☆ 4.5 Article

Exploring the Natural Origins of SARS-CoV-2 in the Light of Recombination

GENOME BIOLOGY AND EVOLUTION (2022)

相关参考文献

注意：仅列出部分参考文献，下载原文获取全部文献信息。

Article Biochemistry & Molecular Biology

The Neighborhood of the Spike Gene Is a Hotspot for Modular Intertypic Homologous and Nonhomologous Recombination in Coronavirus Genomes

Marios Nikolaidis et al.

Summary: Research has shown that coronaviruses have a strong ability for intergenomic recombination, where they can exchange genetic material not only within the same subgenus but also across different CoV genera, other viruses, and even hosts. These events often occur at double crossovers surrounding the Spike ORF, indicating the instability and mobility of this genomic region.

MOLECULAR BIOLOGY AND EVOLUTION (2022)

添加到收藏夹

Article Multidisciplinary Sciences

Bat coronaviruses related to SARS-CoV-2 and infectious for human cells

Sarah Temmam et al.

Summary: SARS-CoV-2-like bat viruses that are potentially infectious for humans circulate in Rhinolophus spp. in the Indochinese peninsula, and they can enter human cells through the hACE2 pathway, indicating the need for further understanding of the origin of the epidemic.

NATURE (2022)

添加到收藏夹

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)

添加到收藏夹

Article Virology

Synonymous mutations and the molecular evolution of SARS-CoV-2 origins

Hongru Wang et al.

Summary: This study analyzed the synonymous divergence between SARS-CoV-2 and related strains, finding that the divergence between bat-derived viruses and SARS-CoV-2 is larger in the RBD compared to GD410721. This supports the hypothesis of recombination between the strains.

VIRUS EVOLUTION (2021)

添加到收藏夹

Editorial Material Multidisciplinary Sciences

Dissecting the early COVID-19 cases in Wuhan

Michael Worobey

SCIENCE (2021)

添加到收藏夹

Article Multidisciplinary Sciences

Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins in Southeast Asia

Supaporn Wacharapluesadee et al.

Summary: A study identified a SARS-CoV-2-related coronavirus (SC2r-CoV), RacCS203, in Rhinolophus acuminatus bats from Thailand, with 91.5% genome similarity to SARS-CoV-2, and demonstrated that sera obtained from bats and Malayan pangolin can neutralize SARS-CoV-2.

NATURE COMMUNICATIONS (2021)

添加到收藏夹

Article Biochemistry & Molecular Biology

Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen

Oscar A. MacLean et al.

Summary: The study suggests that SARS-CoV-2 has undergone limited significant adaptation to humans, with evidence of moderate positive selection concentrated in the early phases of the pandemic. In contrast, bat Sarbecoviruses show evidence of significant positive selection and an adaptive depletion in CpG composition. This indicates that the progenitor of SARS-CoV-2 likely acquired efficient human-human transmission capabilities through evolutionary history in bats, leading to the emergence of a relatively generalist virus.

PLOS BIOLOGY (2021)

添加到收藏夹

Article Multidisciplinary Sciences

A novel SARS-CoV-2 related coronavirus in bats from Cambodia

Deborah Delaune et al.

Summary: The study identified SARS-CoV-2 related coronaviruses in bats sampled in Cambodia, indicating a wider geographic distribution than previously reported. The findings suggest that Southeast Asia may be a key area to consider for future coronavirus surveillance.

NATURE COMMUNICATIONS (2021)

添加到收藏夹

Article Virology

The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus

H. L. Wells et al.

Summary: A study identified three novel sarbecovirus sequences from Rwanda and Uganda that are phylogenetically intermediate to SARS-CoV-1 and SARS-CoV-2 and unable to utilize human ACE2. The study proposed a recombination scenario to explain the observed ACE2 usage pattern among sarbecoviruses, pointing out the need for increased surveillance for sarbecoviruses in regions like southwestern China and Africa.

VIRUS EVOLUTION (2021)

添加到收藏夹

Article Biochemistry & Molecular Biology

Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses

Hong Zhou et al.

Summary: A study in Yunnan province, China, found the existence of bat coronaviruses related to both SARS-CoV-2 and SARS-CoV, with RpYN06 virus being the closest relative of SARS-CoV-2. Ecological modeling predicted the co-existence of up to 23 Rhinolophus bat species, with the largest hot-spots extending from South Laos and Vietnam to southern China. The study highlights the remarkable diversity of bat coronaviruses at the local scale.

CELL (2021)

添加到收藏夹

Review Biochemistry & Molecular Biology

The origins of SARS-CoV-2: A critical review

Edward C. Holmes et al.

Summary: This article critically reviews the current scientific evidence to help clarify the origin of SARS-CoV-2. Recent debate has centered around two competing ideas: a laboratory escape scenario and zoonotic emergence.

CELL (2021)

添加到收藏夹

Editorial Material Multidisciplinary Sciences

The animal origin of SARS-CoV-2

Spyros Lytras et al.

SCIENCE (2021)

添加到收藏夹

Article Multidisciplinary Sciences

Animal sales from Wuhan wet markets immediately prior to the COVID-19 pandemic

Xiao Xiao et al.

Summary: The study documents the sale of 47,381 individuals from 38 species in Wuhan's markets, noting the absence of pangolins and bats which supports the theory that they are not the source of the COVID-19 pandemic. China implemented a temporary ban on wildlife trade and a permanent ban on eating and trading terrestrial wild animals to protect human health, address past inconsistencies, and benefit global biodiversity conservation and animal welfare.

SCIENTIFIC REPORTS (2021)

添加到收藏夹

Article Immunology

A novel SARS-CoV-2 related coronavirus with complex recombination isolated from bats in Yunnan province, China

Li-li Li et al.

Summary: A new SARS-CoV-2 related virus, provisionally named PrC31, was discovered in bat samples from Yunnan province, China. This virus showed high nucleotide identities to SARS-CoV-2 and a common ancestor with it in evolutionary history. Recombination analysis revealed multiple complex recombination events in PrC31 involving SARS-CoV and SARS-CoV-2 sub-lineages.

EMERGING MICROBES & INFECTIONS (2021)

添加到收藏夹

Article Biochemistry & Molecular Biology

Characterizing Transcriptional Regulatory Sequences in Coronaviruses and Their Role in Recombination

Yiyan Yang et al.

Summary: The study found that transcriptional regulatory sequences (TRS) in coronavirus genomes are conserved within different genera, with recombination hotspots frequently colocated with TRS-B sites.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

添加到收藏夹

Article Virology

Synonymous mutations and the molecular evolution of SARS-CoV-2 origins

Hongru Wang et al.

Summary: Human SARS-CoV-2 is genetically closer to bat-derived viruses than pangolin-derived strains, supporting the recombination hypothesis. However, the high synonymous divergence between pangolin strain and SARS-CoV-2 suggests a recombination event into bat-derived viruses. Additionally, there is a significant increase in nonsynonymous mutations in current pandemic strains, indicating a negative impact on viral fitness.

VIRUS EVOLUTION (2021)

添加到收藏夹

Article Virology

The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus

H. L. Wells et al.

Summary: The study introduced a novel sarbecovirus from Rwanda and Uganda, which is phylogenetically intermediate to SARS-CoV-1 and SARS-CoV-2 and is unable to utilize human ACE2. The findings suggest that the observed pattern of ACE2 usage among sarbecoviruses is best explained by recombination of SARS-CoV-1 and its relatives, shedding light on the natural history of ACE2 usage for both SARS-CoV-1 and SARS-CoV-2.

VIRUS EVOLUTION (2021)

添加到收藏夹

Article Multidisciplinary Sciences

Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans

Bas B. Oude Munnink et al.

Summary: Animal experiments have shown that various animals can be infected by SARS-CoV-2, with evidence of animal-to-human transmission within mink farms. Investigation into mink farm outbreaks revealed that the virus was initially introduced by humans and has since evolved, causing transmission between mink farms. Despite enhanced biosecurity measures and culling, transmission occurred between farms in three large clusters with unknown modes of transmission, resulting in a high percentage of infections among mink farm residents and employees.

SCIENCE (2021)

添加到收藏夹

Article Biochemistry & Molecular Biology

HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies

Sergei L. Kosakovsky Pond et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

添加到收藏夹

Article Multidisciplinary Sciences

A new coronavirus associated with human respiratory disease in China

Fan Wu et al.

NATURE (2020)

添加到收藏夹

Article Multidisciplinary Sciences

A pneumonia outbreak associated with a new coronavirus of probable bat origin

Peng Zhou et al.

NATURE (2020)

添加到收藏夹

Article Medicine, General & Internal

Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia

Qun Li et al.

NEW ENGLAND JOURNAL OF MEDICINE (2020)

添加到收藏夹

Article Microbiology

The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

Alexander E. Gorbalenya et al.

NATURE MICROBIOLOGY (2020)

添加到收藏夹

Article Biochemistry & Molecular Biology

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

Alexandra C. Walls et al.

CELL (2020)

添加到收藏夹

Article Multidisciplinary Sciences

Emergence of SARS-CoV-2 through recombination and strong purifying selection

Xiaojun Li et al.

SCIENCE ADVANCES (2020)

添加到收藏夹

Article Multidisciplinary Sciences

Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins

Kangpeng Xiao et al.

NATURE (2020)

添加到收藏夹

Article Multidisciplinary Sciences

Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins

Tommy Tsan-Yuk Lam et al.

NATURE (2020)

添加到收藏夹

Article Microbiology

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

Maciej F. Boni et al.

NATURE MICROBIOLOGY (2020)

添加到收藏夹

Correction Biochemistry & Molecular Biology

A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein (vol 30, 2196.e1, 2020)

Hong Zhou et al.

CURRENT BIOLOGY (2020)

添加到收藏夹

Article Multidisciplinary Sciences

Origin and cross-species transmission of bat coronaviruses in China

Alice Latinne et al.

NATURE COMMUNICATIONS (2020)

添加到收藏夹

Article Biochemistry & Molecular Biology

The SARS-CoV-2 Spike protein has a broad tropism for mammalian ACE2 proteins

Carina Conceicao et al.

PLOS BIOLOGY (2020)

添加到收藏夹

Article Genetics & Heredity

Recombination events are concentrated in the spike protein region of Betacoronaviruses

Louis-Marie Bobay et al.

PLOS GENETICS (2020)

添加到收藏夹

Article Biodiversity Conservation

No Evidence of Coronaviruses or Other Potentially Zoonotic Viruses in Sunda pangolins (Manis javanica) Entering the Wildlife Trade via Malaysia

Jimmy Lee et al.

ECOHEALTH (2020)

添加到收藏夹

Article Virology

Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins (Manis javanica)

Ping Liu et al.

VIRUSES-BASEL (2019)

添加到收藏夹

Article Virology

SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination

Abbas Jariani et al.

VIRUS EVOLUTION (2019)

添加到收藏夹

Letter Virology

Serological Evidence of Bat SARS-Related Coronavirus Infection in Humans, China

Ning Wang et al.

VIROLOGICA SINICA (2018)

添加到收藏夹

Article Immunology

Genomic characterization and infectivity of a novel SARS-like coronavirus in Chinese bats

Dan Hu et al.

EMERGING MICROBES & INFECTIONS (2018)

添加到收藏夹

Article Virology

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10

Marc A. Suchard et al.

VIRUS EVOLUTION (2018)

添加到收藏夹

Article Virology

Extensive diversity of coronaviruses in bats from China

Xian-Dan Lin et al.

VIROLOGY (2017)

添加到收藏夹

Article Biochemistry & Molecular Biology

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

Jaime Huerta-Cepas et al.

MOLECULAR BIOLOGY AND EVOLUTION (2016)

添加到收藏夹

Article Virology

Continuous and Discontinuous RNA Synthesis in Coronaviruses

Isabel Sola et al.

ANNUAL REVIEW OF VIROLOGY, VOL 2 (2015)

添加到收藏夹

Article Biochemistry & Molecular Biology

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

添加到收藏夹

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)

添加到收藏夹

Article Biodiversity Conservation

Bat conservation in China: should protection of subterranean habitats be a priority?

Jinhong Luo et al.

ORYX (2013)

添加到收藏夹

Review Virology

Recombination, Reservoirs, and the Modular Spike: Mechanisms of Coronavirus Cross-Species Transmission

Rachel L. Graham et al.

JOURNAL OF VIROLOGY (2010)

添加到收藏夹

Review Biochemistry & Molecular Biology

Pleistocene climatic cycling drives intra-specific diversification in the intermediate horseshoe bat (Rhinolophus affinis) in Southern China

Xiu Guang Mao et al.

MOLECULAR ECOLOGY (2010)

添加到收藏夹

Article Microbiology

Molecular Mechanisms of Recombination Restriction in the Envelope Gene of the Human Immunodeficiency Virus

Etienne Simon-Loriere et al.

PLOS PATHOGENS (2009)

添加到收藏夹

Article Genetics & Heredity

An exact nonparametric method for inferring mosaic structure in sequence triplets

Maciej F. Boni et al.

GENETICS (2007)

添加到收藏夹

Article Biochemical Research Methods

GARD: a genetic algorithm for recombination detection

Sergei L. Kosakovsky Pond et al.

BIOINFORMATICS (2006)

添加到收藏夹

Article Virology

Recombination patterns in aphthoviruses mirror those found in other picornaviruses

Livio Heath et al.

JOURNAL OF VIROLOGY (2006)

添加到收藏夹

Article Biochemistry & Molecular Biology

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments

Mikita Suyama et al.

NUCLEIC ACIDS RESEARCH (2006)

添加到收藏夹

Article Immunology

A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints

DP Martin et al.

AIDS RESEARCH AND HUMAN RETROVIRUSES (2005)

添加到收藏夹

Article Biochemistry & Molecular Biology

Evaluation of methods for detecting recombination from DNA sequences: Empirical data

D Posada

MOLECULAR BIOLOGY AND EVOLUTION (2002)

添加到收藏夹

Article Multidisciplinary Sciences

Evaluation of methods for detecting recombination from DNA sequences: Computer simulations

D Posada et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)

添加到收藏夹

Article Biochemical Research Methods

Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences

MJ Gibbs et al.

BIOINFORMATICS (2000)

添加到收藏夹

© Peeref 2019-2024. All rights reserved.