Multiple lineages of monkeypox virus detected in the United States, 2021–2022

Gigante, Crystal M.; Korber, Bette T.; Seabolt, Matthew H.; Wilkins, Kimberly; Davidson, Whitni; Rao, Agam K.; Zhao, Hui; Smith, T.; Hughes, Christine M.; Minhaj, Faisal S.; Waltenburg, Michelle A.; Theiler, James; Smole, Sandra; Gallagher, Glen R.; Blythe, David; Myers, Robert; Schulte, Joann; Stringer, Joey; Lee, Philip; Mendoza, Rafael; Griffin-Thomas, LaToya A.; Crain, Jenny; Murray, Jade; Atkinson, Annette; Gonzalez, Anthony H.; Nash, June; Batra, Dhwani; Damon, Inger K.; McQuiston, Jennifer H.; Hutson, Christina L.; McCollum, Andrea M.; Li, Y.

doi:10.1126/science.add4153

Cited by 185 publications

(233 citation statements)

References 37 publications

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“…However, it has been suggested that host APOBEC3 in viral evolution with signs of potential human adaptation of MPXV in ongoing microevolution (Isidro et al, 2022). Gigante et al reported that APOBEC3 activity has been recurrent and dominant in West African MPXV evolution (2017-2022) recently (Gigante et al, 2022). When compared with previous MPXV sequences, many mutations in the 2022 MPXV sequences were 5’ GA-to-AA, suggesting APOBEC3 activity (O’Toole and Rambaut, 2022).…”

Section: Resultsmentioning

confidence: 99%

Recombination shapes 2022 monkeypox outbreak

Yeh

Hsieh

Feehley

et al. 2022

Preprint

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Here we report the first evidence of recombination of monkeypox genome in natural transmission by analyzing six tandem repeats (TRs) among 415 sequences collected between January to July 2022. The 2022 monkeypox viral population has diverged into 11 subgroups based on various TRs and their copy numbers. Here we identify 8 new recombinants (six from Slovenia, one from Australia, one from Italy). Our results indicate that the monkeypox genome is evolving and expanding quickly during the 2022 pandemic (Zeng E = -1.65, Achaz Y=-2.52, p< 0.001). We conclude that, In combination with genomic surveillance, TR analysis is a useful tool to monitor and track phylogenetic dynamics of monkeypox transmission.

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Section: Resultsmentioning

confidence: 99%

Recombination shapes 2022 monkeypox outbreak

Yeh

Hsieh

Feehley

et al. 2022

Preprint

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“…The current Monkeypox outbreak in USA represents the circulation of MPXV lineage A.2 from 2021 which has evolved from lineage A that caused the Nigeria outbreak in 2017-2018. 14 The MPXV genome retrieved from con rmed Monkeypox cases with travel history from UAE to India also demonstrated the circulation of A.2 lineage in UAE. Unfortunately, no epidemiological data is available for the introduction of MPXV to UAE.…”

Section: Laboratory Analysismentioning

confidence: 96%

First two cases of Monkeypox virus infection in travellers returned from UAE to India, July 2022

Yadav

Reghukumar

Sahay

et al. 2022

Preprint

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We report the first two confirmed cases of Monkeypox in foreign returnees from United Arab Emirates who presented with fever, myalgia, and vesicular lesions on the genital area with cervical lymphadenopathy. The oropharyngeal & nasopharyngeal swab, EDTA blood, serum, urine, lesion samples from multiple sites (lesion fluid, lesion roof and lesion base) were collected from both the cases on ninth post onset day of illness. The clinical specimens of both the cases were tested with real time PCR for Orthopoxvirus, Monkeypox virus (MPXV), West African clade specific MPXV. The specimens oropharyngeal & nasopharyngeal swab, urine, lesion samples from multiple sites (lesion fluid, lesion roof and lesion base) were tested positive for MPXV. The complete genome sequences obtained from skin lesions of case 1 and 2 showed similarity of 99.91 and 99.96% respectively with MPXV_USA_2022_FL001 West African clade. Phylogenetic analysis revealed that the two cases were infected with Monkeypox virus strain A.2 which belong to hMPXV-1A lineage of clade 3.

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“…The remaining non-host reads were assembled using SPADES v3.15.3 (Antipov et al, 2016;Prjibelski et al, 2020) in rnaviral mode. A fully ordered MPXV genome sequence was generated using ABACAS v1.3.1 (Assefa et al, 2009), based on the MPXV isolate MPXV_USA_2022_MA001 (Nextstrain subclade IIb lineage B.1) sequence (GenBank #ON563414.3) (Gigante et al, 2022). The independently obtained de novo assemblies and reference-based consensus genomes obtained from swab 353R were aligned using MAFFT v7.475 (Katoh et al, 2019) and visually inspected for variation using Jalview v2.11.0 (Waterhouse et al, 2009).…”

Section: De Novo Assembly and Annotation Of Subclade II Lineage B1 Mp...mentioning

confidence: 99%

“…Among Clade IIb, B1 strains show 16 We propose this genome for sample 353R as a high-quality complete reference genome, HQG 41 . We compared our 198,547 bp HQG to MPXV-M5312_HM12_Rivers (NC_063383.1) and MPXV_USA_2022_MA001 (ON563414.3) 13 (Table 3). Both 353R and ON562414.3 genomes show the same 67 SNPs called against the NC_063383.1 reference genome.…”

Section: A Complete High-quality Monkeypox Genome Assembly and Annota...mentioning

confidence: 99%

“…Clade IIb had been previously imported into the UK 9 , Israel 10 and Singapore 11,12 . The nearest relative of the 2022 outbreak is USA/UT-UPHL-82200022/2022 (Accession number: ON676708), a genome detected in a Nigerian traveler 13 . Although most cases are related to this group of sequences (named lineage B.1), a few 2022 cases reported in the USA, Malaysia, and India form a different lineage (named lineage A.2).…”

Section: Introductionmentioning

confidence: 99%

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Changes in a new type of genomic accordion may open the pallets to increased monkeypox transmissibility

Monzón

Varona

Negredo

et al. 2022

Preprint

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The recent outbreak of Monkeypox displays novel transmission features. The circulating strain is a descendant of a lineage that had been circulating in Nigeria since 2017. The prognosis of monkeypox disease (MPX) with the circulating strain is generally good but the estimated primary reproduction number (R0) among men who have sex with men (MSM) was above 1 suggesting efficient person-to-person transmission. Different mechanisms of viral entry and egress, as well as virus-coded host factors, are the main biological determinants of poxvirus transmissibility. OPXV evolution is driven by gene loss of virus-host interacting genes and selective pressure from host species using unique adaptive strategies at the gene and nucleotide level. In this context, we evaluated the effects of genomic instability in low-complexity-regions, areas that are often neglected during sequencing, during the early stage of the outbreak in Madrid, Spain. We uncovered significant variation in short-tandem repeat areas of the MPXV genome that could be associated with changes in transmissibility. Expression, translation, stability, or function of OPG153 (VACV A26L), OPG204 (VACV B16R) and OPG208 (VACV B19R) could be affected by the changes, in a manner that is consistent with proven genomic accordion strategies of OPXV evolution. Intriguingly, while the changes observed in OPG153 stand out as they are located inside a region under high selective pressure for transmission, in a gene that is clearly considered a core gene involved in attachment and egress; the changes in OPG208, a serine protease inhibitor-like protein that has been identified as an apoptosis inhibitor, host-range factor and virulence factor; and OPG204, a known inhibitor of the Type I interferon system shown to act as a decoy receptor, could also explain phenotypic changes. Further functional studies to complement this comparative genomic study are urgently needed.

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Multiple lineages of monkeypox virus detected in the United States, 2021–2022

Cited by 185 publications

References 37 publications

Recombination shapes 2022 monkeypox outbreak

Recombination shapes 2022 monkeypox outbreak

First two cases of Monkeypox virus infection in travellers returned from UAE to India, July 2022

Changes in a new type of genomic accordion may open the pallets to increased monkeypox transmissibility

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