Singh Pushpendra, Sharma Kuldeep, Shaw Dipika, Bhargava Anudita, Negi Sanjay Singh
Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India.
Front Med (Lausanne). 2023 Jan 23;9:1082846. doi: 10.3389/fmed.2022.1082846. eCollection 2022.
The emergence of the Omicron SARS-CoV-2 variant from various states of India in early 2022 has caused fear of its rapid spread. The lack of such reports from Chhattisgarh (CG), a central state in India, has prompted us to identify the Omicron circulating lineages and their mutational dynamics.
Whole-genome sequencing (WGS) of SARS-CoV-2 was performed in 108 SARS-CoV-2 positive combined samples of nasopharyngeal and oropharyngeal swabs obtained from an equal number of patients.
All 108 SARS-CoV-2 sequences belonged to Omicron of clade 21L (84%), 22B (11%), and 22D (5%). BA.2 and its sub-lineages were predominantly found in 93.5% of patients, BA.5.2 and its sub-lineage BA.5.2.1 in 4.6% of patients, and B.1.1.529 in 2% of patients. Various BA.2 sub-lineages identified were BA.2 (38%), BA.2.38 (32%), BA.2.75 (9.25%), BA.2.56, BA.2.76, and BA.5.2.1 (5% each), BA.2.74 (4.6%), BA.5.2.1 (3.7%), BA.2.43 and B.1.1.529 (1.8% each), and BA.5.2 (0.9%). Maximum mutations were noticed in the spike (46), followed by the nucleocapsid (5), membrane (3), and envelope (2) genes. Mutations detected in the spike gene of different Omicron variants were BA.1.1.529 (32), BA.2 (44), BA.2.38 (37), BA.2.43 (38), BA.2.56 (30), BA.2.74 (31), BA.2.75 (37), BA.2.76 (32), BA.5.2, and BA.5.2.1 (38 similar mutations). The spike gene showed the signature mutations of T19I and V213G in the N-terminal domain (NTD), S373P, S375F, T376A, and D405N in receptor-binding domain (RBD), D614G, H655Y, N679K, and P681H at the furin cleavage site, N764K and D796K in fusion peptide, and Q954H and N969K in heptapeptide repeat sequence (HR)1. Notably, BA.2.43 exhibited a novel mutation of E1202Q in the C terminal. Other sites included ORF1a harboring 13 mutations followed by ORF1b (6), ORF3a (2), and ORF6 and ORF8 (1 mutation each).
BA.2 followed by BA.2.38 was the predominant Omicron lineage circulating in Chhattisgarh. BA.2.75 could supersede other Omicron due to its mutational consortium advantage. The periodical genomic monitoring of Omicron variants is thus required for real-time assessment of circulating strains and their mutational-induced severity.
2022年初，印度多个邦出现了奥密克戎SARS-CoV-2变种，这引发了人们对其快速传播的担忧。印度中部的恰蒂斯加尔邦（CG）缺乏此类报告，这促使我们去识别正在传播的奥密克戎谱系及其突变动态。
对从同等数量患者中采集的108份鼻咽拭子和口咽拭子的SARS-CoV-2阳性混合样本进行了全基因组测序（WGS）。
所有108个SARS-CoV-2序列均属于21L（84%）、22B（11%）和22D（5%）分支的奥密克戎毒株。93.5%的患者主要检测到BA.2及其亚谱系，4.6%的患者检测到BA.5.2及其亚谱系BA.5.2.1，2%的患者检测到B.1.1.529。鉴定出的各种BA.2亚谱系包括BA.2（38%）、BA.2.38（32%）、BA.2.75（9.25%）、BA.2.56、BA.2.76和BA.5.2.1（各占5%）、BA.2.74（4.6%）、BA.5.2.1（3.7%）、BA.2.43和B.1.1.529（各占1.8%）以及BA.5.2（0.9%）。在刺突蛋白（46个）中发现的突变最多，其次是核衣壳蛋白（5个）、膜蛋白（3个）和包膜蛋白（2个）基因。在不同奥密克戎变种的刺突基因中检测到的突变有：B.1.1.529（32个）、BA.2（44个）、BA.2.38（37个）、BA.2.43（38个）、BA.2.56（30个）、BA.2.74（31个）、BA.2.75（37个）、BA.2.76（32个）、BA.5.2和BA.5.2.1（38个相似突变）。刺突基因在N端结构域（NTD）显示出T19I和V213G的特征性突变，在受体结合结构域（RBD）显示出S373P、S375F、T376A和D405N的突变，在弗林蛋白酶切割位点显示出D614G、H655Y、N679K和P681H的突变，在融合肽显示出N764K和D796K的突变，在七肽重复序列（HR）1显示出Q954H和N969K的突变。值得注意的是，BA.2.43在C端表现出E1202Q的新突变。其他位点包括开放阅读框1a有13个突变，其次是开放阅读框1b（6个）、开放阅读框3a（2个）以及开放阅读框6和开放阅读框8（各1个突变）。
BA.2及其后的BA.2.38是恰蒂斯加尔邦主要传播的奥密克戎谱系。由于其突变组合优势，BA.2.75可能会取代其他奥密克戎毒株。因此，需要对奥密克戎变种进行定期的基因组监测，以实时评估传播毒株及其突变引起的严重程度。
