Authored by: Venkat Rao
Leaving aside for at least now the source and origin of the Wuhan SARS-CoV-2 virus that causes COVID-19, more attention is drawn towards newer and more contagious genomic versions of the virus that greatly amplified the COVID-19 pandemic. Newer variants were not only capable of spreading more rapidly, but they were also able to evade the human immune defenses and whatever protection the COVID-19 vaccine afforded to vaccinated individuals.
Just as reports appeared from around the world on the COVID-19 vaccines effectiveness, and around the Thanksgiving season of 2021, scientists in South Africa detected a new variant of coronavirus, which the World Health Organization officially later in November named it, Omicron B.1.1.529. The new South African variant was milder as a pathogen but highly transmissible, evaded the immune surveillance and for the most part rendered vaccines barely effective. The saving grace was that it is a milder pathogen compared to other previous ones.
Omicron also has the dubious reputation as the second most contagious virus in human history, while some researchers regard it as the most contagious virus ever on planet earth. Although the biologic origin of Omicron variant is still under investigation, it was quickly identified and reported in November 2021.
Earlier publications have postulated multiple theories on its origin and rapid spread. A recent study, published a few days ago in Science, provides a better picture of the gradual emergence of Omicron in Africa and spread across almost the entire globe at an incredible speed. According to this international team of German and African scientists, Omicron’s predecessor (genetic variants) was in circulation for over several months in the African continent long before the first case of Omicron-induced COVID-19 was identified and reported.
As the study reports, a crucial observation was made about a year ago with a patient in South Africa infected with the SARS-CoV-2 variant carrying more than 50 mutations to the original virus.
According to these investigators, variants similar to Omicron were in transmission in Africa many months before the arrival of the most transmissible Omicron BA.1. The new variant named, Omicron BA.1 spread to 87 countries around the world within a month, the most spectacularly rapid spread and global transmission of a virus ever known. By the end of December, a vast majority of COVID-19 case reports were tied to the new coronavirus variant. Thus, Omicron BA.1 pretty much displaced dominant Delta and other variants worldwide. Origin of Omicron variant is regarded as the biggest leap in the evolution of SARS-CoV2 reported so far.
As of September 2022, over 6.5 million individuals have died from COVID-19, although the actual number of infection and deaths are likely to be much higher than the officially reported information. This is in part due to a limited diagnostic capacity in much of Africa and other developing nations where COVID-19 pandemic hit the hardest. According to the World Health Organization report, only 14% of all SARS-CoV-2 infections are detected and reported and regional post-mortem data indicates significant underreporting of the COVID-19 clinical cases and fatalities in Africa and other developing nations. Omicron variants are regarded as the second most contagious virus detected on the planet earth, with measles virus considered the most contagious virus known to man. Other reports conclude subvariants BA.4 and BA.5 are regarded by many researchers as the most infectious viruses known to man. The intensity of a viral disease outbreak is often denoted by the expression, Reproduction Number (R0), which provides an estimate on how large a disease outbreak such as Ebola outbreaks in West Africa, H1N1 influenza to grow into a pandemic like the one we witness with COVID-19. R0 refers to the number of cases, on average, an infected person at the peak of infection transmit to others. For example, R1 refers to a transmission rate of just one other person in a susceptible community getting the virus from exposure to an infected individual. Going by this standard definition for the intensity of a disease outbreak, measles has a R factor of 18 (R18), highest ever reported reproduction number for a virus, where on an average measles-infected person could transmit the virus to 18 susceptible individuals causing an exponential outbreak. To illustrate, Omicron cases first reported in Winter of 2021 spread so rapidly that one case gave rise to 6 cases in 4 days, which in turn caused 36 cases in 8 days, and 216 cases in 12 days. In a matter of two-months, by the end of February 2022, Omicron variant accounted for all COVID-19 reported cases in the United States. According to a CDC report, although measles has a short environmental viability of just two hours in ambient air, it is so contagious that up to 90% of all people close to the infected person who are not immune will get infected with the virus. A person infected with measles can spread the virus four days before and for days after they develop the telltale clinical symptoms of the disease.
Omicron variants have a Replication factor of 15 (R15) and considered the second most contagious virus known to man. Soon after its first detection in South Africa, Omicron spread to 87 countries around the world within a month and displaced all prevalent, dominant SARS-CoV-2 variants globally within a few months, a spectacular feature of the COVID-19 pandemic. What makes Omicron so contagious? A remarkable number of mutations in the original Wuhan SARS-CoV-2 virus renders the Omicron variant as the most contagious virus in human history. According to researchers, Omicron has more than 50 mutations compared to the original SARS-COV-2 virus detected in Wuhan, China. More than 30 of the 50 mutations in Omicron are in the spike proteins, the anchor molecule that helps the virus attach to human body host cells. Coronavirus variants that preceded Omicron have only few and no more than 10 mutations on the spike proteins. A crucial mutation on Omicron enables it to escape human immune system surveillance. Another key feature is that Omicron has 15 mutations on its surface to help hide its detection almost completely by the protective mechanism provided by the vaccines. When the virus enters the host, it first gets attached to the host cell surface through the anchor protein, which is also a trigger for the host immune system constantly in surveillance to come to rescue, grab the virus away from the cell surface and prevent infection. COVID-19 vaccines are supposed to enable this protective mechanism, which was rendered ineffective with Omicron-induced COVID-19 disease. Another key feature in Omicron is it preferentially infects upper respiratory tract which makes it easier for person-to-person transmission. Unlike Delta variants which settled in the lower respiratory tract and caused a more serious version of the disease, Omicron’s preferential residence in the upper part of the respiratory tract induced a milder version of COVID disease. There you have it: a highly transmissible variant evading the immune system protection but causes a relatively less severe form of the disease due to its predominant presence in the upper respiratory tract. Nonetheless, the overall impact of Omicron on the global population was far from mild. Rapid transmission caused major COVID-19 disease burden causing medical surge in many parts of the world. United States was hit with record number of hospitalization and deaths both among adults and children. Given the track record of SARS-CoV-2 mutations and its extremely high levels of prevalence worldwide, it is safe to assume many other variants are in circulation and will surface in due course.