Zaman Kamran, Shete Anita M, Mishra Shailendra Kumar, Kumar Abhinendra, Reddy Mahendra M, Sahay Rima R, Yadav Shailendra, Majumdar Triparna, Pandey Ashok K, Dwivedi Gaurav Raj, Deval Hirawati, Singh Rajeev, Behera Sthita Pragnya, Kumar Niraj, Patil Savita, Kumar Ashish, Dudhmal Manisha, Joshi Yash, Shukla Aishwarya, Gawande Pranita, Kavathekar Asif, Kumar Nalin, Kumar Vijay, Kumar Kamlesh, Singh Ravi Shankar, Kumar Manoj, Tiwari Shashikant, Verma Ajay, Yadav Pragya D, Kant Rajni
Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India.
Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology Pune (ICMR-NIV Pune), Pune, India.
Front Med (Lausanne). 2022 Nov 2;9:955930. doi: 10.3389/fmed.2022.955930. eCollection 2022.
Recent studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reveal that Omicron variant BA.1 and sub-lineages have revived the concern over resistance to antiviral drugs and vaccine-induced immunity. The present study aims to analyze the clinical profile and genome characterization of the SARS-CoV-2 variant in eastern Uttar Pradesh (UP), North India.
Whole-genome sequencing (WGS) was conducted for 146 SARS-CoV-2 samples obtained from individuals who tested coronavirus disease 2019 (COVID-19) positive between the period of 1 January 2022 and 24 February 2022, from three districts of eastern UP. The details regarding clinical and hospitalized status were captured through telephonic interviews after obtaining verbal informed consent. A maximum-likelihood phylogenetic tree was created for evolutionary analysis using MEGA7.
The mean age of study participants was 33.9 ± 13.1 years, with 73.5% accounting for male patients. Of the 98 cases contacted by telephone, 30 (30.6%) had a travel history (domestic/international), 16 (16.3%) reported having been infected with COVID-19 in past, 79 (80.6%) had symptoms, and seven had at least one comorbidity. Most of the sequences belonged to the Omicron variant, with BA.1 (6.2%), BA.1.1 (2.7%), BA.1.1.1 (0.7%), BA.1.1.7 (5.5%), BA.1.17.2 (0.7%), BA.1.18 (0.7%), BA.2 (30.8%), BA.2.10 (50.7%), BA.2.12 (0.7%), and B.1.617.2 (1.3%) lineages. BA.1 and BA.1.1 strains possess signature spike mutations S:A67V, S:T95I, S:R346K, S:S371L, S:G446S, S:G496S, S:T547K, S:N856K, and S:L981F, and BA.2 contains S:V213G, S:T376A, and S:D405N. Notably, ins214EPE (S1- N-Terminal domain) mutation was found in a significant number of Omicron BA.1 and sub-lineages. The overall Omicron BA.2 lineage was observed in 79.5% of women and 83.2% of men.
The current study showed a predominance of the Omicron BA.2 variant outcompeting the BA.1 over a period in eastern UP. Most of the cases had a breakthrough infection following the recommended two doses of vaccine with four in five cases being symptomatic. There is a need to further explore the immune evasion properties of the Omicron variant.
近期关于严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的研究表明，奥密克戎变种BA.1及其亚谱系再次引发了人们对抗病毒药物耐药性和疫苗诱导免疫的担忧。本研究旨在分析印度北部北方邦东部地区SARS-CoV-2变种的临床特征和基因组特征。
对2022年1月1日至2022年2月24日期间从北方邦东部三个地区新冠病毒病（COVID-19）检测呈阳性的个体中获取的146份SARS-CoV-2样本进行全基因组测序（WGS）。在获得口头知情同意后，通过电话访谈获取临床和住院状态的详细信息。使用MEGA7创建最大似然系统发育树进行进化分析。
研究参与者的平均年龄为33.9±13.1岁，男性患者占73.5%。在通过电话联系的98例病例中，30例（30.6%）有旅行史（国内/国际），16例（16.3%）报告过去曾感染过COVID-19，79例（80.6%）有症状，7例至少有一种合并症。大多数序列属于奥密克戎变种，包括BA.1（6.2%）、BA.1.1（2.7%）、BA.1.1.1（0.7%）、BA.1.1.7（5.5%）、BA.1.17.2（0.7%）、BA.1.18（0.7%）、BA.2（30.8%）、BA.2.10（50.7%）、BA.2.12（0.7%）和B.1.617.2（1.3%）谱系。BA.1和BA.1.1毒株具有标志性的刺突突变S:A67V、S:T95I、S:R346K、S:S371L、S:G446S、S:G496S、S:T547K、S:N856K和S:L981F，BA.2包含S:V213G、S:T376A和S:D405N。值得注意的是，在大量奥密克戎BA.1及其亚谱系中发现了ins214EPE（S1-N端结构域）突变。奥密克戎BA.2谱系在79.5%的女性和83.2%的男性中被观察到。
当前研究表明，在北方邦东部的一段时间内，奥密克戎BA.2变种占主导地位，超过了BA.1。大多数病例在接种推荐的两剂疫苗后出现突破性感染，五分之四的病例有症状。有必要进一步探索奥密克戎变种的免疫逃逸特性。
