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 third time in a 14-day period. There were 4,478 fewer deaths per day than in the last 14-day period. In the last 14 days, the number of infections has increased by 9 infections per day. This increase in infections over the last four 14-day periods may be secondary to SARS CoV-2 mutants B.1.1.7 (UK isolate), a New York isolate B.1.526, the CAL.20C isolate, the South African isolate and the Brazilian isolate. Increased mask usage and social distancing, which are a part of the Biden 100-day SARS-CoV-2 plan (day 66 of plan) will be necessary to stop spread of these mutants and cause further reductions in infections, hospitalizations and deaths. On 3/26/21, 76,976 new infections occurred in the United States. There were also 1,289 deaths. The number of hospitalized patients is decreasing, and only 8,610 patients are critically ill. The number of critically ill patients has decreased by 3,060 in the last 14 days, while 14,837 new deaths occurred. This still suggests that the number of critically ill patients is decreasing because a large number of patients are still dying each day. 

As of 3/26/21, we have had 561,142 deaths and 30,853,032 SARS-CoV-2 infections in the United States. We have had 792,803 new infections in the last 14 days. We are adding 396,402 infections every 7 days. Each million infections usually results in at least 20,000 deaths. On 3/12/21, twenty states have had greater than 500,000 total infections, and 30 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 3/12/21, in the United States 9.28% of the population has had a documented SARS-CoV-2 infection. In the last 4 months nearly 6% of our country became infected with SARS-CoV-2. 

As of 3/26/21, California was ranked 31st in infection percentage at 9.25%. In North Dakota 13.43% of the population was infected (ranked #1) and in South Dakota 13.20% of the population was infected (ranked #2). Thirty-four states have greater than 9% of their population infected and 45 states have greater than 6% infected. Only two states have less than 3% of their population infected: Vermont (2.96%), and Hawaii (2.06%). 

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

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. 

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. 

SARS-CoV-2, Children, and MIS-C/PIMS

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 1, CDC reported 2,617 cases of MIS-C that meet the case definition and 33 deaths. (As of March 26, 2021, the CDC has not updated its MIS-C data from the March 1 data. We’re sure why the CDC would wait a whole month to update this data.) 

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 AAP’s March 18 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 March 18, A total of 268 child deaths due to COVID-19 were reported in 43 states (an increase of 15 child deaths since March 4). 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 47 (+3) child deaths. Arizona reported 24, California 15 (+1), Georgia 10, Illinois 16, Maryland 10, Pennsylvania 9 (+2), New Jersey 6 (+2) and New York City 21. 

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 66 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 2.6 million vaccinations a day for the last seven days after having opened mass vaccination sites in multiple cities and states. To date, 138 million doses of vaccine have been administered. The new goal of the Biden administration is to administer 200 million doses of vaccine in the first 100 days of his administration. 

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 like B.1.429 + B.1.427 (Cal.20C), the UK, Brazillian and South African 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 starting to see increased numbers of infections occurring in the United States. In the last seven days, we’ve averaged 4,377 infections per day greater than the preceding seven days. In the UK, B.1.1.7, has increased the number of infections, hospitalizations and deaths. This mutant 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 1,039,036 infections and 32,046 deaths in the last 14 days. In South Africa, the total number of infections ever is 1,543,079, and they’ve had 56,602 deaths. Brazil is on track to have more infections and deaths in two weeks 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 four 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. 


COVID-19 Update (5/24/20)

In this post:

  • The United States still leads the world in COVID-19 cases and deaths.
  • We have no effective available oral treatment or preventative drugs, vaccines or hyperimmune intravenous immunoglobulin for COVID-19. Potential therapies are probably 6 to 9 months away. 
  • Despite the data, in the United States our political leaders , federal agencies, and many state public health officials have decided to open back up our country. 
  • In California, although ICU numbers have been stable the last 7 days, COVID-19 cases and deaths are still on the rise. The majority of reported cases (50.8%) are in the 18-49 age group. 
  • We examine the 1918 flu pandemic’s impact on different age groups and compare it with this year’s COVID-19 data in California, concluding that closing schools early was wise and reopening in August would be deadly. 
  • We continue to recommend staying home whenever possible, wearing a mask in public, and staying 6 feet apart from people outside your household. We outline suggestions for businesses and organizations seeking to reopen more safely, highlighting the dangers of congregating in buildings with poor ventilation (which is most buildings).
  • In Monterey County, agricultural workers, health care workers, and first responders are among the occupations most impacted by COVID-19. More than half of COVID-19 patients in the county have no known pre-existing medical condition. 
  • The incomplete nature of the data collected from California’s skilled nursing homes is problematic.  
  • Based on our modeling, we expect to have 2 million COVID-19 infections and 115,357 deaths in the United States by June 7. 
  • By August 4, 2020, at our current rate of new COVID-19 infections and deaths, we anticipate 3,337,190 COVID-19 infected patients and a total of 192,613 deaths. 

By our way of counting, this is Day 145 of the COVID-19 pandemic. To date, we have neither a vaccine nor a widely-available drug to effectively treat or prevent this infection. Our first USA case was identified in Washington State on Day 21 of the pandemic. In those next 124 days (17.7 weeks) the United States, as of 5/22/20, had 1,645,099 known COVID-19 PCR positive infected patients and 97,647 deaths, giving us a still rising death rate of 5.94%. We had 24,197 new cases and 17,109 people in serious or critical condition on that day. That was the fourth day in a row that we’ve had over 17,000 people in serious or critical condition in the United States. We have 1,314,204 more COVID-19 positive infected patients than any other country in the world. The five countries other than the US with the most cases (Brazil, Russia, Spain, the United Kingdom, and Italy) have a total of 1,422,095 cases combined, which is 223,004 fewer cases than in the United States. 

Four rapidly expanding “hot spot” countries are India with 118,226 infections and 6,198 new infections on 5/21/20, Peru with 108,769 infections and 4,749 new infections, Russia had 317,554 infections and 8,849 new infections on   5/21/20, and Brazil had 310,921 infections and 17,564 new infections. Today we’ll focus our discussion on the State of California and Monterey County.

State of California

As of 5/21/20, the State of California has 88,488 total infections, 3,624 new infections, 3,624 total deaths and 110 new deaths. On 5/21/20, California had more new deaths than any other state, with the exception of New York and was 7th in total deaths in the United States, having just surpassed Connecticut’s deaths. On 5/21/20, California reported 4,735 hospitalized COVID-19 patients (on that day) and 1,310 patients in the ICU. If California were a country, it would rank 13th in total number of cases in the world (above China) and 17th in total deaths (between Russia and India). It would rank 10th in new deaths in the world on 5/21/20. It would rank 7th in the world in ICU patients (between Spain and the UK). As of 5/21/20, California reported conducting 1,421,127 COVID-19 tests, which represents 3.57% of California’s population of 39.78 million. However, we know that some people have been tested more than once, so in fact, less that 3.57% of the population has been tested for COVID-19. 

So what can these numbers suggest to us about what public policies would be prudent at this time for California? Here’s what we think:

Keep School Buildings Closed to Protect Youth and the Elderly

From the beginning of the pandemic, it was messaged to us by public health officials and politicians alike that COVID-19 disproportionately affects folks 65 and over and those with underlying health conditions, leading young healthy folks to believe that they would not be infected or become seriously ill. This made it more difficult for young working people to accept the stay-at-home order as the new way of life, and many are counting down the days, hours, and minutes until they can return to work in person, get their hair and nails done, and return to their local bars, restaurants, gyms, and sporting events. 

However, if we look at the data on which age groups are most affected by COVID-19, we see a much different picture. In California, as of 5/21/20, the age group with the largest number of confirmed infections is people 18-49 years of age, with 44,953 infections, compared to 21,461 people 50-64 and 17,864 people 65 and up. The 0-17 age group has 4,049 cases. (Incidentally, the 0-17 age group is also the least-tested group.) We know that 7,908 of those 65+ folks are residents in skilled nursing facilities are infected with COVID-19, so when you take those folks out of the equation, there are only 9,956 other people over the age of 65 infected in California. Deaths in skilled nursing facilities make up 39.5% of the COVID-19 deaths in California. The point is that people over 65 who are not in skilled nursing facilities are not getting infected at the same rate as younger people. Now, it might be a coincidence, but we can’t help noticing that the two age groups that we have essentially mandated stay home since mid-March (school-aged children and senior citizens) have the lowest numbers of infections. Perhaps preventing infections is not as complicated as folks are making it out to be. 

A standard Influenza respiratory epidemic has a U-shaped death curve (see dotted line 1911-1917 curve below), meaning that you have very young and very old people dying. What happened in the 1918 Influenza pandemic is that they had a W-shaped curve (see solid line below). The peak in the middle happened to be people between the ages of 20 and 40.

From 1918 Influenza: the Mother of All Pandemics (Emerging Infectious Diseases) 

If we look at the data from the 2020 COVID-19 pandemic in California, plotted by age group, we can see some similarities and some key differences from the 1918 pandemic. By closing schools and telling older people to stay home in California, we’ve decreased the number of COVID-19 cases in both groups, effectively losing the left arm of the W and flattening out the right arm from the 1918 Influenza graph.

Thanks to early implementation in California of non-essential business closures, school closures, stay-at-home policies, social distancing, and use of masks, we’ve been able to avoid some of the hardships that folks experienced in the 1918 Influenza pandemic.

However, social distancing is not possible in schools–period. Getting children to wear masks safely and wash their hands with soap and warm water before touching their faces, their food, or their classmates is impossible. We won’t even go into how difficult it would be to keep student bathrooms sanitary. Moreover, large class sizes and inadequate ventilation systems (both of which are the norm in California public schools) are not conducive to safe social distancing. In order to make classrooms workable for social distancing, California schools would likely have to triple their teaching staffs, expand facilities, and spend millions of dollars updating air conditioning systems and adding HEPA filter systems. Furthermore, we’ve already been told that school budget cuts are inevitable at this point. Therefore, from our perspective, the only solution for safely educating our children during the next two years of this epidemic would be distance learning. Many school districts are currently surveying parents to collect their input on plans for the upcoming school year. Parents would be prudent to request that their districts offer distance learning for students of all ages.

Wear a Mask in Public

All people should wear masks in public at all times. There is very compelling scientific evidence that masks decrease the incidence of respiratory infections by preventing people’s respiratory droplets from circulating in shared air. We can see correlations between mandated mask-wearing policies and lower numbers of COVID-19 infections and deaths in countries across Asia like Japan, Vietnam, and Taiwan. There are certainly other factors in play that have helped these nations control the spread of COVID-19, like having more socially-distant ways of greeting people, better early education campaigns for COVID-19, prior experience with the SARS epidemic, increased travel restrictions, experimental pharmaceutical interventions (like Japan’s favipiravir) and better contact tracing. However, it’s worth noting that in some countries where most of these factors were not present, masks have been a game-changer, keeping cases and deaths relatively low. Take, for example, the Czech Republic, which mandated face masks in public in late March (along with closing borders, prohibiting public gatherings, and shuttering non-essential businesses). With a population of approximately 10 million, as of 5/23/20, Czechia (as it is also known) had 8,890 total reported cases of COVID-19 and just 314 total deaths. That’s 830 cases per million people and 29 deaths per million, and constitutes a death rate of about 3.5%. In Portugal, whose population is also around 10 million, masks in public were recommended but not required back in April. As of 5/23/20, Portugal had 30,471 total reported cases and 1,302 total deaths. That’s 2,987 cases per million people and 128 deaths per million, for a death rate of 4.3%. Even if we rewind to May 1, before Portugal began partially reopening businesses, we see it had a total of 24,987 cases and 1,007 deaths (death rate 4%), which is 2,450 cases per million and 99 deaths per million. Compare this to Czechia on May 1 with 7,737 total cases and 240 deaths (death rate 3.1%) That’s 722 cases per million and 22 deaths per million. This is not to say we think that mandated mask wearing is solely responsible for the differences in Portugal and Czechia’s numbers, but it certainly couldn’t hurt. 

Avoid Gathering in Enclosed Spaces, Regardless of Restriction Easing

Biologist Erin Bromage from the University of Massachusetts Dartmouth makes some valid points about infection risk in her blog post published on May 6, which was inspired by Jonathan Kay’s April 23 piece in Quillette on COVID-19 superspreader events. We won’t go into detail on the specifics of superspreader events in our post today, but we do have a few things to say about what you can do to stay safe as cities begin to reopen selected businesses and public spaces. 

The keys to preventing transmission of infection are personal protective equipment, washing hands with soap and warm water, and adequate ventilation. Unfortunately, most businesses and public buildings, like schools (see above), restaurants, bars, gyms, and salons (and even many doctor’s offices and hospitals) do not have the HEPA filtered air systems that are required to prevent the spread of COVID-19 and other viruses like influenza. Sanitizing surfaces, erecting barriers, setting up fans, and opening windows will not resolve the air issues in these locations. The reality is, there are few safe buildings when it comes to COVID-19. 

So what are our recommendations for folks who are determined to dine out, get a haircut, join a yoga class, or attend a religious service as soon as their local governments allow it? 

Small businesses need to rethink how they provide services to their patrons. Restaurants, rather than looking for ways to make poorly-ventilated indoor dining rooms safer, should be focused on offering outdoor dining. Hairdressers, barbers, and nail technicians should consider making use of their parking lots to provide their services in the open air, or performing services for their clients in their backyards. Gym owners, likewise, could look for opportunities to move classes outdoors. 

Places of worship should continue to offer services online and should consider outdoor services, where people should wear masks and stay six feet apart. Drive-in services might also be possible for churches with large parking lots, leaving at least one parking space vacant between cars. Of course, some practices, like the distribution of wafers and grape juice or wine for communion, would remain high-risk, whether conducted indoors or outdoors. The bottom line is it’s not safe to be in a public place near people from outside your household who are eating, talking, or singing without wearing masks. 

If you’re going to be around people from outside your household and have the choice to do so outdoors rather than indoors, outdoors would be a significantly safer choice. This is not to say that it’s prudent to have a large backyard barbecue or any large gathering of people outdoors. It’s still best to limit gatherings to no more than 10 people. Stick to video chatting with friends and family who have high risk for exposure to COVID-19 (like essential workers). 

Monterey County

In Monterey County, 40% of the infections are in folks who work in agriculture and 9% of infections are in health care workers and first responders. In 210 (57%) of the cases, patients had no known pre-existing medical conditions. How are people getting infected? In Monterey County, 51% of reported cases are epidemiologically linked to a confirmed case, 43% of cases are community acquired, and 6% are travel-related. In theory, if a county is doing an excellent job of contact tracing, the percentage of community acquired cases would be very low–because cases would be quickly identified and folks could be quarantined before infecting others. The fact that 43% of the cases in our county are community acquired suggests we should be doing better case contact tracing and increase testing for everyone, but especially for essential workers, particularly those who come in close contact with the public. We ought to be testing all agricultural workers, health care workers, and first responders. 

In California, the state public health department reports infections and deaths in skilled nursing facilities. It’s worth noting that since April 23, on any given day, only between 81% and 95% of California’s skilled nursing facilities have reported their COVID-19 cases and deaths to the state health department.  On its website, California Department of Health lists data for COVID-19 infections and deaths for 16 of Monterey County’s skilled nursing facilities. Based on this data, one 103-bed facility, Windsor The Ridge Rehabilitation Center in Salinas (zip code 93906) has reported cases in health care workers and patients. They are also listed as having patient deaths. Because the state of California does not report specific numbers of deaths and cases in skilled nursing facilities unless the number is greater than 11, we do not know how many of the cases and deaths in our county are associated with this facility–the report says fewer than 11. We also reviewed the California Department of Health skilled nursing COVID-19 data base (May11, 2020) and found a total of nine Windsor facilities in California with COVID-19 cases. The site with the most infections was in Solano County where 25 healthcare workers and 60 patients were infected with fewer than 11 deaths. The Monterey County Health Department has not disclosed the number of cases or deaths in the Salinas skilled nursing facility in our county. This data should be made available to the public. In addition, if it has not already been done, all staff and patients at this facility should be tested for COVID-19 by PCR on a routine basis. The state of New York has mandated that each nursing home will test each healthcare provider twice a week for COVID-19. This seems a reasonable approach to any facility with any healthcare provider or patient infection. A more proactive approach would be to test all healthcare providers and patients in skilled nursing facilities. 

Our Updated COVID-19 Projections

The University of Washington’s Institute of Health Metrics (IHME) said on 4/28/20 that we would have a total of 74,000 deaths in the USA by August 5, 2020. In contrast to this, we analyzed the case and death data using our two methods again on 5/22/20.  We estimated that we will reach 2,000,000 infected patients by June 7th (in 15.4 days, 369 hours or 2.2 weeks) and have between 17,710 and 20,513 new deaths for a total number of deaths between 115,357 and 118,156.

All of our predictions from 4/28/20, 5/03/20, 5/08/20 and 5/22/20 for time to reach 2,000,000 infections and the estimate of the number of deaths are listed in the following chart:

A few weeks ago, the University of Washington re-projected the number of deaths by August 4, 2020 to be 134,475. When we checked their website on 5/23/20, they had revised this number to 143,357. (Musical chairs, anyone?)

We don’t usually project out 2 months for total infections and deaths, but if we did, using our methodologies, we would predict that by August 4, 2020 in the United States we will have 3,337,190 COVID-19 infected patients and a total of between 192,613 and 199,229 deaths. If the death rate (now 5.94%) increases, these estimates of the number of deaths will be too low.

On 5/01/20, the FDA finally approved Gilead’s Remdesivir for intravenous treatment of COVID-19 infected patients. Since we initially recommended approval of this drug, another 97,600 Americans have died. Gilead is donating a large amount of drug for free. Unfortunately, it now appears that the government will be involved in the distribution of the drug, which means that university medical centers, hospitals in rural counties, and outpatient clinics like ours will probably not have the opportunity to treat our patients with Remdesivir. If it were up to us, this drug would be sold through normal drug distribution channels. Hopefully use of Remdesivir and/or plasma therapy will alter reported deaths in the next two months. We’re not optimistic based on the United States government’s performance during the first 145 days of the COVID-19 pandemic.  

We have no effective available oral treatment or preventative drugs, vaccines or hyperimmune intravenous immunoglobulin for COVID-19. Potential therapies are probably 6 to 9 months away. In the United States our political leaders (the President and most Governors) and federal agencies (HHS, CDC) and many state public health officials have decided to open back up our country. Viruses (COVID-19, Influenza and perhaps measles) will have many more potential victims this year.

Please think globally and act locally.

Recommended Reading

We Cannot Return to Campus This Fall

1918 Influenza: the Mother of All Pandemics (Emerging Infectious Diseases) 

American Pandemic: The Lost Worlds of the 1918 Influenza Epidemic by Nancy K. Bristow

The Great Influenza: The Story of the Deadliest Pandemic in History by John M. Barry

The Complex Question of Reopening Schools (The New Yorker) 

Public Health Experts Say Many States Are Opening Too Soon To Do So Safely (NPR) 

This Japanese Island Lifted Its Coronavirus Lockdown Too Soon and Became a Warning to the World (Time) 

Tired Of Wearing A Face Mask In Public? New Research Underscores Why You Still Need To (Forbes) 

The airborne lifetime of small speech droplets and their potential importance in SARS-CoV-2 transmission (PNAS) 

Hearts and masks: Czech-Vietnamese solidarity during coronavirus 

California is publicly sharing incomplete data on coronavirus outbreaks at nursing homes (SF Chronicle) 

2019 Novel Coronavirus (2019-NCoV) – Local Data (Monterey County Public Health)