Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India.
Arch Microbiol. 2024 Jan 18;206(2):68. doi: 10.1007/s00203-023-03807-2.
SARS-CoV-2 has expressively changed its sequences during the COVID-19 pandemic situation by encompassing persistent evolutionary mutational changes resulting in the emergence of many clades and lineages. Evolution of these SARS-CoV-2 variants have significantly imparted fitness advantage to the virus, enhanced its transmissibility and severity of the disease. These new variants are a potential threat to the vaccine efficacy as well. It is therefore pertinent to monitor the evolution of these variants and their epidemiological and clinical impact, in a geographic setting. This study has thus looked into the geographic distribution and genetic diversity of SARS-CoV-2 variants and the evolutionary circulation of different clades in Chhattisgarh (CG) state from March 2020 to July 2023. A total of 3018 sequences were retrieved from the GISAID database, in which 558 were submitted by us. The demographic data revealed male preponderance of 56.45% versus 43.54% females, with the overall mean age of 36.5 years. SARS-CoV-2 sequences represented many variants viz., Delta (55%), Omicron (22%) and others (15%) with a small proportion of recombinant (5%), Kappa (2%), and Alpha (1%). The viral clades G was found predominant for a year from initial days of pandemic in March, 2020 to January, 2021 which then subsequently evoluted to subclade GK (Delta B.1.617.2) and remained in circulation in CG till November, 2021. From December 2021, the GRA (Omicron B.1.1.529) variant had replaced GK to become the dominant strain and continues to predominate in present time. GRA clade is however continuously encompassing new recombinant strains, having various non-synonymous mutations especially in spike protein. The non-synonymous mutation P314L in ORF1b, S84L in ORF8 and D614G in spike protein were found as the pan mutation carried over from clade G to GRA. The continuous evolution in SARS-CoV2 warrants periodical geographic genomic surveillance monitoring to timely detect any new variants having the potential of causing future outbreak.
SARS-CoV-2 在 COVID-19 大流行期间明显改变了其序列，包括持续的进化突变，导致出现了许多分支和谱系。这些 SARS-CoV-2 变体的进化显著赋予了病毒适应性优势，增强了其传染性和疾病严重程度。这些新变体也对疫苗功效构成潜在威胁。因此，在地理环境中监测这些变体及其流行病学和临床影响至关重要。本研究因此调查了 2020 年 3 月至 2023 年 7 月恰蒂斯加尔邦（CG）中 SARS-CoV-2 变体的地理分布和遗传多样性，以及不同分支的进化循环。从 GISAID 数据库中总共检索到 3018 个序列，其中 558 个是我们提交的。人口统计学数据显示，男性占 56.45%，女性占 43.54%，平均年龄为 36.5 岁。SARS-CoV-2 序列代表了许多变体，如 Delta（55%）、Omicron（22%）和其他变体（15%），重组变体（5%）、Kappa（2%）和 Alpha（1%）比例较小。在 2020 年 3 月大流行初始阶段至 2021 年 1 月的一年中，发现分支 G 占主导地位，随后进化为亚分支 GK（Delta B.1.617.2），并在 CG 持续传播到 2021 年 11 月。从 2021 年 12 月起，GRA（Omicron B.1.1.529）变体取代了 GK 成为优势株，目前仍占主导地位。然而，GRA 分支不断包含新的重组株，在刺突蛋白中具有各种非同义突变。ORF1b 中的非同义突变 P314L、ORF8 中的 S84L 和刺突蛋白中的 D614G 被发现是从分支 G 到 GRA 的泛突变。SARS-CoV2 的持续进化需要定期进行地理基因组监测，以及时发现任何具有潜在引发未来爆发能力的新变体。
