Patterns of genomic deletions in monkeypox virus during the 2022 outbreak in the United States
Abstract
Abstract Poxviruses have a low overall rate of point mutations but are known to exhibit genomic duplications and deletions that can influence viral evolution. We examine the prevalence of large deletions in clade IIb monkeypox virus (MPXV) genomes during the global 2022 outbreak. We observe thirty-one distinct deletions, ranging from 573 to 21,576 bp among over 2000 MPXV genomes during 2022 − 2023 in the United States (U.S.). Almost all deletions are present in the first 25,000 bp or last 50,000 bp of the MPXV genome, excluding the terminal 500 bp. The large deletions result in extensive predicted gene loss as well as novel predicted gene products. Most unique deletions are observed in one case; however, one 3370 bp deletion mutant predominated in a U.S. state during late 2022 and a different 913 bp deletion may have arisen independently multiple times across several MPXV sub-lineages and multiple countries. The recurrent presence of large deletion mutants provides evidence of a mechanism of poxvirus evolution by genomic deletion and gene loss. While no deletion emerged in a dominant variant during 2022 − 2023, large deletions have the potential to result in viruses in which a therapeutic or diagnostic target is deleted.
Article Details
Authors (37)
Crystal M. Gigante
Daisy McGrath
Sophia Sukkestad
Hui Zhao
Center of Ionic Liquid and Green Energy, Beijing Key Laboratory of Solid State Battery and Energy Storage Process, State Key Laboratory of Mesoscience and Engineering, Institute of Process Engineering
Mengfei Peng
Jade Takakuwa
Kimberly Wilkins
Vaughn Wicker
Audrey Matheny
Theodora Khan
Whitni B. Davidson
Mili Sheth
Alex Burgin
Julie Hand
Gillian Richardson
Danielle Haydel
Mark Burroughs
Jasmine Padilla
Justin S. Lee
Dhwani Batra
Ethan E. Hetrick
Dakota T. Howard
Kyle O’Connell
Jessica L. Rowell
Shatavia Morrison
Sarah Gillani
Michelle Lee
Anil Mangla
David Blythe
Robert Myers
Lynsey Kovar
Matthew H. Seabolt
Michael R. Weigand
Panayampalli S. Satheshkumar
Andrea M. McCollum
Christina L. Hutson
Yu Li