Recombination analysis on the receptor switching event of MERS-CoV and its close relatives: implications for the emergence of MERS-CoV

Su S, Wong G, Shi W, Liu J, Lai ACK, Zhou J, et al. Epidemiology, genetic recombination, and Pathogenesis of coronaviruses. Trends Microbiol. 2016;24(6):490–502. https://doi.org/10.1016/j.tim.2016.03.003.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kesheh MM, Hosseini P, Soltani S, Zandi M. An overview on the seven pathogenic human coronaviruses. Rev Med Virol. 2022;32(2):e2282. https://doi.org/10.1002/rmv.2282.

Article  CAS  PubMed  Google Scholar 

Gupta RS, Khadka B. Conserved Molecular Signatures in the Spike, Nucleocapsid, and Polymerase Proteins Specific for the Genus Betacoronavirus and Its Different Subgenera. Genes (Basel). 2022;13(3):423. https://doi.org/10.3390/genes13030423.

Article  CAS  PubMed  Google Scholar 

Edridge AWD, Kaczorowska J, Hoste ACR, Bakker M, Klein M, Loens K, et al. Seasonal coronavirus protective immunity is short-lasting. Nat Med. 2020;26(11):1691–3. https://doi.org/10.1038/s41591-020-1083-1.

Article  CAS  PubMed  Google Scholar 

Neumann G, Kawaoka Y. Which Virus Will Cause the Next Pandemic? Viruses. 2023;15(1):199. https://doi.org/10.3390/v15010199.

Article  PubMed  PubMed Central  Google Scholar 

World Health Organization WHO Director-General’s opening remarks at the media briefing on COVID-19–11. March 2020. https://www.who.int/director-general/speeches/detail/who-director-general-s-opening-remarks-at-the-media-briefing-on-covid-19---11-march-2020 (2020). Accessed 17 July 2023.

Ruiz-Aravena M, McKee C, Gamble A, Lunn T, Morris A, Snedden CE, et al. Ecology, evolution and spillover of coronaviruses from bats. Nat Rev Microbiol. 2022;20(5):299–314. https://doi.org/10.1038/s41579-021-00652-2.

Article  CAS  PubMed  Google Scholar 

Wang LF, Shi Z, Zhang S, Field H, Daszak P, Eaton BT. Review of bats and SARS. Emerg Infect Dis. 2006;12(12):1834–40. https://doi.org/10.3201/eid1212.060401.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Temmam S, Vongphayloth K, Baquero E, Munier S, Bonomi M, Regnault B, et al. Bat coronaviruses related to SARS-CoV-2 and infectious for human cells. Nature. 2022;604(7905):330–6. https://doi.org/10.1038/s41586-022-04532-4.

Article  CAS  PubMed  Google Scholar 

Memish ZA, Cotten M, Meyer B, Watson SJ, Alsahafi AJ, Al Rabeeah AA, et al. Human infection with MERS coronavirus after exposure to infected camels, Saudi Arabia, 2013. Emerg Infect Dis. 2014;20(6):1012–5. https://doi.org/10.3201/eid2006.140402.

Article  PubMed  PubMed Central  Google Scholar 

Corman VM, Ithete NL, Richards LR, Schoeman MC, Preiser W, Drosten C, et al. Rooting the phylogenetic tree of middle East respiratory syndrome coronavirus by characterization of a conspecific virus from an African bat. J Virol. 2014;88(19):11297–303. https://doi.org/10.1128/JVI.01498-14.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Anthony SJ, Gilardi K, Menachery VD, Goldstein T, Ssebide B, Mbabazi R, et al. Further Evidence for Bats as the Evolutionary Source of Middle East Respiratory Syndrome Coronavirus. mBio. 2017;8(2):e00373-17. https://doi.org/10.1128/mBio.00373-17.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fenton M, Simmons N, Bats. A World of Science and mystery. Chicago, USA: University of Chicago Press; 2014.

Google Scholar 

Wang Q, Qi J, Yuan Y, Xuan Y, Han P, Wan Y, et al. Bat origins of MERS-CoV supported by bat coronavirus HKU4 usage of human receptor CD26. Cell Host Microbe. 2014;16(3):328–37. https://doi.org/10.1016/j.chom.2014.08.009.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Raj VS, Mou H, Smits SL, Dekkers DH, Muller MA, Dijkman R, et al. Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC. Nature. 2013;495(7440):251–4. https://doi.org/10.1038/nature12005.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Xiong Q, Cao L, Ma C, Tortorici MA, Liu C, Si J, et al. Close relatives of MERS-CoV in bats use ACE2 as their functional receptors. Nature. 2022;612(7941):748–57. https://doi.org/10.1038/s41586-022-05513-3.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ma C, Liu C, Xiong Q, Yu X, Chen Y, Si J, et al. Identification of ACE2 as the entry receptor for two novel European Bat Merbecoviruses. bioRxiv (Preprint). 2023. https://doi.org/10.1101/2023.10.02.560486.

Article  PubMed Central  Google Scholar 

Li F, Structure, Function, Evolution of Coronavirus Spike Proteins. Annu Rev Virol. 2016;3(1):237–61. https://doi.org/10.1146/annurev-virology-110615-042301.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nassar A, Ibrahim IM, Amin FG, Magdy M, Elgharib AM, Azzam EB, et al. A Review of Human Coronaviruses’ Receptors: The Host-Cell Targets for the Crown Bearing Viruses. Molecules. 2021;26(21):6455. https://doi.org/10.3390/molecules26216455.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ren W, Qu X, Li W, Han Z, Yu M, Zhou P, et al. Difference in receptor usage between severe acute respiratory syndrome (SARS) coronavirus and SARS-like coronavirus of bat origin. J Virol. 2008;82(4):1899–907. https://doi.org/10.1128/JVI.01085-07.

Article  CAS  PubMed  Google Scholar 

Perez-Losada M, Arenas M, Galan JC, Palero F, Gonzalez-Candelas F. Recombination in viruses: mechanisms, methods of study, and evolutionary consequences. Infect Genet Evol. 2015;30:296–307. https://doi.org/10.1016/j.meegid.2014.12.022.

Article  CAS  PubMed  Google Scholar 

Chabukswar S, Grandi N, Lin LT, Tramontano E. Envelope Recombination: A Major Driver in Shaping Retroviral Diversification and Evolution within the Host Genome. Viruses. 2023;15(9):1856. https://doi.org/10.3390/v15091856.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chiu ES, VandeWoude S. Endogenous Retroviruses Drive Resistance and Promotion of Exogenous Retroviral Homologs. Annu Rev Anim Biosci. 2021;9:225–48. https://doi.org/10.1146/annurev-animal-050620-101416.

Article  CAS  PubMed  Google Scholar 

Wells HL, Bonavita CM, Navarrete-Macias I, Vilchez B, Rasmussen AL, Anthony SJ. The coronavirus recombination pathway. Cell Host Microbe. 2023;31(6):874–89. https://doi.org/10.1016/j.chom.2023.05.003.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database (Oxford). 2020;2020. https://doi.org/10.1093/database/baaa062.

Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–80. https://doi.org/10.1093/molbev/mst010.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25(15):1972–3. https://doi.org/10.1093/bioinformatics/btp348.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, et al. IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020;37(5):1530–4. https://doi.org/10.1093/molbev/msaa015.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the Ultrafast bootstrap approximation. Mol Biol Evol. 2018;35(2):518–22. https://doi.org/10.1093/molbev/msx281.

Article  CAS  PubMed  Google Scholar 

Samson S, Lord E, Makarenkov V. SimPlot++: a Python application for representing sequence similarity and detecting recombination. Bioinformatics. 2022;38(11):3118–20. https://doi.org/10.1093/bioinformatics/btac287.

Article  CAS  PubMed  Google Scholar 

Martin DP, Varsani A, Roumagnac P, Botha G, Maslamoney S, Schwab T, et al. RDP5: a computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets. Virus Evol. 2021;7(1):veaa087. https://doi.org/10.1093/ve/veaa087.

Article  PubMed  Google Scholar 

Martin D, Rybicki E. RDP: detection of recombination amongst aligned sequences. Bioinformatics. 2000;16(6):562–3. https://doi.org/10.1093/bioinformatics/16.6.562.

Article  CAS  PubMed  Google Scholar 

Padidam M, Sawyer S, Fauquet CM. Possible emergence of new geminiviruses by frequent recombination. Virology. 1999;265(2):218–25. https://doi.org/10.1006/viro.1999.0056.

Article  CAS  PubMed  Google Scholar 

Posada D, Crandall KA. Evaluation of methods for detecting recombination from DNA sequences: computer simulation

留言 (0)

沒有登入
gif