COVID-19

Pandemic Year 3 in Review

When my daughter, Emily, and I started writing this blog in the spring of 2020, we did not anticipate that almost three years later, there would still be no end in sight for this pandemic. As we begin a new year, we wish we had better news, but the data continues to tell a grim story, and, as our long-time readers know, we always ground our outlook in the numbers. 

In the United States, from March 2020 to December 31, 2021, we had 55,696,500 SARS CoV-2 infections and 846,905 deaths (66 infections per death). In the last 12 months we have had an additional 46,813,072 new infections and an additional 271,051 deaths (173 infections per death). That’s an average of 742 deaths per day. The majority of these deaths were in people over the age of 65, and all of them were preventable. In November 2022, KFF reported that COVID-19 was still the number 3 cause of death in the United States. It’s also worth noting that the number one cause of death, cardiovascular disease, is a known complication of COVID

In late December 2021 the FDA approved both oral Paxlovid and oral Molnupiravir for outpatient treatment of SARS-CoV-2 with distribution beginning in January 2022. Unfortunately, all of the mask mandates were removed by individual states in 2022, and despite President Biden’s vow to institute a federal mask mandate during his 2020 campaign, the President and his administration adopted a decidedly anti-mask policy this year. CDC Director Rochelle Walensky even went so far as to describe masks as “the scarlet letter of this pandemic.” This irresponsible public health messaging has led to thousands of infections and deaths that could have been otherwise prevented by responsible mask wearing. We continue to urge our patients to protect themselves and others by wearing an N95 (or better) mask in public.

This year, multiple new Omicron variants BA.1, BA.2, BA.4, and BA.5 assaulted the world’s population of humans and other animals. By the time multiple companies made and tested Omicron BA.1 vaccines, BA.1 was no longer the dominant variant; in fact, it was no longer present. On August 31, 2022, the FDA allowed rapid introduction of an Omicron BA.5 bivalent vaccine. However, this has had no effect on new immune evading BQ variants. In December the first highly infectious recombinant variant, XBB, began spreading around the world. An additional variant, XBB.1.5, is now rapidly spreading across the country and the world causing increased numbers of hospitalizations and critically ill patients in the USA. 

At the same time, we have had outbreaks and deaths from Influenza A H3N2 and RSV. Travel and lack of masking and social distancing have exacerbated the spread of these viruses. In addition, Mpox virus outbreaks occurred nationwide, a measles outbreak began in Ohio in unvaccinated children, and several cases of polio in New York were reported. 

Part of why the United States’ vaccine-only approach to COVID-19 is so dangerous is that SARS-CoV-2 mutates, evading immune protection, and spreads more quickly than anyone can make, get approved, and distribute new vaccines. The Omicron BQ.1.1 variant is now being rapidly replaced by XBB.1.5.  As an example, at D4 Labs, we designed, manufactured and packaged a new vaccine for Omicron BQ.1.1 in 6 weeks. Minimal animal testing, IRB approval, human testing, and expedited FDA approval under an EUA would probably require at least another 6 months. Even if we skipped or delayed animal testing, obtained IRB approval, and internally did a standard two-dose immunogenicity study in 20 humans using IgG antibody to the RBD of SARS-CoV-2 as the surrogate marker for protection, it would still take three months in our in-house human testing and assay facility to complete the study. This approach would probably not be acceptable to the FDA for even EUA approval but might be attempted in individual states. The timely production and distribution of any new vaccine against any new SARS-CoV-2 mutant will be difficult to accomplish by any company using the current regulatory framework for approval of vaccines in the United States. Using XBB.1.5 as an example, it is responsible for over 40% of the infections in the United States in the last 28 days. Vaccines would have to be designed, manufactured, and distributed in less than four weeks to stop an outbreak of a virulent, highly-infectious respiratory pathogen. Considerable thought needs to be entertained on how to accomplish this task rapidly. 

Sadly, we do not see things improving in 2023 for respiratory virus control in the United States unless people wear high quality masks (N95 or better) and practice social distancing again. Continued infection and death increases are expected in the next eight weeks with 113 million people expected to travel during the holiday season, schools reopening on January 2, and people returning to work in poorly ventilated spaces. 

Here are our 14-day moving average determinations for SARS-CoV-2 for the United States. 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.

After Delays, CDC Discloses XBB.1.5 Variant Data

On 12/31/22 the CDC estimates that BA.5 accounted for 3.7% of infections (a 49.6% point drop from its peak), BQ.1 accounted for 18.3% (a 12.4% point drop decrease from its peak on 12/17/22), BQ.1.1 accounted for 26.9% (a 11.5% point drop from its peak on 12/17/22), BA.4.6 accounted for 0.3%, BF.7 accounted for 2.1% of infections, BN.1 accounted for 2.4% of isolates, and BA.2.75.2 accounted for 0.1%. XBB is 3.6% of isolates, XBB.1.5 is 40.5% of isolates, BA.5.2.6 is 0.6% of isolates, and BF.11 0.3% of isolates. In the week ending December 31, 2022, BQ isolates accounted for 45.2% of isolates (a 23.9% point decrease in infections caused by these BQ variants since 12/17/22). 

CDC

BQ.1.1 has five spike mutations that are different from BA.5. Four of these mutations allow escape from immunity from monoclonal antibodies, any prior infection (including Omicron BA.5), or any vaccine to include the bivalent Omicron BA.5 vaccine. Infections are still occurring in our clinic in patients that received the Omicron BA.5 bivalent vaccine. The XBB recombinant isolate XBB.1.5  has rapidly become the dominant infection in the USA. It took 28 days to become the cause of 40% of infections in the USA and it now causes over 70% of infections in Regions 1 and 2.

XBB.1.5 Proportion of Sequenced Isolates in the USA

12/03/2212/10/2212/17/2212/24/2212/31/22
1.3%3.7%9.9%21.7%40.5%

XBB.1.5 by Region on 12/31/22

Region12345678910
Percent of isolates identified as XBB.1.575.3%72.2%32.7%19.0%6.0%21.5%8.1%2.1%9.2%18.2%
CDC

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COVID-19

COVID-19 Update (5/8/20)

By our way of counting, this is Day 130 of the COVID-19 pandemic. Our first USA case was identified in Washington State on Day 21 of the pandemic. In those next 109 days (15.5 weeks) the United States, as of 5/08/20, had 1,292,623 known COVID-19 PCR positive infected patients and 76,928 deaths, giving us a still rising death rate of 5.95%. We have 1,035,768 more COVID-19 positive infected patients than any other country in the world. The total number of COVID-19 positive infected patients in Spain, Italy, France, Germany and the United Kingdom is 1,023,649 or 268,974 fewer infected patients than in the United States.  Two new rapidly expanding “hot spot” countries are Russia with 177,160 infections and 11,231 new infections on 5/8/20 and Brazil with 135,693 infections and 9,082 new infections on 5/8/20.

As of 4/28/20:

      USA                                  WORLD

57,812 deaths                      215,461 deaths

1,004,908 infections        3,094,829 infections   

Death rate: 5.75%             Death Rate: 6.96%

As of 5/08/20:

USA                                     WORLD

76,928 deaths                     270,426 deaths

1,292,623 infections        3,913,644 infections   

Death Rate: 5.95%         Death Rate: 6.91%

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 5/08/20.  We now estimate that we will reach 2,000,000 infected patients in 25 days (601 hours or 3.5 weeks) and have between 42,088 and 45,200 new daily deaths for a total number of deaths between 119,017 and 122,128.

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

Recently the University of Washington re-projected the number of deaths by August 4, 2020 to be 134,475.

We don’t usually project out 3 months for total infections and deaths, but if we did, using our methodology, we would predict that by August 4, 2020 in the United States we will have 3,807,104 COVID-19 infected patients and a total of between 207,895 and 231,101 deaths. If the death rate (now 5.95%) continues to increase, these estimates of the number of deaths will be too low.

The FDA finally approved Gilead’s Remdesivir for intravenous treatment of COVID-19 infected patients (5/01/20). Since we initially recommended approval of this drug, another 66,500 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 rural counties and 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 four months. I’m not optimistic based on the United States government’s performance during the first 130 days of the COVID-19 pandemic.  

Please think globally and act locally.

COVID-19

COVID-19 Update (5/3/20)

By our way of counting, this is Day 125 of the COVID-19 pandemic. Our first USA case was identified in Washington State on Day 21 of the pandemic. In those next 104 days (15 weeks) the United States as of  9:32 A.M. on 5/03/20 had 1,138,690 known COVID-19 PCR positive infected patients and 66,570 deaths giving us a still rising death rate of 5.84%. We have 922,108 more COVID-19 positive infected patients than any other country in the world. The total number of COVID-19 positive infected patients in Spain, Italy, France, Germany and the United Kingdom is 944,501 or 194,184 fewer infected patients then the United States. By our modeling method, in the United States we should now reach 2,000,000 COVID-19 positive infected patients in 29.7 days (714 hours or approximately 4.25 weeks). 

As of 4/28/20:

      USA                                  World

57,812 deaths                     215,461 deaths

1,004,908 infections        3,094,829 infections   

Death rate: 5.75%            Death Rate: 6.96%

As of 5/03/20:

USA                                  World

66,570 deaths                     244,911 deaths

1,138,690 infections        3,462,682 infections   

Death rate: 5.84%            Death Rate: 6.43%

The University of Washington’s Institute of Health Metrics said on 4/28/20 that we would a total of 74,000 deaths in the USA by August 5, 2020.

For our prediction on 4/28/20, we used two simple methods to predict the number of deaths and came up with two numbers: in 34.5 days (828 hours or 5 weeks) we should have either  56,166 additional deaths or 57,004 additional deaths from COVID-19. Therefore we predicted  that 5 weeks from  (April 28, 2020), the total number of deaths in the United States would be either 112,641 deaths or 113,479 deaths and we would have 2,000,000 PCR positive COVID-19 infected patients.

We’ve looked at our two methods again 5 days later (5/03/20).  We would now estimate we will now reach 2,000,000 infected patients in 29.7 days (714 hours) and have either 48,400 or 50,587 new deaths, for a total  number of deaths between 114,970 and 117,157.

Other news of interest is that the FDA has finally approved Gilead’s Remdesivir for intravenous treatment of COVID-19 infected patients (5/01/20). Gilead is also donating a large amount of drug for free. Hopefully use of Remdesivir and/or plasma therapy may alter reported deaths in the next month. We recommended that the FDA approve Remdesivir back on March 14.

Please think globally and act locally.

Recommended Reading:

https://www.fda.gov/news-events/press-announcements/coronavirus-covid-19-update-fda-issues-emergency-use-authorization-potential-covid-19-treatment

https://www.cnbc.com/2020/05/03/gilead-ceo-says-remdesivir-available-to-coronavirus-patients-this-week-weve-donated-the-entire-supply.html