Begum Feroza, Mukherjee Debica, Thagriki Dluya, Das Sandeepan, Tripathi Prem Prakash, Banerjee Arup Kumar, Ray Upasana
CSIR-Indian Institute of Chemical Biology, Kolkata, West Bengal, 730032, India.
Academy of Scientific and Innovative Research, Ghaziabad, 201002, India.
F1000Res. 2020 May 18;9:371. doi: 10.12688/f1000research.23805.2. eCollection 2020.
India has recently started sequencing SARS-CoV2 genome from clinical isolates. Currently only few sequences are available from three states in India. Kerala was the first state to deposit complete sequence from two isolates followed by one from Gujarat. On April 27, 2020, the first five sequences from the state of West Bengal (Eastern India) were deposited on GISAID, a global initiative for sharing avian flu data. In this study, we have analysed the spike protein sequences from all five isolates and also compared their similarities or differences with other sequences reported in India and with isolates of Wuhan origin. We report one unique mutation at position 723 and another at 1124 in the S2 domain of spike protein of the isolates from West Bengal only. There was one mutation downstream of the receptor binding domain at position 614 in S1 domain which was common with the sequence from Gujarat (a state of western India). Mutation in the S2 domain showed changes in the secondary structure of the spike protein at region of the mutation. We also studied molecular dynamics using normal mode analyses and found that this mutation decreases the flexibility of S2 domain. Since both S1 and S2 are important in receptor binding followed by entry in the host cells, such mutations may define the affinity or avidity of receptor binding.
印度最近开始对临床分离株中的严重急性呼吸综合征冠状病毒2（SARS-CoV2）基因组进行测序。目前，印度只有三个邦有少量序列可供获取。喀拉拉邦是第一个提交两个分离株完整序列的邦，随后是古吉拉特邦提交了一个序列。2020年4月27日，来自西孟加拉邦（印度东部）的前五个序列提交到了全球共享禽流感数据倡议组织（GISAID）。在本研究中，我们分析了所有五个分离株的刺突蛋白序列，并将它们与印度报告的其他序列以及武汉来源的分离株进行了相似性或差异性比较。我们报告称，仅西孟加拉邦分离株的刺突蛋白S2结构域中，在第723位有一个独特突变，在第1124位有另一个独特突变。在S1结构域的受体结合结构域下游第614位有一个突变，这与古吉拉特邦（印度西部的一个邦）的序列相同。S2结构域中的突变显示，在突变区域刺突蛋白的二级结构发生了变化。我们还使用正常模式分析研究了分子动力学，发现这种突变降低了S2结构域的灵活性。由于S1和S2在受体结合以及随后进入宿主细胞的过程中都很重要，因此这类突变可能决定受体结合的亲和力或亲合力。
