Table_3_Evolutionary dissection of monkeypox virus: Positive Darwinian selection drives the adaptation of virus–host interaction proteins.xlsx

The emerging and ongoing outbreak of human monkeypox (hMPX) in 2022 is a serious global threat. An understanding of the evolution of the monkeypox virus (MPXV) at the single-gene level may provide clues for exploring the unique aspects of the current outbreak: rapidly expanding and sustained human-to-human transmission. For the current investigation, alleles of 156 MPXV coding genes (which account for >95% of the genomic sequence) have been gathered from roughly 1,500 isolates, including those responsible for the previous outbreaks. Using a range of molecular evolution approaches, we demonstrated that intra-species homologous recombination has a negligible effect on MPXV evolution. Despite the fact that the majority of the MPXV genes (64.10%) were subjected to negative selection at the whole gene level, 10 MPXV coding genes (MPXVgp004, 010, 012, 014, 044, 098, 138, 178, 188, and 191) were found to have a total of 15 codons or amino acid sites that are known to evolve under positive Darwinian selection. Except for MPXVgp138, almost all of these genes encode proteins that interact with the host. Of these, five ankyrin proteins (MPXVgp004, 010, 012, 178, and 188) and one Bcl-2-like protein (MPXVgp014) are involved in poxviruses’ host range determination. We discovered that the majority (80%) of positive amino acid substitutions emerged several decades ago, indicating that these sites have been under constant selection pressure and that more adaptable alleles have been circulating in the natural reservoir. This finding was also supported by the minimum spanning networks of the gene alleles. The three positive amino acid substitutions (T/A426V in MPXVgp010, A423D in MPXVgp012, and S105L in MPXVgp191) appeared in 2019 or 2022, indicating that they would be crucial for the virus’ eventual adaptation to humans. Protein modeling suggests that positive amino acid substitutions may affect protein functions in a variety of ways. Further study should focus on revealing the biological effects of positive amino acid substitutions in the genes for viral adaptation to humans, virulence, transmission, and so on. Our study advances knowledge of MPXV’s adaptive mechanism and provides insights for exploring factors that are responsible for the unique aspects of the current outbreak.

2022年暴发且持续蔓延的人类猴痘（human monkeypox, hMPX）疫情，正对全球构成严重威胁。从单基因层面解析猴痘病毒（monkeypox virus, MPXV）的演化规律，或可为探索本次疫情的独特特征——快速扩散且持续的人传人传播——提供关键线索。本研究共收集了约1500株病毒分离株的156个猴痘病毒编码基因的等位基因（allele）序列，该套序列覆盖了病毒基因组95%以上的区域，同时纳入了既往疫情相关的分离株。通过一系列分子演化分析方法，本研究证实种内同源重组（intra-species homologous recombination）对猴痘病毒演化的影响微乎其微。尽管绝大多数猴痘病毒基因（64.10%）在全基因水平处于负选择（negative selection）压力之下，但仍有10个编码基因（MPXVgp004、010、012、014、044、098、138、178、188及191）被检出共15个已知处于达尔文正向选择（positive Darwinian selection）下的密码子或氨基酸位点。除MPXVgp138外，上述基因编码的蛋白几乎均与宿主互作相关。其中，5种锚蛋白（ankyrin protein）（MPXVgp004、010、012、178及188）及1种Bcl-2样蛋白（Bcl-2-like protein，MPXVgp014）参与痘病毒宿主范围的调控。本研究发现，80%的正向氨基酸替换均在数十年前即已出现，这表明这些位点始终处于持续的选择压力之下，且更具适应性的等位基因一直在自然宿主库中流行。这一结论也得到了基因等位基因的最小生成网络（minimum spanning network）分析结果的支持。3个正向氨基酸替换位点——MPXVgp010的T/A426V、MPXVgp012的A423D及MPXVgp191的S105L——出现于2019年或2022年，这提示它们对于病毒最终适应人类宿主具有关键作用。蛋白结构建模（protein modeling）结果显示，正向氨基酸替换可能通过多种途径影响蛋白功能。未来研究应着重揭示这些正向氨基酸替换在病毒适应人类宿主、毒力及传播等相关基因中所发挥的生物学效应。本研究加深了学界对猴痘病毒适应性演化机制的认知，并为探索本次疫情独特传播特征的成因提供了新的研究视角。