infections and only 38 countries have more than 2,000 deaths.

Our new projections for the United States are that by October 4, 2020, we will have had 214,696 total deaths and 7,569,440 infections.

Our new projections for the United States are that by November 4, 2020, we will have had 239,093 total deaths and 8,829,807 total infections.

COVID-19

Monterey County California SARS-CoV-2 update 9/06-9/19/20

In the last 14 days (September 6 – September 19, 2020), 9,289 RT-PCR assays for SARS-CoV-2 (COVID-19) were performed and 996 were positive for an average of 10.60% positive tests per day. We have had 9 deaths in 14 days, an average of 0.643 deaths per day. We have now had a total of 9,467 infections in our county; 10.52% of these infections have occurred in the last 14 days of the pandemic. At our current rate of new infections, 71 per day for the last 14 days, we will reach 10,000 total infections in 8 days. 41 new patients were hospitalized in the last 14 days bringing the total to 549; 7.46% of the total hospitalizations have occurred in the last 14 days. Our hospitalization rate is averaging 2.93 patients per day for the last 14 days. To date, 67 of the 549 patients have died (12.20%). We are not controlling the infection in Monterey County. If our rate of hospitalizations and death rate remain constant, we will reach a total of 100 COVID-19 deaths in our county between 11/3/20 and 11/09/20. If we can get the number of infections down below 1% to 3% per day, we might have a chance to control the pandemic and the deaths per day in our county. 

COVID-19

SARS-CoV-2 Projections 9/14/20

It’s time for our next 14-day moving average determinations and projections for infections and deaths from SARS-CoV-2 (COVID-19) for the United States. 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.

14-Day Moving Averages of SARS-CoV-2 Infections and Deaths

9/12/208/28/208/14/207/31/207/17/20
Average Deaths per day823*9631,0501,070714
Average Infections per day39,951**43,88454,59766,74861,512
*140 fewer deaths/day than 8/28/20 **3,933 fewer infections/day than 8/28/20

The SARS-CoV-2 infections and subsequent deaths have decreased in each of three previous 14-day periods. In the last 14 days, the number of infections has decreased by 3,933 infections per day, and average deaths per day have decreased by 140 deaths per day.

As of 9/11/20 we have had 197,177 deaths and 6,636,247 SARS-CoV-2 infections in the United States.

Our new projections for the United States are that by October 4, 2020 we will have had 211,283 total deaths and 7,507,249 infections.

Our new projections for the United States are that by November 4, 2020 we will have had 241,734 total deaths and 8,972,116 total infections.