Background & objectives: SARS-CoV-2 (Severe acute respiratory syndrome coronavirus-2) is evolving with the progression of the pandemic. This study was aimed to investigate the diversity and evolution of the coronavirus SARS-CoV-2 with progression of the pandemic over time and to identify similarities and differences of viral diversity and evolution across geographical regions (countries).
Methods: Publicly available data on type definitions based on whole-genome sequences of the SARS-CoV-2 sampled during December and March 2020 from 3636 infected patients spread over 55 countries were collected. Phylodynamic analyses were performed and the temporal and spatial evolution of the virus was examined.
Results: It was found that (i) temporal variation in frequencies of types of the coronavirus was significant; ancestral viruses of type O were replaced by evolved viruses belonging to type A2a; (ii) spatial variation was not significant; with the spread of SARS-CoV-2, the dominant virus was the A2a type virus in every geographical region; (iii) within a geographical region, there was significant micro-level variation in the frequencies of the different viral types, and (iv) the evolved coronavirus of type A2a swept rapidly across all continents.
Interpretation & conclusions: SARS-CoV-2 belonging to the A2a type possesses a non-synomymous variant (D614G) that possibly eases the entry of the virus into the lung cells of the host. This may be the reason why the A2a type has an advantage to infect and survive and as a result has rapidly swept all geographical regions. Therefore, large-scale sequencing of coronavirus genomes and, as required, of host genomes should be undertaken in India to identify regional and ethnic variation in viral composition and its interaction with host genomes. Further, careful collection of clinical and immunological data of the host can provide deep learning in relation to infection and transmission of the types of coronavirus genomes.


中文翻译：

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对从55个国家/地区收集的3636个SARS-CoV-2的RNA序列进行的分析揭示了一种病毒的选择性清除


背景与目标： SARS-CoV-2（严重急性呼吸系统综合症冠状病毒-2）随着大流行的发展而发展。这项研究旨在调查冠状病毒SARS-CoV-2随大流行随着时间的推移的多样性和进化，并确定跨地理区域（国家）的病毒多样性和进化的异同。
方法：收集了公开定义的数据，这些数据基于2020年12月至2020年3月在55个国家/地区的3636名感染患者中采样的SARS-CoV-2全基因组序列进行了分类。进行了系统动力学分析，并检查了病毒的时空演变。
结果：发现（i）冠状病毒类型频率的时间变化显着；O型祖传病毒被属于A2a型的进化病毒替代；（ii）空间变化不明显；随着SARS-CoV-2的传播，优势病毒在每个地理区域均为A2a型病毒。（iii）在一个地理区域内，不同病毒类型的频率存在显着的微观变化，并且（iv）进化出的A2a型冠状病毒迅速席卷了所有大洲。
解释和结论：属于A2a类型的SARS-CoV-2具有一个非同源的变体（D614G），该变体可能会减轻病毒进入宿主肺细胞的进入。这可能是A2a型病毒具有感染和生存优势并因此迅速席卷所有地理区域的原因。因此，在印度应该对冠状病毒基因组和宿主基因组进行大规模测序，以鉴定病毒成分及其与宿主基因组相互作用的区域和种族差异。此外，仔细收集宿主的临床和免疫学数据可以提供有关冠状病毒基因组类型感染和传播的深入学习。