The descendants of the B lineage are the most predominant variants among the SARS-CoV-2 virus due to the incorporation of new mutations augmenting the infectivity of the virus. There is a substantial increase in the transition transversion bias, nucleotide diversity and purifying selection on the spike protein in the descendants of the B lineage of the SARS-CoV-2 virus on a temporal scale. A strong bias for C-to-U substitutions is found in the genes encoding spike protein in this lineage. The positive selection has operated on the spike gene of B lineages and its sub-lineages. The B.1 lineage has undergone positive selection on site 501 of the receptor binding domain ultimately reflected in a key substitution N501Y in its three descendant lineages namely B.1.1.7, B.1.351 and P.1. The intensity of purifying selection on the multiple sites of the spike gene has increased substantially in the sub-lineages of B.1 in a timescale. The binding site 501 on the spike protein in B lineage is found to coevolve with other amino acid sites. This study sheds light on the evolutionary trajectory of the B lineage into highly infectious descendants in the recent past under the influence of positive and purifying selection exerted by natural immunity and vaccination of the host.

中文翻译：

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B.1 谱系中 501 结合位点的正选择可能引发了 SARS-CoV-2 的高传染性亚谱系

B 谱系的后代是 SARS-CoV-2 病毒中最主要的变体，因为新突变的结合增强了病毒的感染性。 SARS-CoV-2 病毒 B 谱系的后代中，转换颠换偏差、核苷酸多样性和刺突蛋白的纯化选择在时间尺度上显着增加。在该谱系中编码刺突蛋白的基因中发现了 C-U 取代的强烈偏差。正选择作用于B谱系及其亚谱系的spike基因。 B.1谱系在受体结合结构域的位点501上经历了正选择，最终反映在其三个后代谱系（即B.1.1.7、B.1.351和P.1）中的关键取代N501Y中。在时间尺度上，B.1 亚谱系中刺突基因多个位点上的纯化选择强度显着增加。发现B谱系中刺突蛋白上的结合位点501与其他氨基酸位点共同进化。这项研究揭示了在宿主自然免疫和疫苗接种所施加的正向和纯化选择的影响下，B谱系在最近一段时间内向高传染性后代的进化轨迹。