Genomic annotation and molecular evolution of monkeypox virus outbreak in 2022

Wang, Lulan; Shang, Jingzhe; Weng, Shenghui; Aliyari, Saba R.; Ji, Chengyang; Cheng, Genhong; Wu, Aiping

doi:10.1002/jmv.28036

Cited by 127 publications

(162 citation statements)

References 17 publications

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“…Primers and probe sequences used in the MPV_F3L assay showed >99.4% alignment against the genome database, suggesting its suitability for detection of the MPV-2022 outbreak. Primers used in the MPV_G2R assay designed to detect the West African strain showed a 100% match to the database and 95.6% match for the probe thereby validating previous phylogenetic analysis results that the current MPV lineage belongs to the West Africa clade (20).…”

Section: Resultssupporting

confidence: 79%

Wide mismatches in the sequences of primers and probes for Monkeypox virus diagnostic assays

Oghuan

Gitter

et al. 2022

Preprint

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The current monkeypox outbreak as a global health emergency now spreads into more than 90 counties. Rapid and accurate diagnosis of the infections is fundamental for the viral disease containment. Here, we analyzed the primer and probe sequences in the CDC recommended monkeypox virus (MPV) generic real-time PCR assay by aligning against 683 reported MPV genomes worldwide. Sequence mismatches were found in more than 92% of genomes for the MPV generic forward and reverse primers. We also evaluated the specificity of seven other real-time PCR assays for MPV and orthopoxvirus (OPV) detection, and identified two assays (MPV_F3L and OPV_F8L) with the highest matching score (>99.4%) to the global MPV genome database. Genetic variations on the MPV genomes corresponding with the real-time PCR primer and probe regions were further specified and used to indicate the temporal and spatial emergence pattern of monkeypox disease. Our results show that the current MPV real-time generic assay may be unsuitable to accurately detect MPV highlighting the need to develop new detection assays.

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Section: Resultssupporting

confidence: 79%

Wide mismatches in the sequences of primers and probes for Monkeypox virus diagnostic assays

Oghuan

Gitter

et al. 2022

Preprint

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“…The emergence of this outbreak is regarded as a global threat, and the World Health Organization declared a Public Health Emergency of International Concern on 23 July 2022 [ 1 ]. Since the elimination of the smallpox virus in 1980, MPXV has been considered the most severe orthopoxvirus circulating in humans as an incidental host [ 2 ]. As of 27 July 2022, 20,638 cases have been identified in 77 countries worldwide, 71 of which had never reported an MPXV infection before this outbreak [ 3 ].…”

Section: Introductionmentioning

confidence: 99%

“…The MPXV involved in the 2022 outbreak belongs to Clade 3, lineage B.1 [ 20 ]. Although this double-stranded DNA virus shows a low mutation frequency, a comparison with the strains isolated in 2018 has revealed 46 common mutations among the strains involved in the 2022 outbreak [ 2 , 21 ]. An in-depth mutational analysis also suggested a potential MPXV human adaptation during the ongoing microevolution [ 20 ].…”

Section: Introductionmentioning

confidence: 99%

Monkeypox Virus Infections in Southern Italy: Is There a Risk for Community Spread?

Loconsole

Sallustio

Centrone

et al. 2022

IJERPH

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The ongoing outbreak of the Monkeypox virus (MPXV) is characterized by sustained human-to-human transmission, particularly among men who have sex with men (MSM). The aim of the study was to describe the characteristics of the MPXV infection identified in Southern Italy. Clinical samples for each suspected case identified from 1 June to 1 August 2022 were tested for MPXV, and whole-genome sequencing (WGS) was performed on two strains. Ten cases were identified: eight were young adult males, including six MSMs, and two were female. Nine subjects reported recent sexual exposure. One female subject without sexual exposure only reported attendance at a social gathering. Overall, 7 of 10 skin lesion samples had a high viral load of MPXV DNA, and 6/9 whole blood samples and 6/8 nasopharyngeal swab samples also tested positive. The analyzed sequences belonged to Clade 3, lineage B.1, and B.1.5, respectively. Despite this recent multinational outbreak of MPXV cases having revealed a high proportion of cases occurring among MSM, the identification of cases among heterosexual subjects and in a female subject without sexual risk factors should raise awareness among clinicians about the possible spread of MPXV in the general population.

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“…In France, the first draft genome was released on 25/05/2022 in Southwest France (Croville et al, 2022). Phylogenomic studies of MPX viruses involved in this 2022 outbreak indicated that these viruses belong to clade 3 and likely have a single origin (Isidro et al, 2022b;Wang et al, 2022;Jones et al, 2022). They further indicated that these viruses comprise a lineage named B.1 that derives from the A.1 lineage whose members were associated with the large outbreak in 2017-2018 in Nigeria and with MPX virus exportation from Nigeria to the United Kingdom, Israel and Singapore in 2018-2019 (Mauldin et al, 2022;Isidro et al, 2022b).…”

mentioning

confidence: 98%

“…The copyright holder for this preprint this version posted September 26, 2022. ; https://doi.org/10.1101/2022.09.26.509493 doi: bioRxiv preprint experts-give-virus-variants-new-names)) linked to outbreaks in Democratic Republic of Congo, clade 2 (or WHO clade IIa) linked to West Africa, and clade 3 (or WHO clade IIb) that encompasses viruses originating from the 2017-2018 outbreak that began in Nigeria and now those involved in the current 2022 multicountry outbreak (Berthet et al, 2021;Isidro et al, 2022b, Luna et al, 2022Mauldin et al, 2022;Wang et al, 2022). Although human MPX virus infections imported from subSaharan Africa have occurred in non-endemic countries (Mauldin et al, 2022), they only caused sporadic cases or very limited outbreaks until 2022.…”

mentioning

confidence: 99%

Sequencing of Monkeypox virus from infected patients reveals viral genomes with APOBEC3-like editing, gene inactivation, and bacterial agents of skin superinfection

Colson

Penant

Delerce

et al. 2022

Preprint

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An epidemic of Monkeypox virus (MPX virus) infections has arisen in May 2022 in non-endemic countries particularly in Europe among men having sex with men, whose extent is unprecedented. Since May 2022 we implemented MPX virus diagnosis by real-time PCR at university hospitals of Marseille, southern France. Here, we performed DNA metagenomic analyses of clinical samples from MPX virus-infected patients between June and July 2022, using next-generation sequencing with Illumina or Nanopore technologies. Twenty-five samples from 25 patients were studied. This allowed obtaining a MPX virus genome for 18 patients, essentially from genital skin lesions and rectal swabbing. All 18 genomes were classified in the MPX virus B.1 lineage, and we delineated five sublineages (A-E). We detected a high number of mutations (66-73) scattered along the MPX virus genomes relatively to the genome obtained from a human in Nigeria in 2018. Some non-synonymous mutations occurred in genes encoding central proteins, among which transcription factors and core and envelope proteins. They included two mutations that truncate RNA polymerase subunit RPO132 and a phospholipase D-like protein, which suggests gene inactivation. In addition, we identified that a large majority of nucleotide substitutions (94%) in the 18 MPX virus genomes were G>A or C>T, suggesting the action of human APOBEC3 enzymes. Finally, while we did not detect reads matching with main bacterial agents of sexually transmitted infections, >1,000 reads identified Staphylococcus aureus and Streptococcus pyogenes for 7 and 17 samples, respectively. These findings warrant a close genomic monitoring of MPX virus to get a better picture of this virus genetic evolution and mutational patterns, and they point out the common presence in monkeypox lesions of bacterial agents of skin superinfection, which warrants a close clinical monitoring in monkeypox patients.

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Genomic annotation and molecular evolution of monkeypox virus outbreak in 2022

Cited by 127 publications

References 17 publications

Wide mismatches in the sequences of primers and probes for Monkeypox virus diagnostic assays

Wide mismatches in the sequences of primers and probes for Monkeypox virus diagnostic assays

Monkeypox Virus Infections in Southern Italy: Is There a Risk for Community Spread?

Sequencing of Monkeypox virus from infected patients reveals viral genomes with APOBEC3-like editing, gene inactivation, and bacterial agents of skin superinfection

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