An isolated epidemic of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) causing Coronavirus Diseases (C0VID-19) originating in Wuhan, China has now rapidly emerged into a global pandemic affecting millions of people worldwide. Molecular detection of SARS-CoV-2 using reverse transcription polymerase chain reaction (RT-PCR) forms the mainstay in screening, diagnosis and epidemiology of disease. The virus has been evolving through base substitutions. The recent availability of genomes of SARS-CoV-2 isolates from different countries including India motivated us to assess the presence and potential impact of variations in target sites for the oligonucleotide primers and probes used in molecular diagnosis. We catalogued a total of 132 primers or probes sequences from the literature and the public domain. Our analysis revealed a total of 125 unique genetic variants in 80 either primers or probes binding sites. A total of 13 unique variants had allele frequency of ≥ 1% in Indian SARS-CoV-2 genomes mapped to the primers or probes binding sites. A total of 15 primers or probes binding sites had cumulative variant frequency of ≥ 1% in the SARS-CoV-2 genomes. These included primers or probes sites which are widely used in India and across the world for molecular diagnosis as well as approved by national and international agencies. This highlights the need for sequencing genomes of emerging pathogens to make evidence based policies for development and approval of diagnostics. To the best of our knowledge, ours is the most comprehensive analysis of genomic variants in genomes of SARS-CoV-2 isolates from India and their potential impact on efficacy of molecular diagnostics. Keywords: COVID-19, genomes, SARS-CoV-2, variations, reverse transcription polymerase chain reaction, Gibbs free energy

中文翻译：

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印度SARS-CoV-2基因组中基因组变异对分子诊断分析的潜在影响分析

严重的急性呼吸系统综合症冠状病毒2（SARS-CoV-2）的一种流行病原发于武汉，目前已迅速发展成为一种全球性大流行病，影响了全球数百万人，冠状病毒病（C0VID-19）起源于武汉。使用逆转录聚合酶链反应（RT-PCR）进行SARS-CoV-2分子检测是疾病筛查，诊断和流行病学研究的主要内容。该病毒一直通过碱基取代而发展。来自包括印度在内的不同国家的SARS-CoV-2分离株的基因组的最新可用性促使我们评估用于分子诊断的寡核苷酸引物和探针的靶位点变异的存在和潜在影响。我们从文献和公共领域对总共132个引物或探针序列进行了分类。我们的分析揭示了在80个引物或探针结合位点中共有125个独特的遗传变异。在映射到引物或探针结合位点的印度SARS-CoV-2基因组中，共有13个独特变体的等位基因频率≥1％。在SARS-CoV-2基因组中，共有15个引物或探针结合位点的累积变异频率≥1％。其中包括在印度和世界范围内广泛用于分子诊断并得到国家和国际机构认可的引物或探针位点。这突出显示了对新兴病原体的基因组进行测序的必要性，以制定基于证据的诊断学开发和批准政策。据我们所知，我们对印度SARS-CoV-2分离株的基因组变异及其对分子诊断功效的潜在影响进行了最全面的分析。关键词：COVID-19，基因组，SARS-CoV-2，变异，逆转录聚合酶链反应，吉布斯自由能