Evolution of SARS-CoV-2: impact of variants on hosts, COVID-19 vaccines and countermeasures

Book excerpt: The ‘novel coronavirus disease’ (COVID-19) has caused significant global morbidity, mortality and economic damage on a scale similar to the influenza pandemic of 1918. The causative ‘severe acute respiratory syndrome virus 2’ (SARS-CoV-2) is a RNA virus which is evolving rapidly, accumulating mutations, and existing as a cloud of variants with quasispecies diversity. We have tens of thousands of variants, of which currently two are ‘variants of interest’ (Lambda, Mu) and another four ‘variants of concern’ (Alpha, Beta, Gamma, Delta, Omicron) to the World Health Organization (WHO). Variants of interest often emerge as variants under investigation in one or more countries, as seen with the Omicron (initially denoted as Nu in South Africa). They become variants of concern when there is evidence of increased transmissibility, greater case severity, loss of neutralization by antibodies, and reduced effectiveness of countermeasures. Some SARS-CoV-2 variants can infect new hosts (for instance, the Alpha, Beta and Gamma variants of concern can infect wild type mice which is a species that cannot be vaccinated or controlled easily), and/or reduce the effectiveness of vaccines and therapies (especially Beta and Delta); diagnostic tests have also been reported to be affected. Currently, we do not yet have any ‘variant of high consequence’ with confirmed attributes such as widespread diagnostic test failures, significant reduction in the effectiveness of vaccines and/or therapies, with greater disease severity and deaths. It remains to be seen if Omicron would be the first to be declared by the WHO as a variant of high consequence; more variants of concern are also likely to be declared by the WHO over the next couple of years. Therefore, our ability to control and conquer this pandemic over the long run is dependent on predicting and keeping up with the evolution of this virus, its new hosts, as well as understanding and mitigating its impact on diagnostics, vaccines and therapies.