4.7 Article

Insights into the Evolution and Host Adaptation of the Monkeypox Virus from a Codon Usage Perspective: Focus on the Ongoing 2022 Outbreak

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Real-world effectiveness of a single dose of mpox vaccine in males

Yael Wolff Sagy et al.

Summary: The effectiveness of one subcutaneous dose of MVA-BN vaccine in preventing mpox virus infection was estimated to be 86% in a cohort study of vaccine-eligible males in Israel. The study provides evidence supporting the use of MVA-BN vaccine to control the outbreak of mpox virus. This observational study evaluated the real-world effectiveness of a single dose of MVA-BN vaccine in a high-risk cohort and found that vaccination was associated with a significantly lower risk of MPXV infection.

NATURE MEDICINE (2023)

Article Microbiology

A comprehensive analysis of Usutu virus (USUV) genomes revealed lineage-specific codon usage patterns and host adaptations

Jianglin Zhou et al.

Summary: This study investigated the evolution and codon usage patterns of the Usutu virus (USUV). They found that USUV is influenced by various factors in its codon usage, including natural selection, mutation pressure, and dinucleotide abundance. The study also observed a complex interaction of codon usage between USUV and its host, suggesting a potential risk of cross-species transmission and subsequent outbreaks. Therefore, further epidemiologic surveys, diversity monitoring, and pathogenetic research are warranted.

FRONTIERS IN MICROBIOLOGY (2023)

Article Virology

Genomic annotation and molecular evolution of monkeypox virus outbreak in 2022

Lulan Wang et al.

Summary: Monkeypox virus (MPXV) has been circulating in West and Central Africa. Recent outbreaks in nonendemic countries were analyzed, revealing that the MPXV-2022 strains belong to the same lineage as the 2018 strain with several new mutations. Some specific proteins were found to be more prone to mutation in the MPXV genome. This study provides insights into the ongoing MPXV outbreak and identifies novel mutations for further research.

JOURNAL OF MEDICAL VIROLOGY (2023)

Article Biology

Multi-valent mRNA vaccines against monkeypox enveloped or mature viron surface antigens demonstrate robust immune response and neutralizing activity

Niubing Zhang et al.

Summary: Monkeypox has been declared a global health emergency with 86,000 confirmed cases and 111 deaths reported across 110 countries as of March 2023. A study developed multi-valent mRNA vaccines against monkeypox virus and examined their efficacy and mechanism of action. The mRNA vaccines elicited a dynamic immune response and strong IgG response, with the combination of EV and MV antigens providing the strongest protection against VACV. The findings provide insight into the protective mechanism of multi-valent mRNA vaccines and lay the foundation for further development of effective vaccines against monkeypox virus outbreak.

SCIENCE CHINA-LIFE SCIENCES (2023)

Review Infectious Diseases

Human monkeypox infection threat: A comprehensive overview

Yue Kang et al.

Summary: This review provides fundamental knowledge for the prevention and control of future monkeypox outbreaks, including diagnosis, treatment, and prevention measures.

PLOS NEGLECTED TROPICAL DISEASES (2023)

Article Immunology

Rational development of multicomponent mRNA vaccine candidates against mpox

Rong-Rong Zhang et al.

Summary: The re-emerging mpox virus has become a public health emergency of international concern and developing a safe and effective mRNA vaccine against it is a top priority. Using a lipid nanoparticle-encapsulated mRNA vaccine platform, a panel of multicomponent MPXV vaccine candidates were constructed and prepared, which elicited strong immune responses in mice. Particularly, the penta- and tetra-component vaccine candidates showed superior capability of inducing neutralizing antibodies and protecting mice from VACV challenge. This study provides critical insights for understanding the protection mechanism of MPXV infection and supports further clinical development of these multicomponent mRNA vaccine candidates.

EMERGING MICROBES & INFECTIONS (2023)

Article Infectious Diseases

Monkeypox (mpox) virus: Classification, origin, transmission, genome organization, antiviral drugs, and molecular diagnosis

Aysel Karagoz et al.

Journal of Infection and Public Health (2023)

Article Biochemistry & Molecular Biology

Monkeypox virus quadrivalent mRNA vaccine induces immune response and protects against vaccinia virus

Ye Sang et al.

Summary: Monkeypox has been declared a public health emergency by the World Health Organization. Two mRNA vaccines, mRNA-A-LNP and mRNA-B-LNP, based on specific proteins of the monkeypox virus, have been developed and shown to induce immune responses in mice, including specific antibodies and cellular immunity. These vaccines also provide protection against vaccinia virus challenge in mice and have the potential to be used against other orthopoxviruses.

SIGNAL TRANSDUCTION AND TARGETED THERAPY (2023)

Article Immunology

Exportation of Monkeypox Virus From the African Continent

Matthew R. Mauldin et al.

Summary: There is no direct linkage between the individuals who exported the monkeypox cases from Nigeria, but there is limited genetic variation among the viruses, suggesting a possible common source or independent infections within a small geographic area.

JOURNAL OF INFECTIOUS DISEASES (2022)

Article Tropical Medicine

The changing epidemiology of human monkeypox—A potential threat? A systematic review

Eveline M. Bunge et al.

PLoS Neglected Tropical Diseases (2022)

Article Infectious Diseases

Community transmission of monkeypox in the United Kingdom, April to May 2022

Roberto Vivancos et al.

Summary: Between 7 and 25 May, 86 cases of monkeypox have been confirmed in the UK, with only one case known to have traveled to a monkeypox virus endemic country. The majority of the cases were males, among which 66 reported being gay, bisexual, or men who have sex with men. This is the first sustained human-to-human transmission of monkeypox in the UK, occurring through close contacts, including sexual networks. Ongoing efforts are being made to improve case identification and prevent further transmission.

EUROSURVEILLANCE (2022)

Article Microbiology

Genomic Sequencing and Analysis of a Novel Human Cowpox Virus With Mosaic Sequences From North America and Old World Orthopoxvirus

Diana Diaz-Canova et al.

Summary: In this study, the complete genome sequence of an atypical cowpox virus (CPXV-No-H2) isolated from a human in Norway was determined. The virus showed a mosaic genome with genes most similar to other orthopoxviruses and multiple potential recombination events were identified. Phylogenetic analysis revealed that CPXV-No-H2 formed a distinct clade with German CPXV isolates and clustered closely with the ECTV-OPXV Abatino clade.

FRONTIERS IN MICROBIOLOGY (2022)

Article Microbiology

Evolution of monkeypox virus from 2017 to 2022: In the light of point mutations

Perumal Arumugam Desingu et al.

Summary: According to the available sequence data, monkeypox virus exhibits point mutations in multiple proteins, which contribute to the potential for a multi-country outbreak. The analysis also reveals codon usage bias and a favorable trend for human adaptation in the mutated genes. Furthermore, selection pressure plays a significant role in the evolution of these mutated genes.

FRONTIERS IN MICROBIOLOGY (2022)

Letter Medicine, General & Internal

Evidence of human-to- dog transmission of monkeypox virus

Sophie Seang et al.

LANCET (2022)

Article Biochemistry & Molecular Biology

Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus

Joana Isidro et al.

Summary: In this study, shotgun metagenomics were used to rapidly reconstruct and characterize the genome sequences of the largest monkeypox virus outbreak in non-endemic countries so far. The findings indicate that the outbreak most likely has a single origin and that the virus belongs to clade 3. Furthermore, the study suggests the involvement of host APOBEC3 in viral evolution and reveals signs of ongoing microevolution in the virus.

NATURE MEDICINE (2022)

Article Medicine, General & Internal

Monkeypox Virus Infection in Humans across 16 Countries - April-June 2022

John P. Thornhill et al.

Summary: This report describes 528 cases of monkeypox in 16 countries. Common clinical findings include rash, mucosal lesions, fever, lethargy, and lymphadenopathy. Few patients required hospitalization.

NEW ENGLAND JOURNAL OF MEDICINE (2022)

Letter Surgery

Monkeypox outbreak: New zoonotic alert after the COVID-19 pandemic

Amit Sharma et al.

INTERNATIONAL JOURNAL OF SURGERY (2022)

Article Public, Environmental & Occupational Health

Monkeypox Outbreak — Nine States, May 2022

Faisal S. Minhaj et al.

MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT (2022)

Article Multidisciplinary Sciences

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

Crystal M. Gigante et al.

Summary: Monkeypox, a viral zoonotic disease endemic in Central and West Africa, has recently been reported in non-endemic countries. A study found two lineages of monkeypox virus (MPXV) in US cases, with one being the major variant of the 2022 outbreak and the other being a minor variant. Analysis suggests that APOBEC3 gene activity may be a dominant driver of MPXV evolution in the current outbreak.

SCIENCE (2022)

Article Public, Environmental & Occupational Health

Phylogenomic analysis of the monkeypox virus (MPXV) 2022 outbreak: Emergence of a novel viral lineage?

Nicolas Luna et al.

Summary: Since May 13, 2022, there has been an increasing number of suspected and confirmed cases of monkeypox reported in non-endemic regions worldwide. Analysis of the virus genomes revealed three distinct clades, including a newly emerging clade from the 2022 outbreak. The surge in cases and widespread geographical spread suggest multiple factors driving the current outbreak dynamics.

TRAVEL MEDICINE AND INFECTIOUS DISEASE (2022)

Article Biochemical Research Methods

Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2

Yashpal Singh Malik et al.

Summary: The interaction between the SARS-CoV-2 spike glycoprotein and the ACE2 cell receptor is crucial for virus attachment to human cells, and certain mutations in the S-protein can strengthen binding affinity to ACE2. Recombination events in SARS-CoV-2 strains are frequent, suggesting a common origin with predecessors and genetic exchange between potential reservoirs and human hosts. Comprehensive analysis of codon bias in SARS-CoV-2 indicates adaptation in other animal hosts and potential use in experimental animal models for drug and vaccine development research.

BRIEFINGS IN BIOINFORMATICS (2021)

Review Virology

Here, There, and Everywhere: The Wide Host Range and Geographic Distribution of Zoonotic Orthopoxviruses

Natalia Ingrid Oliveira Silva et al.

Summary: The global spread of zoonotic poxviruses poses a significant threat to human and animal health, with potential outbreaks and viral dissemination to new regions. Current epidemiological understanding of the geographical distribution and host ranges of poxviruses, particularly orthopoxviruses with epidemic potential, highlights the need for enhanced monitoring and preventive measures to curb further spread of these viruses.

VIRUSES-BASEL (2021)

Article Virology

RDP5: a computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets

Darren P. Martin et al.

Summary: The RDP project has developed an automated recombination analysis tool, RDP5, which is faster and more efficient than its predecessor, RDP4. Users can now analyze larger and more complex datasets with minimal manual intervention, allowing for greater flexibility and output options.

VIRUS EVOLUTION (2021)

Article Microbiology

Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype

Fusheng Si et al.

Summary: The study revealed a low codon usage bias in the PEDV genome, with natural selection being the dominant factor influencing codon usage bias. Genotype II PEDV strains showed the highest level of adaptation to Sus scrofa compared to other divergent clades. This comprehensive report provides insights into PEDV evolution, adaptation, and fitness towards their hosts.

FRONTIERS IN MICROBIOLOGY (2021)

Article Genetics & Heredity

Use ggbreak to Effectively Utilize Plotting Space to Deal With Large Datasets and Outliers

Shuangbin Xu et al.

Summary: ggbreak is an R package based on ggplot2 that helps users effectively tackle data visualization issues with large datasets, enhancing the interpretative capability of the data.

FRONTIERS IN GENETICS (2021)

Article Microbiology

Base Composition and Host Adaptation of the SARS-CoV-2: Insight From the Codon Usage Perspective

Ayan Roy et al.

Summary: The study found that SARS-CoV-2 exhibits complex compositional features, including avoidance of certain codon pairs and strict avoidance of CpG dinucleotides, possibly to evade human immune responses.

FRONTIERS IN MICROBIOLOGY (2021)

Article Virology

Evolutionary Signatures Governing the Codon Usage Bias in Coronaviruses and Their Implications for Viruses Infecting Various Bat Species

Naveen Kumar et al.

Summary: This study investigates the codon usage trends in bat-hosted coronaviruses, revealing the potential ancestors of SARS-CoV-2 and uncovering specific characteristics of the virus. Furthermore, it dissects the evolution and specificity of various CoVs in hosts, shedding light on the latent diversity of coronaviruses in mammals that has yet to be fully explored.

VIRUSES-BASEL (2021)

Article Microbiology

Edging on Mutational Bias, Induced Natural Selection From Host and Natural Reservoirs Predominates Codon Usage Evolution in Hantaan Virus

Galal Ata et al.

Summary: The study revealed that natural selection is the primary determinant of biased codon choices in Hantaan virus (HTNV), exceeding the mutational bias effect. Phylogenetic analysis of HTNV strains identified three distinct clades: South Korean, Russian, and Chinese.

FRONTIERS IN MICROBIOLOGY (2021)

Article Biochemistry & Molecular Biology

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Bui Quang Minh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Biochemistry & Molecular Biology

Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design

Aikaterini Alexaki et al.

JOURNAL OF MOLECULAR BIOLOGY (2019)

Editorial Material Infectious Diseases

Monkeypox - Enhancing public health preparedness for an emerging lethal human zoonotic epidemic threat in the wake of the smallpox post- eradication era

Eskild Petersen et al.

INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES (2019)

Article Biochemistry & Molecular Biology

UFBoot2: Improving the Ultrafast Bootstrap Approximation

Diep Thi Hoang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Evolutionary Biology

Evolution of Synonymous Codon Usage Bias in West African and Central African Strains of Monkeypox Virus

Sudeesh Karumathil et al.

EVOLUTIONARY BIOINFORMATICS (2018)

Article Biochemical Research Methods

ModelFinder: fast model selection for accurate phylogenetic estimates

Subha Kalyaanamoorthy et al.

NATURE METHODS (2017)

Article Immunology

Evolution of codon usage in Zika virus genomes is host and vector specific

Azeem Mehmood Butt et al.

EMERGING MICROBES & INFECTIONS (2016)

Article Public, Environmental & Occupational Health

Introduction of Monkeypox into a Community and Household: Risk Factors and Zoonotic Reservoirs in the Democratic Republic of the Congo

Leisha Diane Nolen et al.

AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE (2015)

Article Multidisciplinary Sciences

Genome-Wide Analysis of Codon Usage and Influencing Factors in Chikungunya Viruses

Azeem Mehmood Butt et al.

PLOS ONE (2014)

Article Immunology

Genomic Variability of Monkeypox Virus among Humans, Democratic Republic of the Congo

Jeffrey R. Kugelman et al.

EMERGING INFECTIOUS DISEASES (2014)

Article Biochemistry & Molecular Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)