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Transmission of SARS-CoV-2 in South Asian countries: molecular evolutionary model based phylogenetic and mutation analysis

机译：SARS-CoV-2在南亚的传播国家:分子进化模型的基础系统发育和基因突变分析

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Abstract The on-going coronavirus disease 19 (COVID-19) pandemic?has caused a very high number of infections and deaths around the globe. The absence of vaccine/drugs to counter COVID-19 has scrambled scientific communities to repurpose available medicines/vaccines. As the virus is known to mutate, using the whole genome sequences, the transmission dynamics and molecular evolutionary models were evaluated for South Asian countries to determine the evolutionary rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Phylogenetic analyses were done using the data available on National Center for Biotechnology Information (NCBI). Different nucleotide substitution models and molecular evolutionary models were analyzed to see how SARS-CoV-2 was transmitted in the populations. Models for the viral ‘S’ and ‘N’ protein from selected strains were constructed, validated, and analyzed to determine the mutations and discover the potential therapeutics against this deadly viral disease. We found that the Hasegawa-Kishino-Yano (HKY) nucleotide substitution model was the best model with the lowest Bayesian information criterion (BIC) scores. Molecular clock RelTime analysis showed the evolutionary rate of SARS-CoV-2 substitutions in the genome was at 95% confidence interval, and heterogeneity was observed. Several mutations in the viral S-protein were found with one in the receptor-binding domain concerning SARS-CoV-2/Wuhan-1/S-Protein. Nucleocapsid protein also showed mutations in the strains from India and Sri Lanka. Our analysis suggests that SARS-CoV-2 is evolving at a diverse rate. The mutation leading to substitution in the nucleotide sequence occurred in the genome during the transmission of COVID-19 among individuals in the South Asian countries.
机译：摘要持续19冠状病毒疾病(COVID-19)大流行?全球的感染和死亡。没有疫苗/药物对抗COVID-19科学社区重新炒可用的药物和疫苗。使用全基因组突变,序列,动力学和传播分子进化的模型进行评估南亚国家来确定严重急性呼吸系统的进化速率综合症冠状病毒2 (SARS-CoV-2)。分析使用的数据可用国家生物技术信息中心(NCBI)。和分子进化模型进行了分析看到SARS-CoV-2是如何传播的人群。蛋白质所选菌株的构建,验证和分析来确定突变和发现潜在的治疗对这种致命的病毒性疾病。Hasegawa-Kishino-Yano (HKY)核苷酸替换模型是最好的模型贝叶斯信息准则(BIC)最低分数。的进化速率SARS-CoV-2替换在95%置信区间的基因组,异质性被观察到。病毒S-protein被发现的受体结合域有关SARS-CoV-2 / Wuhan-1 / S-Protein。蛋白质还显示突变菌株印度和斯里兰卡。SARS-CoV-2发展速度不同。突变导致的替换核苷酸序列发生在基因组中的传播COVID-19个体南亚国家。

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