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Open Access 01-12-2024 | Middle Eastern Respiratory Syndrome | Research

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

Authors: Jarel Elgin Tolentino, Spyros Lytras, Jumpei Ito, Kei Sato

Published in: Virology Journal | Issue 1/2024

Abstract

Background

PlMERS-CoV is a coronavirus known to cause severe disease in humans, taxonomically classified under the subgenus Merbecovirus. Recent findings showed that the close relatives of MERS-CoV infecting vespertillionid bats (family Vespertillionidae), named NeoCoV and PDF-2180, use their hosts’ ACE2 as their entry receptor, unlike the DPP4 receptor usage of MERS-CoV. Previous research suggests that this difference in receptor usage between these related viruses is a result of recombination. However, the precise location of the recombination breakpoints and the details of the recombination event leading to the change of receptor usage remain unclear.

Methods

We used maximum likelihood-based phylogenetics and genetic similarity comparisons to characterise the evolutionary history of all complete Merbecovirus genome sequences. Recombination events were detected by multiple computational methods implemented in the recombination detection program. To verify the influence of recombination, we inferred the phylogenetic relation of the merbecovirus genomes excluding recombinant segments and that of the viruses’ receptor binding domains and examined the level of congruency between the phylogenies. Finally, the geographic distribution of the genomes was inspected to identify the possible location where the recombination event occurred.

Results

Similarity plot analysis and the recombination-partitioned phylogenetic inference showed that MERS-CoV is highly similar to NeoCoV (and PDF-2180) across its whole genome except for the spike-encoding region. This is confirmed to be due to recombination by confidently detecting a recombination event between the proximal ancestor of MERS-CoV and a currently unsampled merbecovirus clade. Notably, the upstream recombination breakpoint was detected in the N-terminal domain and the downstream breakpoint at the S2 subunit of spike, indicating that the acquired recombined fragment includes the receptor-binding domain. A tanglegram comparison further confirmed that the receptor binding domain-encoding region of MERS-CoV was acquired via recombination. Geographic mapping analysis on sampling sites suggests the possibility that the recombination event occurred in Africa.

Conclusion

Together, our results suggest that recombination can lead to receptor switching of merbecoviruses during circulation in bats. These results are useful for future epidemiological assessments and surveillance to understand the spillover risk of bat coronaviruses to the human population.

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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.CrossRefPubMedPubMedCentral

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.CrossRefPubMed

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.CrossRefPubMed

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.CrossRefPubMed

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

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.CrossRefPubMed

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.CrossRefPubMedPubMedCentral

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.CrossRefPubMed

10.

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.CrossRefPubMedPubMedCentral

11.

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.CrossRefPubMedPubMedCentral

12.

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.CrossRefPubMedPubMedCentral

13.

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

14.

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.CrossRefPubMedPubMedCentral

15.

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.CrossRefPubMedPubMedCentral

16.

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.CrossRefPubMedPubMedCentral

17.

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.CrossRefPubMedCentral

18.

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.CrossRefPubMedPubMedCentral

19.

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.CrossRefPubMedPubMedCentral

20.

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.CrossRefPubMed

21.

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.CrossRefPubMed

22.

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.CrossRefPubMedPubMedCentral

23.

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.CrossRefPubMed

24.

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.CrossRefPubMedPubMedCentral

25.

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.

26.

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.CrossRefPubMedPubMedCentral

27.

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.CrossRefPubMedPubMedCentral

28.

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.CrossRefPubMedPubMedCentral

29.

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.CrossRefPubMed

30.

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.CrossRefPubMed

31.

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.CrossRefPubMed

32.

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.CrossRefPubMed

33.

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.CrossRefPubMed

34.

Posada D, Crandall KA. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci U S A. 2001;98(24):13757–62. https://doi.org/10.1073/pnas.241370698.CrossRefPubMedPubMedCentral

35.

Smith JM. Analyzing the mosaic structure of genes. J Mol Evol. 1992;34(2):126–9. https://doi.org/10.1007/BF00182389.CrossRefPubMed

36.

Martin DP, Posada D, Crandall KA, Williamson C. A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res Hum Retroviruses. 2005;21(1):98–102. https://doi.org/10.1089/aid.2005.21.98.CrossRefPubMed

37.

Gibbs MJ, Armstrong JS, Gibbs AJ. Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics. 2000;16(7):573–82. https://doi.org/10.1093/bioinformatics/16.7.573.CrossRefPubMed

38.

Lam HM, Ratmann O, Boni MF. Improved algorithmic complexity for the 3SEQ recombination detection algorithm. Mol Biol Evol. 2018;35(1):247–51. https://doi.org/10.1093/molbev/msx263.CrossRefPubMed

39.

Fei D, Guo Y, Fan Q, Wang H, Wu J, Li M, et al. Phylogenetic and recombination analyses of two deformed wing virus strains from different honeybee species in China. PeerJ. 2019;7:e7214. https://doi.org/10.7717/peerj.7214.CrossRefPubMedPubMedCentral

40.

Martin DP, Murrell B, Golden M, Khoosal A, Muhire B. RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evol. 2015;1(1):vev003. https://doi.org/10.1093/ve/vev003.CrossRefPubMedPubMedCentral

41.

Larsson A. AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics. 2014;30(22):3276–8. https://doi.org/10.1093/bioinformatics/btu531.CrossRefPubMedPubMedCentral

42.

Revell L. Phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol Evol. 2011;3(2):217–23. https://doi.org/10.1111/j.2041-210X.2011.00169.x.CrossRef

43.

Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–3. https://doi.org/10.1093/bioinformatics/btu033.CrossRefPubMedPubMedCentral

44.

Kobert K, Salichos L, Rokas A, Stamatakis A. Computing the Internode Certainty and related measures from partial gene trees. Mol Biol Evol. 2016;33(6):1606–17. https://doi.org/10.1093/molbev/msw040.CrossRefPubMedPubMedCentral

45.

Wang Y, Liu D, Shi W, Lu R, Wang W, Zhao Y, et al. Origin and possible genetic recombination of the Middle East Respiratory Syndrome Coronavirus from the First Imported Case in China: Phylogenetics and Coalescence Analysis. mBio. 2015;6(5):e01280–15. https://doi.org/10.1128/mBio.01280-15.CrossRefPubMedPubMedCentral

46.

Luo CM, Wang N, Yang XL, Liu HZ, Zhang W, Li B, et al. Discovery of Novel Bat Coronaviruses in South China That Use the Same Receptor as Middle East Respiratory Syndrome Coronavirus. J Virol. 2018;92(13):e00116–18. https://doi.org/10.1128/JVI.00116-18.CrossRefPubMedPubMedCentral

47.

Lau SKP, Zhang L, Luk HKH, Xiong L, Peng X, Li KSM, et al. Receptor usage of a novel Bat lineage C Betacoronavirus reveals evolution of Middle East Respiratory syndrome-related Coronavirus Spike Proteins for Human Dipeptidyl Peptidase 4 binding. J Infect Dis. 2018;218(2):197–207. https://doi.org/10.1093/infdis/jiy018.CrossRefPubMed

48.

Tan CCS, Trew J, Peacock TP, Mok KY, Hart C, Lau K, et al. Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential. Nat Commun. 2023;14(1):3322. https://doi.org/10.1038/s41467-023-38717-w.CrossRefPubMedPubMedCentral

49.

Yang Y, Du L, Liu C, Wang L, Ma C, Tang J, et al. Receptor usage and cell entry of bat coronavirus HKU4 provide insight into bat-to-human transmission of MERS coronavirus. Proc Natl Acad Sci U S A. 2014;111(34):12516–21. https://doi.org/10.1073/pnas.1405889111.CrossRefPubMedPubMedCentral

50.

Lau SKP, Fan RYY, Zhu L, Li KSM, Wong ACP, Luk HKH, et al. Isolation of MERS-related coronavirus from lesser bamboo bats that uses DPP4 and infects human-DPP4-transgenic mice. Nat Commun. 2021;12(1):216. https://doi.org/10.1038/s41467-020-20458-9.CrossRefPubMedPubMedCentral

51.

Chen J, Yang X, Si H, Gong Q, Que T, Li J, et al. A bat MERS-like coronavirus circulates in pangolins and utilizes human DPP4 and host proteases for cell entry. Cell. 2023;186(4):850-863.e16. https://doi.org/10.1016/j.cell.2023.01.019.CrossRefPubMedPubMedCentral

52.

Letko M. Functional assessment of cell entry and receptor use for merbecoviruses. bioRxiv (Preprint). 2024. https://doi.org/10.1101/2024.03.13.584892.CrossRef

53.

Lytras S, Hughes J, Martin D, Swanepoel P, de Klerk A, Lourens R, et al. Exploring the Natural Origins of SARS-CoV-2 in the Light of Recombination. Genome Biol Evol. 2022;14(2):evac018. https://doi.org/10.1093/gbe/evac018.CrossRef

54.

Tamura T, Ito J, Uriu K, Zahradnik J, Kida I, Anraku Y, et al. Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants. Nat Commun. 2023;14(1):2800. https://doi.org/10.1038/s41467-023-38435-3.CrossRefPubMedPubMedCentral

55.

van Boheemen S, de Graaf M, Lauber C, Bestebroer TM, Raj VS, Zaki AM, et al. Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans. mBio. 2012;3(6):e00473–12. https://doi.org/10.1128/mBio.00473-12.CrossRefPubMedPubMedCentral

56.

Dudas G, Rambaut A. MERS-CoV recombination: implications about the reservoir and potential for adaptation. Virus Evol. 2016;2(1):vev023. https://doi.org/10.1093/ve/vev023.CrossRefPubMedPubMedCentral

57.

Pollett S, Conte MA, Sanborn M, Jarman RG, Lidl GM, Modjarrad K, et al. A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic. Sci Rep. 2021;11(1):17365. https://doi.org/10.1038/s41598-021-96626-8.CrossRefPubMedPubMedCentral

58.

Sabir JS, Lam TT, Ahmed MM, Li L, Shen Y, Abo-Aba SE, et al. Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia. Science. 2016;351(6268):81–4. https://doi.org/10.1126/science.aac8608.CrossRefPubMed

59.

Patino-Galindo JA, Filip I, Rabadan R. Global patterns of recombination across human viruses. Mol Biol Evol. 2021;38(6):2520–31. https://doi.org/10.1093/molbev/msab046.CrossRefPubMedPubMedCentral

60.

Ma C, Liu C, Xiong Q, Gu M, Shi L, Wang C, et al. Broad host tropism of ACE2-using MERS-related coronaviruses and determinants restricting viral recognition. Cell Discov. 2023;9(1):57. https://doi.org/10.1038/s41421-023-00566-8.CrossRefPubMedPubMedCentral

61.

Forni D, Cagliani R, Sironi M. Recombination and Positive Selection Differentially Shaped the Diversity of Betacoronavirus Subgenera. Viruses. 2020;12(11):1313. https://doi.org/10.3390/v12111313.CrossRefPubMedPubMedCentral

62.

de Klerk A, Swanepoel P, Lourens R, Zondo M, Abodunran I, Lytras S, et al. Conserved recombination patterns across coronavirus subgenera. Virus Evol. 2022;8(2):veac054. https://doi.org/10.1093/ve/veac054.CrossRefPubMedPubMedCentral

63.

Mohd HA, Al-Tawfiq JA, Memish ZA. Middle East respiratory syndrome coronavirus (MERS-CoV) origin and animal reservoir. Virol J. 2016;13:87. https://doi.org/10.1186/s12985-016-0544-0.CrossRefPubMedPubMedCentral

64.

Zech F, Schniertshauer D, Jung C, Herrmann A, Cordsmeier A, Xie Q, et al. Spike residue 403 affects binding of coronavirus spikes to human ACE2. Nat Commun. 2021;12(1):6855. https://doi.org/10.1038/s41467-021-27180-0.CrossRefPubMedPubMedCentral

65.

Dufloo J, Andreu-Moreno I, Valero-Rello A, Sanjuan R. Viral entry is a weak barrier to zoonosis. bioRxiv (Preprint). 2024. https://doi.org/10.1101/2024.01.22.576693v1.CrossRef

66.

Markotter W, Coertse J, De Vries L, Geldenhuys M, Mortlock M. Bat-borne viruses in Africa: a critical review. J Zool (1987). 2020;311(2):77–98. https://doi.org/10.1111/jzo.12769.CrossRefPubMed

Title: Recombination analysis on the receptor switching event of MERS-CoV and its close relatives: implications for the emergence of MERS-CoV
Authors: Jarel Elgin Tolentino
Spyros Lytras
Jumpei Ito
Kei Sato
Publication date: 01-12-2024
Publisher: BioMed Central
Keywords: Middle Eastern Respiratory Syndrome
Coronavirus
Published in: Virology Journal / Issue 1/2024
Electronic ISSN: 1743-422X
DOI: https://doi.org/10.1186/s12985-024-02358-2

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