Host adaptation of codon usage in SARS-CoV-2 from mammals indicates potential natural selection and viral fitness.
Host adaptation of codon usage in SARS-CoV-2 from mammals indicates potential natural selection and viral fitness.
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哺乳动物 SARS-CoV-2 密码子使用的宿主适应表明潜在的自然选择和病毒适应性
DOI：
10.1007/s00705-022-05612-6
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发表时间：
2022-12
影响因子：
2.7
通讯作者：
中科院分区：
文献类型：
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作者：
SARS-CoV-2感染是COVID-19大流行的原因，已在各种动物宿主中扩展，该病毒可在水貂中特别有效地传播。目前尚不清楚SARS-CoV-2是如何在其宿主中被选择和进化的，或者突变如何影响病毒适应性。本研究分析了从人和动物宿主中分离的SARS-CoV-2的序列，并比较了刺突蛋白结合人ACE 2和水貂受体的结合能和能力。密码子适应指数（CAI）分析表明，在一些动物，如蝙蝠和水貂的病毒密码子的优化，和中性图表明，自然选择有更大的影响，一些SARS-CoV-2序列比突变压力。分子动力学模拟结果表明，水貂SARS-CoV-2中的Y 453 F和N501 T突变可以增强病毒刺突与水貂受体的结合，表明这些突变参与了自然选择和病毒适应性。受体结合分析显示，貂SARS-CoV-2刺突与貂受体的相互作用比与人受体的相互作用更强。追踪SARS-CoV-2的变异和密码子偏好性有助于了解该病毒在病毒传播、致病和免疫逃避中的适应性。在线版本包含补充材料，可通过10.1007/s 00705 -022-05612-6获得。
SARS-CoV-2 infection, which is the cause of the COVID-19 pandemic, has expanded across various animal hosts, and the virus can be transmitted particularly efficiently in minks. It is still not clear how SARS-CoV-2 is selected and evolves in its hosts, or how mutations affect viral fitness. In this report, sequences of SARS-CoV-2 isolated from human and animal hosts were analyzed, and the binding energy and capacity of the spike protein to bind human ACE2 and the mink receptor were compared. Codon adaptation index (CAI) analysis indicated the optimization of viral codons in some animals such as bats and minks, and a neutrality plot demonstrated that natural selection had a greater influence on some SARS-CoV-2 sequences than mutational pressure. Molecular dynamics simulation results showed that the mutations Y453F and N501T in mink SARS-CoV-2 could enhance the binding of the viral spike to the mink receptor, indicating the involvement of these mutations in natural selection and viral fitness. Receptor binding analysis revealed that the mink SARS-CoV-2 spike interacted more strongly with the mink receptor than the human receptor. Tracking the variations and codon bias of SARS-CoV-2 is helpful for understanding the fitness of the virus in virus transmission, pathogenesis, and immune evasion. The online version contains supplementary material available at 10.1007/s00705-022-05612-6.
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影响因子：
5.5
作者：
Puigbo, Pere;Bravo, Ignacio G.;Garcia-Vallve, Santiago
通讯作者：
Garcia-Vallve, Santiago
SARS-COV-2在人类和貂皮之间的貂皮农场上传播，然后回到人类。
DOI：
10.1126/science.abe5901
发表时间：
2021-01-08
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Oude Munnink BB;Sikkema RS;Nieuwenhuijse DF;Molenaar RJ;Munger E;Molenkamp R;van der Spek A;Tolsma P;Rietveld A;Brouwer M;Bouwmeester-Vincken N;Harders F;Hakze-van der Honing R;Wegdam-Blans MCA;Bouwstra RJ;GeurtsvanKessel C;van der Eijk AA;Velkers FC;Smit LAM;Stegeman A;van der Poel WHM;Koopmans MPG
通讯作者：
Koopmans MPG
影响因子：
5
作者：
Dutta, Rupam;Buragohain, Lukumoni;Borah, Probodh
通讯作者：
Borah, Probodh
鲤科疱疹病毒3型密码子使用偏差分析及该病毒对宿主的适应
影响因子：
2.5
作者：
Ma, Y. P.;Liu, Z. X.;Ke, H.
通讯作者：
Ke, H.
影响因子：
64.8
作者：
Hale VL;Dennis PM;McBride DS;Nolting JM;Madden C;Huey D;Ehrlich M;Grieser J;Winston J;Lombardi D;Gibson S;Saif L;Killian ML;Lantz K;Tell RM;Torchetti M;Robbe-Austerman S;Nelson MI;Faith SA;Bowman AS
通讯作者：
Bowman AS