SARS-CoV-2 is an appropriate name for the new coronavirus

Wu, Yuntao; Ho, Wen‐Zhe; Huang, Yao‐Wei; Jin, Dong-Yan; Li, Shiyue; Liu, Shan-Lu; Li, Xuefeng; Qiu, Jianming; Sang, Yongming; Wang, Qiuhong; Yuen, Kwok‐Yung; Zheng, Zhi-Ming

doi:10.1016/s0140-6736(20)30557-2

Cited by 317 publications

(270 citation statements)

References 6 publications

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“…When the first genome sequence of SARS-CoV-2, Wuhan-Hu-1, was released on January 10 2020 on Virological.org by a consortium led by Yong-Zhen Zhang it enabled the immediate analyses of its ancestry. Across a large region of its genome, corresponding approximately to ORF1b , it did not cluster with any of the known bat coronaviruses indicating that recombination likely played a role in the evolutionary history of these viruses (Lu et al, 2020;Wu et al 2020b). Subsequently, a bat sarbecovirus -RaTG13 sampled from a Rhinolophus affinis horseshoe bat in 2013 in Yunnan province -was reported that clusters with SARS-CoV-2 in almost all genomic regions with approximately 96% genome sequence identity (Zhou et al, 2020b).…”

Section: Introductionmentioning

confidence: 99%

“…In December 2019, a cluster of pneumonia cases epidemiologically linked to an open-air wet market in city of Wuhan (Hubei Province), China Zhou et al, 2020b) led local health officials to issue an epidemiological alert to the Chinese Center for Disease Control and Prevention (China CDC) and the World Health Organization's (WHO) China Country Office. In early January, the etiological agent of the pneumonia cases was found to be a coronavirus (World Health Organization, 2020a), subsequently named SARS-CoV-2 by an International Committee on Taxonomy of Viruses (ICTV) Study Group (Gorbalenya et al, 2020), (also named hCoV-19 by (Wu et al, 2020b)). The first available sequence data placed this novel human pathogen in the Sarbecovirus subgenus of Coronaviridae (Lu et al, 2020), the same sub-genus as the SARS virus that caused a global outbreak of nearly 8000 cases in [2002][2003].…”

Section: Introductionmentioning

confidence: 99%

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

Boni

Lemey

Jiang

et al. 2020

Preprint

359

531

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There are outstanding evolutionary questions on the recent emergence of coronavirus in Hubei province that caused the COVID-19 pandemic, including (1) the relationship of the new virus to the SARS-related coronaviruses, (2) the role of bats as a reservoir species, (3) the potential role of other mammals in the emergence event, and (4) the role of recombination in viral emergence. Here, we address these questions and find that the sarbecoviruses -the viral subgenus responsible for the emergence of SARS-CoV and SARS-CoV-2 -exhibit frequent recombination, but the SARS-CoV-2 lineage itself is not a recombinant of any viruses detected to date. In order to employ phylogenetic methods to date the divergence events between SARS-CoV-2 and the bat sarbecovirus reservoir, recombinant regions of a 68-genome sarbecovirus alignment were removed with three independent methods. Bayesian evolutionary rate and divergence date estimates were consistent for all three recombination-free alignments and robust to two different prior specifications based on HCoV-OC43 and MERS-CoV evolutionary rates. Divergence dates between SARS-CoV-2 and the bat sarbecovirus reservoir were estimated as 1948 (95% HPD: 1879-1999), 1969 (95% HPD: 1930-2000), and 1982 (95% HPD: 1948-2009). Despite intensified characterization of sarbecoviruses since SARS, the lineage giving rise to SARS-CoV-2 has been circulating unnoticed for decades in bats and been transmitted to other hosts such as pangolins. The occurrence of a third significant coronavirus emergence in 17 years together with the high prevalence and virus diversity in bats implies that these viruses are likely to cross species boundaries again. : bioRxiv preprint 3 / 25 In BriefThe Betacoronavirus SARS-CoV-2 is a member of the sarbecovirus subgenus which shows frequent recombination in its evolutionary history. We characterize the extent of this genetic exchange and identify non-recombining regions of the sarbecovirus genome using three independent methods to remove the effects of recombination. Using these non-recombining genome regions and prior information on coronavirus evolutionary rates, we obtain estimates from three approaches that the most likely divergence date of SARS-CoV-2 from its most closely related available bat sequences ranges from 1948 to 1982. Key Points RaTG13 is the closest available bat virus to SARS-CoV-2; a sub-lineage of these bat viruses is able to infect humans. Two sister lineages of the RaTG13/SARS-CoV-2 lineage infect Malayan pangolins. The sarbecoviruses show a pattern of deep recombination events, indicating that there are high levels of co-infection in horseshoe bats and that the viral pool can generate novel allele combinations and substantial genetic diversity; the sarbecoviruses are efficient 'explorers' of phenotype space. The SARS-CoV-2 lineage is not a recent recombinant, at least not involving any of the bat or pangolin viruses sampled to date. Non-recombinant regions of the sarbecoviruses can be identified, allowing for phylogenetic inference and dating...

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Boni

Lemey

Jiang

et al. 2020

Preprint

359

531

View full text Add to dashboard Cite

show abstract

“…En décembre 2019, l'apparition de plusieurs cas de pneumopathies d'origine inconnue dans la province de Hubei en Chine, a conduit à l'identification, en janvier 2020, d'un nouveau coronavirus [8], appelé SARS-CoV-2 par le groupe de travail Coronavirus du comité international de taxonomie des virus [9]. Il s'agit d'un Betacoronavirus probablement transmis à l'homme par le pangolin, sur le marché de fruits de mer de Huanan, situé dans la ville de Wuhan [10].…”

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COVID-19 : caractéristiques cliniques, biologiques et radiologiques chez l’adulte, la femme enceinte et l’enfant. Une mise au point au cœur de la pandémie

Plaçais

Richier

2020

La Revue de Médecine Interne

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publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. J o u r n a l P r e -p r o o f 1 RésuméLa propagation du nouveau coronavirus SARS-CoV-2, découvert en Chine en janvier 2020, a mené à une pandémie dès mars 2020, obligeant chaque système de soins des pays touchés à une adaptation rapide. Pour mieux faire face à cette crise sanitaire majeure, qui a donné lieu à de nombreuses publications scientifiques, nous avons synthétisé les principales études cliniques originales afin de faciliter la prise en charge au quotidien des patients atteints de COVID-19.Nous détaillons les premiers signes et l'évolution de la maladie ainsi que les différentes formes cliniques, y compris extra-pulmonaires, telles qu'elles sont connues au début de cette pandémie.Nous insistons sur les marqueurs cliniques, biologiques et scannographiques prédictifs de sévérité ou de mortalité. Enfin, nous discutons de l'impact de l'infection par le SARS-CoV-2 dans les populations suspectes d'être à haut risque de formes sévères. AbstractThe spread of the new coronavirus SARS-CoV-2, discovered in China in January 2020, led to a pandemic as early as March 2020, forcing every health care system in the affected countries to adapt quickly. In order to better address this major health crisis, which has given rise to numerous scientific publications, we have synthesized the main original clinical studies to facilitate the day-to-day management of patients with COVID-19.We detail the early signs and progression of the disease as well as the different clinical forms, including extra-pulmonary, as known at the beginning of this pandemic. We focus on clinical, biological and CT markers predictive of severity or mortality. Finally, we discuss the impact of SARS-CoV-2 infection in populations suspected to be at high risk of severe forms.

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“…In December 2019, a novel pneumonia resulting from SARS-CoV2, named coronavirus disease 2019 (COVID-19), emerged in Wuhan [1,2]. Due to the high viral contagiousness and transmission during the presymptomatic phase [3,4], COVID-19 progressively spread throughout China and has since become a global health issue [5].…”

Section: Introductionmentioning

confidence: 99%

COVID-19 in a patient with long-term use of glucocorticoids: A study of a familial cluster

Han

Jiang

Xia

et al. 2020

Clinical Immunology

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A B S T R A C TClusters of patients with novel coronavirus disease 2019 (COVID-19) have been successively reported globally. Studies show clear person-to-person transmission. The average incubation period is 2-14 days, and mostly 3-7 days. However, in some patients, this period may be longer. Here, we report a familial cluster of COVID-19 where a 47-year-old woman with long-term use of glucocorticoids did not develop any symptoms within the 14day quarantine period but was confirmed with COVID-19 by tested positive of antibody on day 40 after she left Wuhan. Almost at the same time, her father and sister were diagnosed with COVID-19. The results suggest that the long-term use of glucocorticoids might cause atypical infections, a long incubation period, and extra transmission of COVID-19.

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SARS-CoV-2 is an appropriate name for the new coronavirus

Cited by 317 publications

References 6 publications

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

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

COVID-19 : caractéristiques cliniques, biologiques et radiologiques chez l’adulte, la femme enceinte et l’enfant. Une mise au point au cœur de la pandémie

COVID-19 in a patient with long-term use of glucocorticoids: A study of a familial cluster

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