Sahni Chetan, Basu Roy Chowdhury Priyoneel, Devadas Deepa, Ashish Ashish, Singh Nitish K, Yadav Abhay, Kaur Manpreet, Mishra Shivani, Vishwakarma Shani, Singh Royana
Anatomy, Institute of Medical Sciences (IMS) Banaras Hindu University (BHU), Varanasi, IND.
Zoology, Kalinga Institute of Social Sciences Deemed University, Bhubaneswar, IND.
Cureus. 2022 Sep 24;14(9):e29544. doi: 10.7759/cureus.29544. eCollection 2022 Sep.
India had faced a devastating second outbreak of COVID-19 infection, in which a majority of the viral sequences were found to be of the B.1.617.2 lineage (Delta-variant). While India and the world focused on vaccination, reports of vaccine-immunity evasion by the virus, termed "breakthrough cases", emerged worldwide. Our study was focused on the primary objective to identify the mutations associated with breakthrough infections SARS-CoV-2.
In our study, we extracted the SARS-CoV-2 RNA (ribonucleic acid) from reverse transcription-polymerase chain reaction (RT-PCR) positive COVID-19 patients, and 150 random samples were sent for sequencing to the Centre for Cellular & Molecular Biology, Hyderabad. Whole genome sequences of 150 SARS-CoV-2 viral samples were analyzed thoroughly. We mostly found B.1.617 and its sub-lineages in the genomic sequencing results.
On further analysis of patient data, it was seen that nine patients had been vaccinated against the SARS-CoV-2 previously. These nine patients had B.1.617/B.1 or A strains, and all of them had similar genomic variations in spike proteins as well as non-structural proteins (NSPs). The mutations seen in these sequences in the Spike (S), NSPs, and open reading frame (ORF) regions would have produced amino acid changes known to improve viral replication, confer drug resistance, influence host-cell interaction, and lead to antigenic drift.
Increased virulence culminating in vaccine immunity evasion may be inferred from these specific mutations. Our study adds to the growing body of evidence linking rapidly emerging mutations in the S (Spike) and ORF genes of the SARS-CoV-2 genome to immune evasion.
印度曾面临第二波毁灭性的新冠病毒感染疫情，在此期间发现大多数病毒序列属于B.1.617.2谱系（德尔塔变种）。当印度和全球都聚焦于疫苗接种时，全球出现了关于病毒逃避疫苗免疫的报道，即“突破性病例”。我们的研究主要目标是确定与新冠病毒突破性感染相关的突变。
在我们的研究中，我们从逆转录聚合酶链反应（RT-PCR）呈阳性的新冠患者中提取了新冠病毒核糖核酸（RNA），并将150个随机样本送往海得拉巴细胞与分子生物学中心进行测序。对150个新冠病毒样本的全基因组序列进行了全面分析。我们在基因组测序结果中大多发现了B.1.617及其亚谱系。
对患者数据的进一步分析显示，有9名患者此前已接种过新冠疫苗。这9名患者感染的是B.1.617/B.1或A毒株，他们在刺突蛋白以及非结构蛋白（NSPs）方面都有相似的基因组变异。在这些序列的刺突（S）、NSPs和开放阅读框（ORF）区域中发现的突变会导致氨基酸变化，已知这些变化可改善病毒复制、赋予耐药性、影响宿主细胞相互作用并导致抗原漂移。
从这些特定突变中可以推断出毒力增加最终导致疫苗免疫逃避。我们的研究进一步证明了新冠病毒基因组中S（刺突）和ORF基因中迅速出现的突变与免疫逃避之间的联系。
