Molecular Mechanisms of Poxvirus Evolution

Brennan, Greg; Stoian, Ana M. M.; Yu, Huibin; Rahman, M. Julhasur; Banerjee, Shefali; Stroup, Jeannine N.; Park, Chorong; Tazi, Loubna; Rothenburg, Stefan

doi:10.1128/mbio.01526-22

Cited by 39 publications

(32 citation statements)

References 119 publications

(165 reference statements)

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“…It is worthy to note that virus attenuation was previously observed with the Myxoma virus in rabbits. 58,65 Another interesting observation in the present study is the high number of mutations (between 64 and 73) in MPXV genomes obtained here compared to the NC_063383.1 genome obtained from a human specimen collected in Nigeria in August 2018, which is in the same range than recently reported. 5,7,13,42 This corresponds to a greater mutation rate than that expected based on previous assessment for orthopoxviruses that was estimated to be 1−2 nucleotide substitutions per genome per year (i.e., approximately 10 −5 substitutions per site per year), 15,66 and might represent accelerated evolution.…”

Section: Metagenomic Analysis Of Ngs Runssupporting

confidence: 77%

“…Anyway, gene loss is a known trait of poxvirus evolution, and it was notably suspected to be associated with a restricted host range but also with an efficient human‐to‐human spread in orthopoxviruses 1,33,57–59 . For instance, it was observed in MPXV genomes recovered from 10 of 60 specimens collected from humans between 2005 and 2007 in the Democratic Republic of the Congo 60 .…”

Section: Discussionmentioning

confidence: 99%

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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. 2023

Journal of Medical Virology

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A large outbreak of Monkeypox virus (MPXV) infections has arisen in May 2022 in nonendemic countries. Here, we performed DNA metagenomics using next‐generation sequencing with Illumina or Nanopore technologies for clinical samples from MPXV‐infected patients diagnosed between June and July 2022. Classification of the MPXV genomes and determination of their mutational patterns were performed using Nextclade. Twenty‐five samples from 25 patients were studied. A MPXV genome was obtained for 18 patients, essentially from skin lesions and rectal swabbing. All 18 genomes were classified in clade IIb, lineage B.1, and we identified four B.1 sublineages (B.1.1, B.1.10, B.1.12, B.1.14). We detected a high number of mutations (range, 64−73) relatively to a 2018 Nigerian genome (genome GenBank Accession no. NC_063383.1), which were harbored by a large part of a set of 3184 MPXV genomes of lineage B.1 recovered from GenBank and Nextstrain; and we detected 35 mutations relatively to genome ON563414.3 (a B.1 lineage reference genome). Nonsynonymous mutations occurred in genes encoding central proteins, among which transcription factors and core and envelope proteins, and included two mutations that would truncate a RNA polymerase subunit and a phospholipase d‐like protein, suggesting an alternative start codon and gene inactivation, respectively. A large majority (94%) of nucleotide substitutions were G > A or C > U, suggesting the action of human APOBEC3 enzymes. Finally, >1000 reads were identified as from Staphylococcus aureus and Streptococcus pyogenes for 3 and 6 samples, respectively. These findings warrant a close genomic monitoring of MPXV to get a better picture of the genetic micro‐evolution and mutational patterns of this virus, and a close clinical monitoring of skin bacterial superinfection in monkeypox patients.

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Section: Metagenomic Analysis Of Ngs Runssupporting

confidence: 77%

Section: Discussionmentioning

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. 2023

Journal of Medical Virology

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“…However, it is also well accepted that poxviruses can recombine under specific conditions to give chimeric viruses. The mechanisms include recombination, and horizontal gene transfer to acquire new genes [ 69 ]. The first experiments to show recombination between different orthopoxviruses were conducted in the 1960s [ 70 , 71 , 72 ].…”

Section: Introductionmentioning

confidence: 99%

“…Marker rescue studies were carried out to demonstrate how homologous recombination could be used to generate recombinant poxviruses with novel inserts [ 73 ] and this subsequently evolved into making recombinant poxvirus-based vaccines [ 74 ]. Poxviruses under specific stresses can duplicate genes to adapt to new conditions [ 69 , 75 , 76 ]. However, there was minimal evidence that Capripoxviruses would recombine in the field [ 77 ].…”

Section: Introductionmentioning

confidence: 99%

Lumpy Skin Disease—An Emerging Cattle Disease in Europe and Asia

2023

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Lumpy skin disease virus (LSDV) is a member of the Capripoxvirus genus, mainly infecting cattle and buffalo, which until relatively recently was only endemic in parts of Africa and then spread to the Middle East and lately Europe and Asia. Lumpy skin disease (LSD) is a notifiable disease with a serious impact on the beef industry as it causes mortality of up to 10% and has impacts on milk and meat production, as well as fertility. The close serological relationship between LSDV, goat poxvirus (GTPV) and sheep poxvirus (SPPV) has led to live attenuated GTPV and SPPV vaccines being used to protect against LSD in some countries. There is evidence that the SPPV vaccine does not protect from LSD as well as the GTPV and LSDV vaccines. One of the LSD vaccines used in Eastern Europe was found to be a combination of different Capripoxviruses, and a series of recombination events in the manufacturing process resulted in cattle being vaccinated with a range of recombinant LSDVs resulting in virulent LSDV which spread throughout Asia. It is likely that LSD will become endemic throughout Asia as it will be very challenging to control the spread of the virus without widespread vaccination.

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“…The origin and evolution of poxviruses remain obscure, despite evidence that poxviruses emerged thousands of years ago. Poxvirus genomes evolved through the acquisition and loss of genes, especially gene replication and horizontal gene transfer, to adapt to and combat the host’s antiviral immune defenses to establish successful infection [ 3 ]. Parapoxvirus belongs to Chordopoxvirinae, a vertebrate Poxviridae, and is one of the most commonly studied genera of poxvirus.…”

Section: Introductionmentioning

confidence: 99%

Rapid Onsite Visual Detection of Orf Virus Using a Recombinase-Aided Amplification Assay

Guan

Li³

et al. 2023

Life

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Orf is an important zoonotic disease caused by the Orf virus (ORFV) which can cause contagious pustular dermatitis in goats and sheep. Orf is widespread in most sheep-raising countries in the world, causing huge economic losses. Although diagnostic methods for ORFV infection already exist, it is still necessary to develop a time-saving, labor-saving, specific, low-cost and visual diagnostic method for rapid detection of ORFV in the field and application in grassroots laboratories. This study establishes a DNA extraction–free, real-time, visual recombinase–aided amplification (RAA) method for the rapid detection of ORFV. This method is specific to ORFV and does not cross-react with other common DNA viruses. The detection limits of the real-time RAA and visual judgment of the RAA assay at 95% probability were 13 and 21 copies per reaction for ORFV, respectively. Compared with qPCR, the sensitivity and specificity of the real-time RAA assay were 100%, and those of the visual RAA assay were 92.31% and 100.0%, respectively. The DNA extraction–free visual detection method of RAA established in this study can meet the needs of rapid onsite detection and grassroots laboratories and has important reference value and significance for the early diagnosis of diseased animals.

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Molecular Mechanisms of Poxvirus Evolution

Cited by 39 publications

References 119 publications

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

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

Lumpy Skin Disease—An Emerging Cattle Disease in Europe and Asia

Rapid Onsite Visual Detection of Orf Virus Using a Recombinase-Aided Amplification Assay

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