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.

自新型冠状病毒（SARS-CoV-2）疫情暴发以来，该病毒持续演化出携带潜在突变的变异株，这些突变与传播能力增强、可能逃逸中和抗体以及疾病严重程度升高相关。尽管全球范围内正开展密集研究以解析该病毒的突变模式，但学界仍担忧其可能改变病毒传播动态，并由此对公共卫生产生不良影响。南非新型冠状病毒大流行的疫情进程呈现四轮主要感染流行波特征。本研究针对2020-2021年基因组监测周期内，南非自由州省四轮流行波中循环传播的新型冠状病毒变异株，报告其基因组流行病学特征。为分析循环传播的变异株，研究团队共纳入1290份经实时荧光定量聚合酶链反应（qPCR）确认的新型冠状病毒阳性样本，对其开展病毒RNA提取、基因组扩增及测序实验。分别采用PANGOLIN工具与新型冠状病毒基因组注释器完成病毒序列的变异株分型及突变位点鉴定。分析结果显示，在第一波疫情初期，自由州省曾流行B.1、B.1.1、B.1.1.53、B.1.1.448及B.1.237变异株，该波疫情后期则出现了贝塔（Beta）变异株B.1.351。尽管多数初期检出的变异株在第二波疫情中消失，但贝塔（Beta）变异株B.1.351仍持续存在。第三波疫情初期，贝塔（Beta）变异株B.1.351占据主导优势，随后被德尔塔（Delta）亚谱系AY.45取代。第四波疫情则以奥密克戎（Omicron）亚变异株BA.1的首次出现为主要特征。本研究数据进一步显示，在四轮感染流行波期间，自由州省的新型冠状病毒在刺突蛋白上累积了氨基酸突变。每一轮感染流行波均由一组独特的新型冠状病毒变异株组合所驱动。本研究结果凸显了持续开展基因组监测与循环变异株监测的重要性，此举可为公共卫生防控工作提供科学依据，并确保对当前大流行实施有效管控。