SARS-CoV2. Figure by A, Solodovnibov and V. Arkhipova. Wikimedia Commons
(Click on the following link to listen to an audio version of this blog … SARS CoV2 and Waves of Transmission
Last week I described the structure of the SARS-CoV2 virus (the virus that causes the disease COVID-19). I noted that the virus uses its activated Spike Proteins to attach itself to the lining epithelial cells of an exposed person’s upper respiratory tract primarily via the epithelial cell’s surface ACE2 protein receptors. Once attached, the virus envelope fuses with the cell membrane of the epithelial cell, and the virus releases its RNA molecule into the host cell’s cytoplasm. The virus then shuts down normal cellular metabolism and converts the infected cell into a virus manufacturing machine. The accumulating viral load eventually causes the host cell to burst open releasing large numbers of newly synthesized viruses which then are able to infect more cells along the respiratory tract. These abundant viruses along with a mixture of cellular debris trigger the initial symptoms of COVID-19 (sore throat, dry cough, fever, etc.).
Exposure graphic. Howard County Maryland. Wikimedia Commons
The CDC currently indicates that people infected with the SARS-CoV2 virus will begin to show symptoms in 2 to 14 days. The newest variants of the SARS-CoV2 virus tend to have very short (2 to 4 days) incubation times. The onset of symptoms indicates that abundant viruses are present in the infected host’s respiratory tract and, consequently, these viruses are being expelled into the surrounding environment with each cough! It is very important to note, though, that viruses may be shed even before symptoms arise! Typically, a person will produce and shed active SARS-CoV2 viruses for 5 to 10 days, although longer periods of viral shedding have been observed.
A study at the Bundeswehr Institute of Microbiology (Munich Germany) indicated that many of the examined COVID-19 patients had upper respiratory infections (and associated “common cold”-like symptoms). All infected patients, though, regardless of the mildness or severity of their symptoms, were actively producing and shedding viruses. The first five days with symptoms correlated with the maximum rate of viral production and release, but, in this study, viruses continued to be shed for up to one week after symptoms had abated.
The original, or “wild type,” SARS-CoV2 differed from its other two related coronaviruses (SARS-CoV and MERS-CoV) in two ways: 1. It is more infectious and more easily transmitted from person to person, and 2. It is less lethal (death rate for SARS was 10% and for MERS, 23%, while death rate for SARS-CoV2 is between 1 and 2%).
Viruses are not conscious entities, they are not even alive. They do not “want” things, they do not “strive” to accomplish anything. They just are. According to Richard Dawkins, though, and I am not sure if this idea is a metaphor or not, nucleic acids do impose a drive for replication upon the life forms they create. This “selfish gene” hypothesis does explain many observations concerning the evolution, reproduction and observed behaviors in a large number of animal species (including ourselves!). It may also be the foundational explanation behind our observations over the past two years of the evolution of the new forms and variants of SARS-CoV2. The nucleic acid of SARS-CoV2 “wants” to replicate! The more viral RNA created, the better!
SARS-CoV2. Photo by NIAD-NIH. Wikimedia Commons
The evolution of SARS-CoV2 is reflected in the five epidemic waves that have occurred since the virus was first detected in China in late 2019. The first wave was, of course, the early 2020 spread of the original form of the SARS-CoV2 virus (often referred to as the “wild type” SARS-CoV2). The subsequent major waves of infection involved the Alpha Variant, then the Delta Variant, then the Omicron Variant and, most recently and currently, the B.A.5 Omicron variant.
(The data for the numbers of cases and deaths for each SARS-CoV2 variant were derived from the World Health Oragnization’s (WHO) weekly data compilation graphs. The number of cases and the number of deaths presented for each variant are those cases and deaths recorded on the WHO graphs during each Wave’s indicated time interval. These data, then, are estimates made with the underlying assumption that the particular viral variant was the major infectious agent during its wave period of ascendency.)
“Waves” of SARS-CoV2
- First Wave: Original (“wild type”) SARS-CoV2
Timing of spread in United States: January, 2020 to March, 2021 (15 months)
Total Number of cases worldwide: 100,271,284 (6,684,752 cases per month)
Total number of deaths worldwide: 2,729,257 (181,950 deaths per month)
Worldwide death rate: 2.7%
The first official case of a SARS-CoV-2 infection was reported in Wuhan, China on December 31, 2019. This first officially described patient had an atypical pneumonia. It is thought that the SARS-CoV2 virus emerged some weeks before from bats, or, possibly, from civet cats that had picked up the virus from bats, that were all being sold at a “wet market” in Wuhan. The virus then slowly and steadily infected and spread through a growing number of people first in the immediate area of the market and then in more distant locations due to person to person transmissions. Many initial SARS-CoV2 cases, undoubtedly, went undetected.
SARS-CoV2 is closely related to SARS-CoV (the virus that caused the SARS outbreak in 2003). This new form of the SARS virus, though, had adaptations that made it more contagious than the original SARS-CoV and also better at avoiding the immune system’s detection. Alterations in the amino acid sequences of the S-1 protein subunits of the Spike Proteins of the virus may have contributed to both of these features of SARS-CoV2. Also, a mutation in the virus that allowed human cellular enzymes to trigger S-1 and S-2 cleavage in the Spike Protein (a step which forms the enzyme that catalyzes the attachment of the S-1 to the potential host cell’s surface protein receptor (typically an ACE2 protein)) may have made this new form of the SARS virus increasingly virulent and infectious.
SARS-CoV2 in human lung. Photo by NAID-NIH, Wikimedia Commons
Within a month after its official detection, the SARS-CoV2 virus had spread across the globe. By January 20, 2020 it was detected in Washington State, and then within days it was detected in Illinois and Arizona. These initial cases were seen in people who had recently traveled to China, but by the end of January, 2020 cases were spreading via local transmission. The first death in the U.S. was reported on February 29, 2020 in Washington State.
On March 11, 2020 the WHO declared a global pandemic. There were then 118,000 cases of COVID-19 worldwide and 4,281 deaths. By April 4, 2020 there were 1 million cases of COVID-19 worldwide.
In the United States case numbers went up exponentially: 2 million cases by June 10, 2020, 3 million cases by July 7, 2020. 5.4 million cases by August 17, 2020. In August deaths from COVID-19 exceeded 1000 per day, and by September 22, 2020 the deaths from COVID-19 in the United States reached 200,000 individuals. By September 28, 2020 deaths worldwide reached 1 million people. By March 2021, the designated “end” of this first wave of viral transmission the worldwide death total had reached 2,728, 257 people! The estimated death rate of this “wild type” SARS-CoV2 (based on the over 100 million cases recorded) was 2.7%!
(I will continue these waves of SARS-CoV2 next week!)