On 11 February 2020, the ICTV introduced the name "severe acute respiratory syndrome coronavirus 2" (SARS-CoV-2) to refer to the virus strain previously known as 2019-nCoV. Earlier the same day, the WHO officially renamed the disease caused by the virus strain from "2019-nCoV acute respiratory disease" to coronavirus disease 2019 (COVID-19).
Human-to-human transmission of the virus has been confirmed and occurs primarily via respiratory droplets from coughs and sneezes within a range of about 6 feet (1.8 m). Viral RNA has also been found in stool samples from infected patients.
It is possible that the virus can be infectious even during the incubation period, but this has not been proven, and the WHO stated on 1 February 2020 that "transmission from asymptomatic cases is likely not a major driver of transmission" at this time.
Animals sold for food were originally suspected to be the reservoir or intermediary hosts of SARS-CoV-2 because many of the first individuals found to be infected by the virus were workers at the Huanan Seafood Market. A market selling live animals for food was also blamed in the SARS outbreak in 2003; such markets are considered to be incubators for novel pathogens. The outbreak has prompted a temporary ban on the trade and consumption of wild animals in China. However, some researchers have suggested that the Huanan Seafood Market may not be the original source of viral transmission to humans.
Researchers from Guangzhou claim to have found a "99% identical" viral nucleic acid sequence in a pangolin sample. As of 12 February 2020[update], the sequence remains unavailable, and all information comes from a university announcement. Pangolins are protected under Chinese law, but poaching and trading of pangolins for traditional medicine remains common. A metagenomic study published in 2019 previously revealed that SARS-CoV was the most widely distributed coronavirus among a sample of Malayan pangolins. Microbiologists and geneticists in Texas have independently found evidence of recombination in coronaviruses suggesting pangolin origins of SARS-CoV-2; they acknowledged remaining unknown factors while urging continued examination of other mammals.
Like the SARS-related coronavirus strain implicated in the 2003 SARS outbreak, SARS-CoV-2 is a member of the subgenus Sarbecovirus (Beta-CoV lineage B). Its RNA sequence is approximately 30,000 bases in length.
With a sufficient number of sequenced genomes, it is possible to reconstruct a phylogenetic tree of the mutation history of a family of viruses. By 12 January 2020, five genomes of SARS-CoV-2 had been isolated from Wuhan and reported by the Chinese Center for Disease Control and Prevention (CCDC) and other institutions; the number of genomes increased to 81 by 11 February 2020. A phylogenic analysis of the samples shows they are "highly related with at most seven mutations relative to a common ancestor", implying that the first human infection occurred in November or December 2019.
Protein modeling experiments on the spike (S) protein of the virus suggest that it has sufficient affinity to the angiotensin converting enzyme 2 (ACE2) receptors of human cells to use them as a mechanism of cell entry. On 22 January 2020, a group in China working with the full virus genome and a group in the United States using reverse genetics methods independently and experimentally demonstrated that ACE2 could act as the receptor for SARS-CoV-2. Studies have shown that SARS-CoV-2 has a higher affinity to human ACE2 than the original SARS virus strain. An atomic-level image of the S protein has been created using cryogenic electron microscopy.
The first known human infection by the strain occurred in early December 2019. Proliferation of SARS-CoV-2 was first detected in Wuhan, China, in mid-December 2019, likely originating from a single infected animal. The virus subsequently spread to all provinces of China and to more than two dozen other countries in Asia, Europe, North America, Africa, and Oceania. Human-to-human spread of the virus has been confirmed in all of these regions except Africa. On 30 January 2020, 2019-nCoV was designated a Public Health Emergency of International Concern by the WHO.
As of 20 February 2020[update] (15:30 UTC), there were 75,752 confirmed cases of infection, of which 74,579 were within mainland China. One mathematical model estimated the number of people infected in Wuhan alone at 75,815 as of 25 January 2020. Nearly all cases outside China have occurred in people who either traveled from Wuhan, or were in direct contact with someone who traveled from the area. While the proportion of infections that result in confirmed infection or progress to diagnosable disease remains unclear, the total number of deaths attributed to the virus was 2,130 as of 20 February 2020[update] (15:30 UTC); over 95% of all deaths have occurred in Hubei province, where Wuhan is located.
The basic reproduction number (, pronounced R-nought or R-zero) of the virus has been estimated to be between 1.4 and 3.9. This means that, when unchecked, the virus typically results in 1.4 to 3.9 new cases per established infection. It has been established that the virus is able to transmit along a chain of at least four people.
^ abcdGorbalenya AE (11 February 2020). "Severe acute respiratory syndrome-related coronavirus – The species and its viruses, a statement of the Coronavirus Study Group". bioRxiv. doi:10.1101/2020.02.07.937862. License:CC-BY-NC-ND 4.0.
^World Health Organization (2020). Surveillance case definitions for human infection with novel coronavirus (nCoV): interim guidance v1, January 2020 (Report). World Health Organization. hdl:10665/330376. WHO/2019-nCoV/Surveillance/v2020.1.
^ abc"CoV2020". GISAID EpifluDB. Archived from the original on 12 January 2020. Retrieved 12 January 2020.
^ abcChan JF, Yuan S, Kok KH, et al. (January 2020). "A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster". Lancet. 395 (10223): 514–523. doi:10.1016/S0140-6736(20)30154-9. PMID31986261.
^ abBenvenuto D, Giovanetti M, Ciccozzi A, et al. (January 2020). "The 2019-new coronavirus epidemic: Evidence for virus evolution". Journal of Medical Virology. 92 (4): 455–459. doi:10.1002/jmv.25688. PMID31994738.
^ abHui DS, I Azhar E, Madani TA, et al. (February 2020). "The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health - The latest 2019 novel coronavirus outbreak in Wuhan, China". Int. J. Infect. Dis. 91: 264–6. doi:10.1016/j.ijid.2020.01.009. PMID31953166.
^Wong, MC; Cregeen, SJJ; Ajami, NJ; Petrosino, JF (2020). "Evidence of recombination in coronaviruses implicating pangolin origins of nCoV-2019". bioRxiv. doi:10.1101/2020.02.07.939207.
^Zhu N, Zhang D, Wang W, et al. (January 2020). "A Novel Coronavirus from Patients with Pneumonia in China, 2019". New England Journal of Medicine. 382 (8): 727–733. doi:10.1056/NEJMoa2001017. PMID31978945.
^Xu X, Chen P, Wang J, et al. (January 2020). "Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission". Science China Life Sciences. doi:10.1007/s11427-020-1637-5. PMID32009228.
^Letko M, Munster V (22 January 2020). "Functional assessment of cell entry and receptor usage for lineage B β-coronaviruses, including 2019-nCoV". bioRxiv. doi:10.1101/2020.01.22.915660.
^Wrapp, Daniel; Wang, Nianshuang; Corbett, Kizzmekia S.; Goldsmith, Jory A.; Hsieh, Ching-Lin; Abiona, Olubukola; Graham, Barney S.; McLellan, Jason S. (15 February 2020). "Cryo-EM Structure of the 2019-nCoV Spike in the Prefusion Conformation". bioRxiv. doi:10.1101/2020.02.11.944462.
^Wu JT, Leung K, Leung GM (January 2020). "Nowcasting and forecasting the potential domestic and international spread of the 2019-nCoV outbreak originating in Wuhan, China: a modelling study". Lancet. doi:10.1016/S0140-6736(20)30260-9. PMID32014114.
^Li Q, Guan X, Wu P, et al. (January 2020). "Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia". New England Journal of Medicine. doi:10.1056/NEJMoa2001316. PMID31995857.
^Liu T, Hu J, Kang M, Lin L (25 January 2020). "Transmission dynamics of 2019 novel coronavirus (2019-nCoV)". bioRxiv. doi:10.1101/2020.01.25.919787.
^Read JM, Bridgen JR, Cummings DA, Ho A, Jewell CP (28 January 2020). "Novel coronavirus 2019-nCoV: early estimation of epidemiological parameters and epidemic predictions". MedRxiv. doi:10.1101/2020.01.23.20018549. License:CC-BY-NC-ND 4.0.
World Health Organization (2020). Laboratory testing of human suspected cases of novel coronavirus (nCoV) infection: interim guidance, 10 January 2020 (Report). World Health Organization. hdl:10665/330374. WHO/2019-nCoV/laboratory/2020.1.
World Health Organization (2020). WHO R&D Blueprint: informal consultation on prioritization of candidate therapeutic agents for use in novel coronavirus 2019 infection, Geneva, Switzerland, 24 January 2020 (Report). World Health Organization. hdl:10665/330680. WHO/HEO/R&D Blueprint (nCoV)/2020.1.