SARS-CoV-2 variants from COVID-19 positive cases in the Free State province, South Africa from July 2020 to December 2021

Since the COVID-19 outbreak emerged, SARS-CoV-2 has continuously evolved into variants with underlying mutations associated with increased transmissibility, potential escape from neutralizing antibodies, and disease severity. Although intensive research is ongoing around the world to understand the mutational patterns of the virus, there are concerns about the potential to alter the dynamics and the resultant public health impact. The SARS-CoV-2 pandemic in South Africa has been characterized by periods of infections with four major epidemic waves. Here, we report on the genomic epidemiology of SARS-CoV-2 variants circulating in the Free State province in each of the four waves during the 2020-2021 genomic surveillance period. For analysis of the circulating variants, a total of 1290 samples from qPCR confirmed SARS-CoV-2 positive individuals were subjected to viral RNA extraction, genomic amplification, and sequencing. Variant assignment of the viral sequences and mutation identification were conducted using PANGOLIN and SARS-CoV-2 genome annotator, respectively. Our analysis revealed that during the initial part of the first wave, B.1, B.1.1, B.1.1.53, B.1.1.448 and B.1.237 circulated in the Free State province, followed by Beta variant, B.1.351 later in the wave. Although most of the initially detected variants disappeared during the second wave, the Beta variant, B.1.351, persisted. Early in the third wave, the Beta variant, B.1.351, predominated but was replaced by the Delta sub-lineage, AY.45. The fourth wave was characterized by unique emergence of the Omicron sub-variant, BA.1. The data further indicates that SARS-CoV-2 in the Free State accumulated amino acid mutations on the spike protein across the four waves of infections. Each wave of infection was driven by a unique combination of SARS-CoV-2 variants. Findings from this study highlight the importance of continued genomic surveillance and monitoring of the circulating SARS-CoV-2 variants to inform public health efforts and ensure adequate control of the ongoing pandemic.