Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding
- R. Lu, Xiang-rong Zhao, W. Tan
- BiologyThe Lancet
- 30 January 2020
A new coronavirus associated with human respiratory disease in China
- Fan Wu, Su Zhao, Yong‐Zhen Zhang
- Biology, MedicineNature
- 3 February 2020
Phylogenetic and metagenomic analyses of the complete viral genome of a new coronavirus from the family Coronaviridae reveal that the virus is closely related to a group of SARS-like coronaviruses found in bats in China.
The proximal origin of SARS-CoV-2
- K. Andersen, A. Rambaut, W. Lipkin, E. Holmes, R. Garry
- BiologyNature Network Boston
- 17 March 2020
It is shown that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus, and scenarios by which they could have arisen are discussed.
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
- A. Rambaut, E. Holmes, O. Pybus
- BiologyNature Microbiology
- 15 July 2020
A rational and dynamic virus nomenclature that uses a phylogenetic framework to identify those lineages that contribute most to active spread and is designed to provide a real-time bird’s-eye view of the diversity of the hundreds of thousands of genome sequences collected worldwide.
A Metagenomic Survey of Microbes in Honey Bee Colony Collapse Disorder
- D. Cox-Foster, S. Conlan, W. Lipkin
- BiologyScience
- 12 October 2007
The observation that irradiated combs from affected colonies can be repopulated with naive bees suggests that infection may contribute to colony collapse disorder (CCD).
Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins
The discovery of multiple lineages of pangolin coronavirus and their similarity to SARS-CoV-2 suggests that pangolins should be considered as possible hosts in the emergence of new coronaviruses and should be removed from wet markets to prevent zoonotic transmission.
Redefining the invertebrate RNA virosphere
- M. Shi, Xian-dan Lin, Yong‐Zhen Zhang
- BiologyNature
- 22 December 2016
A view of the RNA virosphere is presented that is more phylogenetically and genomically diverse than that depicted in current classification schemes and provide a more solid foundation for studies in virus ecology and evolution.
Rates of evolutionary change in viruses: patterns and determinants
- S. Duffy, L. A. Shackelton, E. Holmes
- BiologyNature reviews genetics
- 1 April 2008
It is shown that the high rate of nucleotide substitution in RNA viruses is matched by some DNA viruses, suggesting that evolutionary rates in viruses are explained by diverse aspects of viral biology, such as genomic architecture and replication speed, and not simply by polymerase fidelity.
New World Bats Harbor Diverse Influenza A Viruses
- S. Tong, Xueyong Zhu, R. Donis
- BiologyPLoS Pathogens
- 1 October 2013
Using consensus degenerate RT-PCR, a novel influenza A virus is identified in a flat-faced fruit bat from Peru, indicating that bats constitute a potentially important and likely ancient reservoir for a diverse pool of influenza viruses.
Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region.
- P. Simmonds, E. Holmes, M. Urdea
- BiologyJournal of General Virology
- 1 November 1993
A new nomenclature for HCV variants is proposed in this communication that reflects the two-tiered nature of sequence differences between different viral isolates and describes criteria that would enable new variants to be assigned within the classification as they are discovered.
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