Phylogenomic and Structural Analysis of the Monkeypox Virus Shows Evolution towards Increased Stability

Yadav, Priya; Devasurmutt, Yashas; Tatu, Utpal

doi:10.3390/v15010127

Cited by 13 publications

(10 citation statements)

References 34 publications

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“…The dominant clade of circulating MPXV in Ireland was suggested to accumulate mutations at a rate that was at least an order of magnitude higher than previously reported (Babkin et al, 2022), which is in keeping with recent data from a number of other studies (Yadav et al, 2022; Luna et al, 2022). The Bayesian-inferred population model suggested an increase in the effective population size early on in the outbreak that gave origin to many of the different subclades, as a probable consequence of the extensive human-to-human transmission events and adaptation and modification by the human host immune response (Yang et al, 2023).…”

Section: Discussionsupporting

confidence: 88%

Multiple Introductions of Mpox virus to Ireland during the 2022 International Outbreak

Gonzalez,

Carr,

Kelleher

et al. 2023

Preprint

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Background: mpox (formerly Monkeypox) virus (MPXV) was considered a rare zoonotic disease prior to May 2022, when a global epidemic of cases in non-endemic countries led to the declaration of a Public Health Emergency of International Concern. Previously, mpox infection was associated with symptoms similar to smallpox, although substantially less severe, including fever, an extensive characteristic rash and swollen lymph nodes. Aim: Elucidating the origin and molecular characteristics of the virus circulating in the Republic of Ireland in the period between May and November 2022. Methods: Whole-genome sequencing of all MPXV cases (80%; n=178/219) analysed against sequences from public databases (n=2695). Bayesian approaches were used to infer the divergence time between sequences from different subclades and transmission events involving different countries. Results: The circulating virus belonged to the clade IIb B.1 lineage and, notably, the presence of twelve separable and highly-supported subclades consistent with multiple introductions into the country. Such a hypothesis of multiple importation events was supported further by the estimation of the time to the divergence of subclades. Additionally, inferred MPXV transmissions involving different countries and continents were indicative of an extended international spread. The analysis of the mutations in the Irish sequences revealed 93% of the mutations were from cytosine to thymine (or from guanine to adenine), leading to a high number of non-synonymous mutations across the subclades. Conclusion: In the context of extremely high national sequencing coverage, we provide new insights into the international origin and transmission dynamics supporting multiple introductions into the Republic of Ireland.

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Section: Discussionsupporting

confidence: 88%

Multiple Introductions of Mpox virus to Ireland during the 2022 International Outbreak

Gonzalez,

Carr,

Kelleher

et al. 2023

Preprint

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“…Reference of Protein names and functions. [25][26][27][28] Our analysis revealed A26L/A30L membrane-associated protein in the A.2.1 study sequences exhibits the highest number of deletions, indicating a high degree of variation. This protein family facilitates virion entry through endocytic vesicles and aids in cell attachment by binding to laminins.…”

Section: Discussionmentioning

confidence: 69%

“…Furthermore, we identified two novel nonsynonymous substitutions, V98I in OPG046 and P600S in OPG109, within genes involved in transcription. 25 These substitutions or deletions add to the genetic diversity observed in the study sequence and warrant further investigation to ascertain their functional significance.…”

Section: Discussionmentioning

confidence: 98%

Genomic characterization of the first mpox and varicella‐zoster co‐infection in Pakistan (2023) through next‐generation sequencing

Umair,

Jamal,

Haider

et al. 2023

Journal of Medical Virology

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The global mpox outbreak spanning 2022–2023 has affected numerous countries worldwide. In this study, we present the first report on the detection, whole‐genome sequence, and coinfection of the mpox virus and varicella zoster virus (VZV) from Pakistan. During April–May 2023, samples from 20 suspected cases of mpox were tested at the National Institutes of Health, Islamabad among which 4 tested positive. All four cases had a travel history of Saudi Arabia. All the suspected samples were processed by using a Zymo research kit for DNA extraction, followed by qRT‐PCR amplification by using a DaAn Gene detection kit for the mpox virus. Further, two of the positive samples with a low Ct value (<20) were subjected to whole‐genome sequencing using a metagenomic approach on the iSeq (Illumina) platform. The sequencing results revealed Clade IIb and genotype A.2.1 of MPXV, which clustered with viruses from Slovenia and the UK in July and June 2022, respectively. Our analysis identified two novel nonsynonymous substitutions in mpox virus, namely V98I in OPG046 and P600S in OPG109. Furthermore, we successfully retrieved the complete genome of VZV from the same sample, belonging to Clade 5. This study represents the first positive case of MPXV in Pakistan and the coinfection of mpox and VZV by using a metagenome approach providing insights into their complete genomes. Our results highlight the importance of surveillance at the point of entries, strengthening lab capacities including next‐generation sequencing, and using differential diagnosis for timely and accurate detection of mpox cases.

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“…Also, they used timeseries models to predict the cases which was incremental till august 2022. So far, one mutation analysis has been found for monkeypox which worked with GenBank dataset and figured out the 2022 substitution mutation rate as 38.63 worldwide [ 32 ]. Though we have observed a significant number of studies in this field, the amount of work to analyze the monkeypox data compared with COVID-19 is pretty low.…”

Section: Literature Reviewmentioning

confidence: 99%

Monkeypox genome mutation analysis using a timeseries model based on long short-term memory

Pathan,

Uddin,

Paul

et al. 2023

PLoS ONE

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Monkeypox is a double-stranded DNA virus with an envelope and is a member of the Poxviridae family’s Orthopoxvirus genus. This virus can transmit from human to human through direct contact with respiratory secretions, infected animals and humans, or contaminated objects and causing mutations in the human body. In May 2022, several monkeypox affected cases were found in many countries. Because of its transmitting characteristics, on July 23, 2022, a nationwide public health emergency was proclaimed by WHO due to the monkeypox virus. This study analyzed the gene mutation rate that is collected from the most recent NCBI monkeypox dataset. The collected data is prepared to independently identify the nucleotide and codon mutation. Additionally, depending on the size and availability of the gene dataset, the computed mutation rate is split into three categories: Canada, Germany, and the rest of the world. In this study, the genome mutation rate of the monkeypox virus is predicted using a deep learning-based Long Short-Term Memory (LSTM) model and compared with Gated Recurrent Unit (GRU) model. The LSTM model shows “Root Mean Square Error” (RMSE) values of 0.09 and 0.08 for testing and training, respectively. Using this time series analysis method, the prospective mutation rate of the 50th patient has been predicted. Note that this is a new report on the monkeypox gene mutation. It is found that the nucleotide mutation rates are decreasing, and the balance between bi-directional rates are maintained.

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Phylogenomic and Structural Analysis of the Monkeypox Virus Shows Evolution towards Increased Stability

Cited by 13 publications

References 34 publications

Multiple Introductions of Mpox virus to Ireland during the 2022 International Outbreak

Multiple Introductions of Mpox virus to Ireland during the 2022 International Outbreak

Genomic characterization of the first mpox and varicella‐zoster co‐infection in Pakistan (2023) through next‐generation sequencing

Monkeypox genome mutation analysis using a timeseries model based on long short-term memory

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