SARS-CoV-2 evolution in Botswana

Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) is a virus with fatal health outcomes and its associated disease, Corona Virus 2019 (COVID-19), has claimed many lives worldwide. Viruses are subject to evolutionary pressures and often mutate at the epitopes to cause immune escape and in some instances resistance to antiviral drugs and broadly neutralising antibodies. As COVID-19 vaccines and antiviral drugs become available and are being implemented, it is crucial to monitor the evolution of SARS-CoV-2 within a population. To increase the understanding of SARS-CoV-2 evolution at population level, viral diversity and signatures of immune selection can be studied using dominant virus population as well as intra-host quasispecies (well-defined distribution of mutants that is generated by a mutation-selection process). Genomic surveillance has played a key role in the response to the COVID-19 pandemic and data from sequences provide information on transmission patterns and virus evolution. Choga’s study aims to track emerging lineages of SARS-CoV-2 in Botswana and evaluate the impact of emerging mutations including those detected at minority levels (<20%). Furthermore, it is expected that 15-20% of the sequences will be from people living with HIV (PLWH) which is the prevalence of HIV in the general population of Botswana. PLWH who are treatment naïve often have sub-optimal immune environments which has been associated with continued and increased mutagenesis of SARS-CoV-2. This study will further investigate, at population level, the genome-wide diversity and minority variants of SARS-CoV-2 among different risk groups among PLWH.