Recombination shapes 2022 monkeypox outbreak

Background On July 23, 2022, the WHO declared monkeypox outbreak a global health emergency. Here we analyze monkeypox virus (MPXV) sequences during 2022 pandemic to investigate whether the virus is adapting for better survival and transmission among the human population. Methods By studying tandem repeats (TRs) and linkage disequilibrium (LD), we analyzed 415 MPXV sequences from January 1 to July 20, 2022 worldwide. Finding The 2022 MPXV population has diverged into 4 lineages and 11 subgroups based on various TRs and their copy numbers. LD analysis also shows that virus has evolved into 3 new lineages. We identify 8 new recombinants (six from Slovenia, one from Australia, one from Italy) using TR analysis and 3 recombinants (two from Germany, one from Spain) using LD analysis. Conclusion Our results indicate that the MPXV genome is evolving and expanding quickly during the 2022 pandemic. We conclude that in combination with genomic surveillance, TR analysis, as well as LD analysis, are useful tools with which to monitor and track phylogenetic dynamics and recombination of monkeypox transmission. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This study did not receive any funding. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: NCBI, https://www.ncbi.nlm.nih.gov/nuccore DOI: 10.6084/m9.figshare.20486313 DOI: 10.6084/m9.figshare.21387525 I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All sequence data are available at Figshare website: DOI: 10.6084/m9.figshare.20486313. TRAL analysis is available at Figshare website DOI: 10.6084/m9.figshare.21387525