ORF-Interrupting Mutations in Monkeypox Virus Genomes from Washington and Ohio, 2022

• Published in: Viruses 2022-10, Vol.14 (11), p.2393
• Main Authors: Sereewit, Jaydee, Lieberman, Nicole A P, Xie, Hong, Bakhash, Shah A K Mohamed, Nunley, B Ethan, Chung, Benjamin, Mills, Margaret G, Roychoudhury, Pavitra, Greninger, Alexander L
• Format: Article
• Language: English
• Subjects: Automation; B21R; C-Terminus; DNA sequencing; DNA viruses; DNA-directed RNA polymerase; essential gene; Frameshift mutation; Genes; Genetic aspects; Genomes; genomic deletion; Host-pathogen interactions; Humans; Immunogenicity; Laboratories; monkeypox virus; Monkeypox virus - genetics; Mpox; Mpox (monkeypox) - diagnosis; Mutation; Nucleotide sequencing; Ohio; Open Reading Frames; Orthopoxvirus; Physiological aspects; Proteins; RNA polymerase; RNA viruses; serology; Virulence; Washington; Whole genome sequencing
• ISSN: 1999-4915; 1999-4915
• DOI: 10.3390/v14112393

Monkeypox virus, the causative agent of the 2022 monkeypox outbreak, is a double-stranded DNA virus in the genus of the family. Genes in terminal regions of genomes mostly code for host-pathogen interaction proteins and are prone to selective pressure and modification events. Using viral whole genome sequencing, we identified twenty-five total clinical samples with ORF-disrupting mutations, including twenty samples encoding nonsense mutations in MPXVgp001/191 (OPG001), MPXVgp004/188 (OPG015), MPXVgp010 (OPG023), MPXVgp030 (OPG042), MPXVgp159 (OPG0178), or MPXVgp161 (OPG181). Additional mutations include a frameshift leading to an alternative C-terminus in MPXVgp010 (OPG023) and an insertion in an adenine homopolymer at the beginning of the annotated ORF for MPXVgp153 (OPG151), encoding a subunit of the RNA polymerase, suggesting the virus may instead use the start codon that encodes Met9 as annotated. Finally, we detected three samples with large (>900 bp) deletions. These included a 913 bp deletion that truncates the C-terminus of MPXVgp010 (OPG023); a 4205 bp deletion that eliminates MPXVgp012 (OPG025), MPXVgp013 (OPG027), and MPXVgp014 (OPG029) and truncates MPXVgp011 (OPG024; D8L) and MPXVgp015 (OPG030); and a 6881 bp deletion that truncates MPXVgp182 (OPG210) and eliminates putative ORFs MPXVgp184, MPXVgp185 (OPG005), and MPXVgp186, as well as MPXVgp187 (OPG016), and MPXVgp188 (OPG015) from the 3' ITR only. MPXVgp182 encodes the monkeypox-specific, highly immunogenic surface glycoprotein B21R which has been proposed as a serological target. Overall, we find greater than one-tenth of our sequenced MPXV isolates have at least one gene inactivating mutation and these genes together comprised greater than one-tenth of annotated MPXV genes. Our findings highlight non-essential genes in monkeypox virus that may be evolving as a result of selective pressure in humans, as well as the limitations of targeting them for therapeutics and diagnostic testing.