Viral and host factors related to the clinical outcome of COVID-19.
Adolescent
Adult
Aged
Aged, 80 and over
Aging
Animals
Asymptomatic Infections
/ epidemiology
Betacoronavirus
/ classification
COVID-19
China
/ epidemiology
Cohort Studies
Coronavirus Infections
/ complications
Critical Illness
/ epidemiology
Disease Progression
Evolution, Molecular
Female
Genetic Variation
Genome, Viral
/ genetics
Hospitalization
/ statistics & numerical data
Host-Pathogen Interactions
/ immunology
Humans
Inflammation Mediators
/ immunology
Interleukin-6
/ blood
Interleukin-8
/ blood
Lymphocyte Count
Lymphopenia
/ complications
Male
Middle Aged
Pandemics
Phylogeny
Pneumonia, Viral
/ complications
Respiratory Distress Syndrome
/ complications
SARS-CoV-2
T-Lymphocytes
/ cytology
Time Factors
Treatment Outcome
Virulence
/ genetics
Virus Shedding
Young Adult
Zoonoses
/ transmission
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
07 2020
07 2020
Historique:
received:
14
03
2020
accepted:
13
05
2020
pubmed:
21
5
2020
medline:
22
7
2020
entrez:
21
5
2020
Statut:
ppublish
Résumé
In December 2019, coronavirus disease 2019 (COVID-19), which is caused by the new coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified in Wuhan (Hubei province, China)
Identifiants
pubmed: 32434211
doi: 10.1038/s41586-020-2355-0
pii: 10.1038/s41586-020-2355-0
doi:
Substances chimiques
Inflammation Mediators
0
Interleukin-6
0
Interleukin-8
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
437-440Commentaires et corrections
Type : CommentIn
Références
Zhu, N. et al. A novel coronavirus from patients with pneumonia in China, 2019. N. Engl. J. Med. 382, 727–733 (2020).
doi: 10.1056/NEJMoa2001017
pubmed: 31978945
pmcid: 7092803
Zhou, P. et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579, 270–273 (2020).
doi: 10.1038/s41586-020-2012-7
pubmed: 32015507
pmcid: 7095418
Lam, T. T. et al. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature (2020).
Li, Q. et al. Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia. N. Engl. J. Med. 382, 1199–1207 (2020).
doi: 10.1056/NEJMoa2001316
pubmed: 31995857
pmcid: 7121484
Guan, W. J. et al. Clinical characteristics of coronavirus disease 2019 in China. N. Engl. J. Med. 382, 1708–1720 (2020).
doi: 10.1056/NEJMoa2002032
pubmed: 32109013
Chan, J. F. et al. A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet 395, 514–523 (2020).
doi: 10.1016/S0140-6736(20)30154-9
pubmed: 31986261
pmcid: 7159286
Lu, R. et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet 395, 565–574 (2020).
doi: 10.1016/S0140-6736(20)30251-8
pubmed: 32007145
pmcid: 7159086
Andersen, K. G., Rambaut, A., Lipkin, W. I., Holmes, E. C. & Garry, R. F. The proximal origin of SARS-CoV-2. Nat. Med. 26, 450–452 (2020).
doi: 10.1038/s41591-020-0820-9
pubmed: 32284615
MacLean, O. A., Orton, R., Singer, J. B. & Robertson, D. L. Response to “On the origin and continuing evolution of SARS-CoV-2”, http://virological.org/t/response-to-on-the-origin-and-continuing-evolution-of-sars-cov-2/418 (2020).
Tang, X. et al. On the origin and continuing evolution of SARS-CoV-2. Natl Sci. Rev. https://doi.org/10.1093/nsr/nwaa036 (2020).
Ren, L. L. et al. Identification of a novel coronavirus causing severe pneumonia in human: a descriptive study. Chin. Med. J. (Engl.) 133, 1015–1024 (2020).
doi: 10.1097/CM9.0000000000000722
Wong, R. S. et al. Haematological manifestations in patients with severe acute respiratory syndrome: retrospective analysis. Br. Med. J. 326, 1358–1362 (2003).
doi: 10.1136/bmj.326.7403.1358
Tian, S. et al. Pulmonary pathology of early-phase 2019 novel coronavirus (COVID-19) pneumonia in two patients with lung cancer. J. Thorac. Oncol. 15, 700–704 (2020).
doi: 10.1016/j.jtho.2020.02.010
pubmed: 32114094
pmcid: 7128866
Xu, Z. et al. Pathological findings of COVID-19 associated with acute respiratory distress syndrome. Lancet Respir. Med. 8, 420–422 (2020).
doi: 10.1016/S2213-2600(20)30076-X
pubmed: 32085846
pmcid: 7164771
Wang, C. et al. Alveolar macrophage activation and cytokine storm in the pathogenesis of severe COVID-19. Preprint at https://doi.org/10.21203/rs.3.rs-19346/v1 (2020).
Shan, C. et al. Infection with novel coronavirus (SARS-CoV-2) causes pneumonia in the Rhesus macaques. Preprint at https://doi.org/10.21203/rs.2.25200/v1 (2020).
National Health Commission of the People’s Republic of China Diagnosis and Treatment Protocol for COVID-19 (Trial Version 7) http://en.nhc.gov.cn/2020-03/29/c_78469.htm (2020).
Quick, J. et al. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat. Protocols 12, 1261–1276 (2017).
doi: 10.1038/nprot.2017.066
pubmed: 28538739
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
doi: 10.1093/bioinformatics/btp324
pubmed: 19451168
pmcid: 2705234
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
pubmed: 19505943
pmcid: 2723002
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
doi: 10.1093/bioinformatics/btu170
pubmed: 24695404
pmcid: 4103590
Fedonin, G. G., Fantin, Y. S., Favorov, A. V., Shipulin, G. A. & Neverov, A. D. VirGenA: a reference-based assembler for variable viral genomes. Brief. Bioinform. 20, 15–25 (2019).
doi: 10.1093/bib/bbx079
pubmed: 28968771
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
doi: 10.1093/molbev/mst010
pubmed: 23329690
pmcid: 3603318
Hadfield, J. et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 34, 4121–4123 (2018).
doi: 10.1093/bioinformatics/bty407
pubmed: 29790939
pmcid: 6247931
Nguyen, L. T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).
doi: 10.1093/molbev/msu300
pubmed: 25371430
Sagulenko, P., Puller, V. & Neher, R. A. TreeTime: maximum-likelihood phylodynamic analysis. Virus Evol. 4, vex042 (2018).
doi: 10.1093/ve/vex042
pubmed: 29340210
pmcid: 5758920