Phylogenetic analysis of all available monkeypox virus strains shows the close relatedness of contemporary ones

Benkő, Mária; Harrach, Balázs; Kaján, Gyözö L.

doi:10.1016/j.heliyon.2023.e12895

Cited by 5 publications

(4 citation statements)

References 13 publications

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“…Poxviruses are usually known to have low genomic variability, in contrast to RNA viruses such as SARS‐CoV‐2 which tend to mutate constantly and spread more quickly 34,35 . However, the dispersion of hMPVX during the 2022 outbreak in more than 110 countries and the possible emergence of a new sub‐lineage with higher infectious capacity caused concern around the world.…”

Section: Discussionmentioning

confidence: 99%

“…Poxviruses are usually known to have low genomic variability, in contrast to RNA viruses such as SARS-CoV-2 which tend to mutate constantly and spread more quickly. 34,35 However, the dispersion of which the substitution rate is estimated for each sub-lineage and not by clade or lineage, as has been described on several occasions. [36][37][38][39][40] Interestingly who detected a rate 350 times higher between epidemic/endemic lineages in Amerindian tribes.…”

Section: Hmpxv Substitution Rates and Dispersionmentioning

confidence: 99%

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Sub‐lineage B.1.6 of hMPXV in a global context: Phylogeny and epidemiology

Molina,

Jimenez‐Vasquez,

Lizarraga

et al. 2023

Journal of Medical Virology

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During the 2022 COVID‐19 pandemic, monkeypox emerged as a significant threat to global health. The virus responsible for the disease, the human monkeypox virus (hMPXV), underwent various genetic changes, resulting in the emergence of over a dozen distinct lineages, which could be identified by only a small number of unique mutations. As of January 25, 2023, genomic information of hMPXV generated had reached 4632 accessions in the GISAID database. In this study, we aimed to investigate the epidemiological and phylogenetic characteristics of the B.1.6 sub‐lineage of hMPXV in Peru, compared with other circulating sub‐lineages during the global outbreak. The B.1.6 sub‐lineage, characterized by the 111029G>A mutation, was estimated to have emerged in June 2022 and was found mainly in Peru. Most cases (95.8%) were men with an average age of 33 years, and nearly half of the patients had HIV, of whom only 77.35% received antiretroviral therapy. Our findings revealed that the B.1.6, B.1.4, and B.1.2 sub‐lineages were well represented and had a higher number of mutations despite having the lowest media substitution rates per site per year. Moreover, it was estimated that B.1.2 and B.1.4 appeared in February 2022 and were the first two sub‐lineages to emerge. A mutation profile was also obtained for each sub‐lineage, reflecting that several mutations had a pattern similar to the characteristic mutation. This study provides the first estimation of the substitution rate and ancestry of each monkeypox sub‐lineage belonging to the 2022 outbreak. Based on our findings, continued genomic surveillance of monkeypox is necessary to understand better and track the evolution of the virus.

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Section: Discussionmentioning

confidence: 99%

Section: Hmpxv Substitution Rates and Dispersionmentioning

confidence: 99%

Sub‐lineage B.1.6 of hMPXV in a global context: Phylogeny and epidemiology

Molina,

Jimenez‐Vasquez,

Lizarraga

et al. 2023

Journal of Medical Virology

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“…Several genomic studies have been published on the 2022 outbreak in different countries around the world to understand the transmission and the evolution of the virus; however, most of these studies were limited by the number of genomes analyzed (n < 402) [4,[10][11][12][13][14][15][16][17][18][19][20][21][22][23]. Studying the intra-host genomic diversity of MPXV can provide additional resolution [4,15] to study virus transmission networks.…”

Section: Introductionmentioning

confidence: 99%

Genomic Epidemiology of Monkeypox Virus During the 2022 Outbreak in New York City

Akther,

Su,

Wang

et al. 2024

Preprint

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New York City (NYC) was one of the hotspots of monkeypox virus (MPXV) infections in the United States during the multi-country mpox outbreak in 2022. This study used the most comprehensive dataset to date to investigate the genomic characteristics of MPXV in NYC. We performed Nextclade lineage assignment, phylogenetic and mutational analyses on 1,138 specimens from 748 individuals at the NYC Public Health Lab in the context of 2,968 MPXV sequences sampled globally. Nextclade lineage assignment showed B.1.12 as a NYC specific lineage and phylogenetic analysis showed NYC and North America specific clades. The majority of mutations showed signatures of APOBEC3 activity. When looking at the intra-host genomic diversity for MPXV, distinct MPXV genomic profiles were observed in 6.4% of individuals with multiple sampled specimens, with at least 4.2% of NYC cases due to multiple MPXV infections from distinct viral strains. Further, 13% of the sequences in infected patients had a lack of concordance between epidemiologic and genetic linkages. This study identified NYC-specific MPXV genomic profiles and provided a conservative estimate of simultaneous infections with multiple MPXV variants, likely due to behavioral risk factors during the peak of the outbreak in July 2022. Improving concordance between genomic and epidemiological clusters for mpox investigations may require expanding partnerships with testing labs, clinics, and community groups to enhance the representativeness of MPXV samples that are available for sequencing.

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“…Viruses from Clade I (former Congo Basin clade) cause more clinically severe disease in humans, with higher mortality rates and transmissibility, while those from Clade IIa (former West African clade) have a milder clinical presentation with lower mortality rates and transmissibility. The isolates from the most recent 2022 outbreak are placed in Clade IIb and closely related to the virus responsible for the 2017-2019 outbreaks in the same clade [8][9][10].…”

Section: Introductionmentioning

confidence: 99%

Development of an extraction-free LAMP method for the generic detection of Orthopoxvirus and for the specific detection of Mpox virus

Sinha

Zhang

et al. 2023

Preprint

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Mpox is a neglected zoonotic disease endemic in West and Central Africa. The 2022 Mpox outbreak with more than 18,000 cases worldwide generated great concern about future outbreaks and highlighted the need for a simple and rapid diagnostic test. The Mpox virus, MPXV, is a member of the Orthopoxvirus genus that also contains other pathogenic viruses including variola virus, vaccinia virus, camelpox virus, and cowpox virus. Phylogenomic analysis of all available Orthopoxvirus genomes identified 10 distinct phylogroups, with isolates from infected humans distributed across various phylogroups interspersed with isolates from animal sources, indicating the zoonotic potential of these viruses. In this study, we developed a simple and sensitive colorimetric pan-Orthopoxvirus LAMP assay for broader Orthopoxvirus detection. We also developed an MPXV-specific probe that differentiates MPXV from other Orthopoxviruses on the N1R gene which differs by only a few nucleotides. In addition, we described an extraction-free protocol for use directly with swab eluates in LAMP assays, thereby eliminating the time and resources needed to extract DNA from the sample. Our direct LAMP assays are well-suited for low-resource settings and provide a valuable tool for rapid and scalable diagnosis and surveillance of Orthopoxviruses and MPXV.

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Phylogenetic analysis of all available monkeypox virus strains shows the close relatedness of contemporary ones

Cited by 5 publications

References 13 publications

Sub‐lineage B.1.6 of hMPXV in a global context: Phylogeny and epidemiology

Sub‐lineage B.1.6 of hMPXV in a global context: Phylogeny and epidemiology

Genomic Epidemiology of Monkeypox Virus During the 2022 Outbreak in New York City

Development of an extraction-free LAMP method for the generic detection of Orthopoxvirus and for the specific detection of Mpox virus

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