Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins ( Manis javanica )
Ping Liu,Wu Chen,Jin-Ping Chen +2 more
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TLDR
This is the first report on the viral diversity of pangolins, expanding the understanding of the virome in endangered species, and providing insight into the overall diversity of viruses that may be capable of directly or indirectly crossing over into other mammals.Citations
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The proximal origin of SARS-CoV-2.
Kristian G. Andersen,Kristian G. Andersen,Andrew Rambaut,W. Ian Lipkin,Edward C. Holmes,Robert F. Garry +5 more
TL;DR: 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.
Journal ArticleDOI
Characteristics of SARS-CoV-2 and COVID-19
TL;DR: The basic virology of SARS-CoV-2 is described, including genomic characteristics and receptor use, highlighting its key difference from previously known coronaviruses.
Journal ArticleDOI
Transmission routes of 2019-nCoV and controls in dental practice.
TL;DR: Dental professionals play great roles in preventing the transmission of 2019-nCoV, and the infection control measures during dental practice are recommended to block the person-to-person transmission routes in dental clinics and hospitals.
Journal ArticleDOI
Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins.
Tommy Tsan-Yuk Lam,Na Jia,Ya-Wei Zhang,Marcus Ho-Hin Shum,Jia-Fu Jiang,Hongbo Zhu,Yigang Tong,Yongxia Shi,Xue-Bing Ni,Yunshi Liao,Wen-Juan Li,Bao-Gui Jiang,Wei Wei,Ting-Ting Yuan,Kui Zheng,Xiao-Ming Cui,Jie Li,Guangqian Pei,Xin Qiang,William Yiu-Man Cheung,Lian-Feng Li,Fang-Fang Sun,Si Qin,Jicheng Huang,Gabriel M. Leung,Edward C. Holmes,Yan-Ling Hu,Yi Guan,Wu-Chun Cao +28 more
TL;DR: 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.
Journal ArticleDOI
On the origin and continuing evolution of SARS-CoV-2
Xiaolu Tang,Changcheng Wu,Xiang Li,Yuhe Song,Yuhe Song,Xinmin Yao,Xinkai Wu,Yuange Duan,Hong Zhang,Yirong Wang,Zhaohui Qian,Jie Cui,Jian Lu +12 more
TL;DR: The results suggest that the development of new variations in functional sites in the receptor-binding domain (RBD) of the spike seen in SARS-CoV-2 and viruses from pangolin SARSr-CoVs are likely caused by natural selection besides recombination.
References
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Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Journal ArticleDOI
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Kazutaka Katoh,Daron M. Standley +1 more
TL;DR: This version of MAFFT has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update.
Journal ArticleDOI
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Weizhong Li,Adam Godzik +1 more
TL;DR: Cd-hit-2d compares two protein datasets and reports similar matches between them; cd- Hit-est clusters a DNA/RNA sequence database and cd- hit-est-2D compares two nucleotide datasets.
Journal ArticleDOI
W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis.
TL;DR: W-IQ-TREE supports multiple sequence types in common alignment formats and a wide range of evolutionary models including mixture and partition models, performing fast model selection, partition scheme finding, efficient tree reconstruction, ultrafast bootstrapping, branch tests, and tree topology tests.
Journal ArticleDOI
Bats are natural reservoirs of SARS-like coronaviruses.
Wendong Li,Zhengli Shi,Meng Yu,Wuze Ren,Craig Smith,Jonathan H. Epstein,Hanzhong Wang,Gary Crameri,Zhihong Hu,Huajun Zhang,Jianhong Zhang,Jennifer A. McEachern,Hume Field,Peter Daszak,Bryan T. Eaton,Shuyi Zhang,Lin-Fa Wang +16 more
TL;DR: It is reported that species of bats are a natural host of coronaviruses closely related to those responsible for the SARS outbreak, and these viruses display greater genetic variation than SARS-CoV isolated from humans or from civets.
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