SARS-CoV-2

By ¹Sackey Lyanne, ²Kwakye Sylvester, ³Obiri Darko Stella.

From apsf

Covid 19 is caused by the SARs-CoV-2 virus previously known as the 2019 novel coronavirus. The virus was first identified in the city of Wuhan, Hubei, China. SARS-CoV-2 is believed to have genetic similarity to the bat coronaviruses suggesting it emerged from that source.

COVID-19 can be spread in a number of ways but is mainly spread by human-to-human transmission. This can occur mainly via respiratory droplets from coughs and sneezes within six feet. Speaking can also be an additional mode of transmission of the virus. One can also be infected via indirect contact with contaminated surfaces. The most dominant initial site of infection by the virus is the nostrils and the virus later gets seeded in the lungs. About 17% of COVID-19 cases are asymptomatic and asymptomatic individuals are 42% less likely to transmit the virus. Although reinfection by the virus is not common, it can occur.

Viruses constantly change through mutation and sometimes these mutations result in a new variant of the virus. The SARS-CoV-2 virus is no exception to that. Some of the variants are of importance due to their potential for increased transmissibility, increased virulence or reduced effectiveness of the vaccine against them. A lot of variants exist but the current variants of concern by WHO are the alpha, beta, gamma, delta and omicron variants.

Alpha variant

First detected in October 2020 during the COVID-19 pandemic in the United Kingdom from a sample taken the previous month in Kent, lineage B.1.1.7, labelled Alpha Variant by the WHO, was previously known as the first Variant Under Investigation in December 2020 (VUI — 202012/01) and later notated VOC-202012/01. It is also known as 20I (V1), 20I/501Y.V1](formerly 20B/501Y.V1), or 501Y.V1. From October to December 2020, its prevalence doubled every 6.5 days, the presumed generational interval. It is correlated with a significant increase in the rate of the infection in the United Kingdom, associated partly with the N501Y mutation. The alpha variant has 40–80% increased transmissibility (with most estimates lying around the middle to higher end of this range), and early analyses suggested an increase in lethality, though later work found no evidence of increased virulence. As of May 2021, the Alpha variant had been detected in some 120 countries

Beta variant

It was first detected on December 18, 2020, in South Africa. Its prevalence was shown to be higher among young people with no underlying health conditions and results in serious illness. It was indicated by the South African Health department that it spreads at a more rapid pace than the earlier variants and may be driving the second wave in the country. the variant contains several mutations that allow it to attach more easily to human cells because of the following three mutations in the receptor binding domain (RBD) in the spike glycoprotein of the virus: N501Y, K417N, and E484K. The N501Y mutation has also been detected in the United Kingdom.

Gamma Variant

It was detected in Tokyo on 6 January 2021 by the National Institute of Infectious Diseases (NIID). It has been labelled as Gamma variant by WHO. The new variant was first identified in four people who arrived in Tokyo having travelled from the Brazilian Amazonas State on 2 January 2021. This variant of SARS-CoV-2 has been named lineage P.1 (although it is a descendant of B.1.1.28, the name B.1.1.28.1 is not permitted and thus the resultant name is P.1), and has 17 unique amino acid changes, 10 of which in its spike protein, including the three concerning mutations: N501Y, E484K and K417T. infections by Gamma can produce nearly ten times more viral load compared to persons infected by one of the other lineages identified in Brazil (B.1.1.28 or B.1.195). Gamma also showed 2.2 times higher transmissibility with the same ability to infect both adults and older persons, suggesting P.1 and P.1-like lineages are more successful at infecting younger humans irrespective of sex. A study found that people fully vaccinated with Pfizer or Moderna have significantly decreased neutralization effect against Gamma, although the actual impact on the course of the disease is uncertain. Preliminary data from two studies indicate that the Oxford- AstraZeneca is effective against the Gamma variant, although the exact level of efficacy has not yet been released.

Delta variant

It is a globally dominant variant that spread to about 185 countries. It was labelled a variant of concern after they flagged evidence that it spreads more quickly than the original version of the virus and could spread quicker or as quickly as Alpha. It carries L452R and P681R mutations in Spike; unlike Kappa it carries T478K but not E484Q. It spread twice as fast as the alpha variant and occurred in vaccinated individuals. In June 2021, reports began to appear of a variant of Delta with the K417N mutation. The mutation, also present in the Beta and Gamma variants, raised concerns about the possibility of reduced effectiveness of vaccines and antibody treatments and increased risk of reinfection.

Omicron variant

The Omicron variant, known as lineage B.1.1.529, was declared a variant of concern by the World Health Organization on 26 November 2021. The variant has a large number of mutations, of which some are concerning. The number of cases in the B.1.1.529 lineage is increasing in all areas of South Africa. Some evidence shows that this variant has an increased risk of reinfection. Studies are underway to evaluate the exact impact on transmissibility, mortality, and other factors. Identified in November 2021 in Botswana and South Africa one case had travelled to Hong Kong, one confirmed case was identified in Israel in a traveler returning from Malawi along with two who returned from South Africa and one from Madagascar. One confirmed case in Belgium, who had apparently acquired it in Egypt before November 11.

References

UK Research and Innovation

World Health Organization

Wikipedia

National Center for Biotechnology Information

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