The emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) in 2002 and Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 has generated enormous interest in the biodiversity, genomics and cross-species transmission potential of coronaviruses, especially those from bats, the second most speciose order of mammals. Herein, we identified a novel coronavirus, provisionally designated Rousettus bat coronavirus GCCDC1 (Ro-BatCoV GCCDC1), in the rectal swab samples of Rousettus leschenaulti bats by using pan-coronavirus RT-PCR and next-generation sequencing. Although the virus is similar to Rousettus bat coronavirus HKU9 (Ro-BatCoV HKU9) in genome characteristics, it is sufficiently distinct to be classified as a new species according to the criteria defined by the International Committee of Taxonomy of Viruses (ICTV). More striking was that Ro-BatCoV GCCDC1 contained a unique gene integrated into the 3’-end of the genome that has no homologs in any known coronavirus, but which sequence and phylogeny analyses indicated most likely originated from the p10 gene of a bat orthoreovirus. Subgenomic mRNA and cellular-level observations demonstrated that the p10 gene is functional and induces the formation of cell syncytia. Therefore, here we report a putative heterologous inter-family recombination event between a single-stranded, positive-sense RNA virus and a double-stranded segmented RNA virus, providing insights into the fundamental mechanisms of viral evolution.

Background Between mid‐January and early February, provinces of mainland China outside the epicentre in Hubei province were on high alert for importations and transmission of COVID‐19. Many properties of COVID‐19 infection and transmission were still not yet established. Methods We collated and analysed data on 449 of the earliest COVID‐19 cases detected outside Hubei province to make inferences about transmission dynamics and severity of infection. We analysed 64 clusters to make inferences on serial interval and potential role of pre‐symptomatic transmission. Results We estimated an epidemic doubling time of 5.3 days (95% confidence interval (CI): 4.3, 6.7) and a median incubation period of 4.6 days (95% CI: 4.0, 5.2). We estimated a serial interval distribution with mean 5.7 days (95% CI: 4.7, 6.8) and standard deviation 3.5 days, and effective reproductive number was 1.98 (95% CI: 1.68, 2.35). We estimated that 32/80 (40%) of transmission events were likely to have occurred prior to symptoms onset in primary cases. Secondary cases in clusters had less severe illness on average than cluster primary cases. Conclusions The majority of transmissions are occurring around illness onset in an infected person, and pre‐symptomatic transmission does play a role. Detection of milder infections among the secondary cases may be more reflective of true disease severity.

Background The relative contributions of asymptomatic, pre-symptomatic and symptomatic transmission of SARS-CoV-2 have not been clearly measured although control measures may differ in response to the risk of spread posed by different types of cases. Methods We collected detailed information on transmission events and symptom status based on laboratory-confirmed patient data and contact tracing data from four provinces and one municipality in China. We estimated the variation in risk of transmission over time, and the severity of secondary infections, by symptomatic status of the infector. Results There were 393 symptomatic index cases with 3136 close contacts and 185 asymptomatic index cases with 1078 close contacts included into the study. The secondary attack rate among close contacts of symptomatic and asymptomatic index cases were 4.1% (128/3136) and 1.1% (12/1078), respectively, corresponding to a higher transmission risk from symptomatic cases than from asymptomatic cases (OR: 3.79, 95% CI: 2.06, 6.95). Approximately 25% (32/128) and 50% (6/12) of the infected close contacts were asymptomatic from symptomatic and asymptomatic index cases, respectively, while more than one third (38%) of the infections in the close contacts of symptomatic cases were attributable to exposure to the index cases before symptom onset. Infected contacts of asymptomatic index cases were more likely to be asymptomatic and less likely to be severe. Conclusions Asymptomatic and pre-symptomatic transmission play an important role in spreading infection, although asymptomatic cases pose a lower risk of transmission than symptomatic cases. Early case detection and effective test-and-trace measures are important to reduce transmission.

Background COVID-19 has posed an enormous threat to public health around the world. Some severe and critical cases have bad prognoses and high case fatality rates, unraveling risk factors for severe COVID-19 are of significance for predicting and preventing illness progression, and reducing case fatality rates. Our study focused on analyzing characteristics of COVID-19 cases and exploring risk factors for developing severe COVID-19. Methods The data for this study was disease surveillance data on symptomatic cases of COVID-19 reported from 30 provinces in China between January 19 and March 9, 2020, which included demographics, dates of symptom onset, clinical manifestations at the time of diagnosis, laboratory findings, radiographic findings, underlying disease history, and exposure history. We grouped mild and moderate cases together as non-severe cases and categorized severe and critical cases together as severe cases. We compared characteristics of severe cases and non-severe cases of COVID-19 and explored risk factors for severity. Results The total number of cases were 12 647 with age from less than 1 year old to 99 years old. The severe cases were 1662 (13.1%), the median age of severe cases was 57 years [Inter-quartile range(IQR): 46–68] and the median age of non-severe cases was 43 years (IQR: 32–54). The risk factors for severe COVID-19 were being male [adjusted odds ratio (aOR) = 1.3, 95% CI: 1.2–1.5]; fever (aOR = 2.3, 95% CI: 2.0–2.7), cough (aOR = 1.4, 95% CI: 1.2–1.6), fatigue (aOR = 1.3, 95% CI: 1.2–1.5), and chronic kidney disease (aOR = 2.5, 95% CI: 1.4–4.6), hypertension (aOR = 1.5, 95% CI: 1.2–1.8) and diabetes (aOR = 1.96, 95% CI: 1.6–2.4). With the increase of age, risk for the severity was gradually higher [20–39 years (aOR = 3.9, 95% CI: 1.8–8.4), 40–59 years (aOR = 7.6, 95% CI: 3.6–16.3), ≥ 60 years (aOR = 20.4, 95% CI: 9.5–43.7)], and longer time from symtem onset to diagnosis [3–5 days (aOR = 1.4, 95% CI: 1.2–1.7), 6–8 days (aOR = 1.8, 95% CI: 1.5–2.1), ≥ 9 days(aOR = 1.9, 95% CI: 1.6–2.3)]. Conclusions Our study showed the risk factors for developing severe COVID-19 with large sample size, which included being male, older age, fever, cough, fatigue, delayed diagnosis, hypertension, diabetes, chronic kidney diasease, early case identification and prompt medical care. Based on these factors, the severity of COVID-19 cases can be predicted. So cases with these risk factors should be paid more attention to prevent severity.