Decoding the evolution and transmissions of the novel pneumonia coronavirus (SARS-CoV-2 / HCoV-19) using whole genomic data.
利用全基因组数据解码新型肺炎冠状病毒 (SARS-CoV-2 / HCoV-19) 的进化和传播。
- 作者列表："Yu WB","Tang GD","Zhang L","Corlett RT
:The outbreak of COVID-19 started in mid-December 2019 in Wuhan, China. Up to 29 February 2020, SARS-CoV-2 (HCoV-19 / 2019-nCoV) had infected more than 85 000 people in the world. In this study, we used 93 complete genomes of SARS-CoV-2 from the GISAID EpiFlu TM database to investigate the evolution and human-to-human transmissions of SARS-CoV-2 in the first two months of the outbreak. We constructed haplotypes of the SARS-CoV-2 genomes, performed phylogenomic analyses and estimated the potential population size changes of the virus. The date of population expansion was calculated based on the expansion parameter tau ( τ) using the formula t= τ/2 u. A total of 120 substitution sites with 119 codons, including 79 non-synonymous and 40 synonymous substitutions, were found in eight coding-regions in the SARS-CoV-2 genomes. Forty non-synonymous substitutions are potentially associated with virus adaptation. No combinations were detected. The 58 haplotypes (31 found in samples from China and 31 from outside China) were identified in 93 viral genomes under study and could be classified into five groups. By applying the reported bat coronavirus genome (bat-RaTG13-CoV) as the outgroup, we found that haplotypes H13 and H38 might be considered as ancestral haplotypes, and later H1 was derived from the intermediate haplotype H3. The population size of the SARS-CoV-2 was estimated to have undergone a recent expansion on 06 January 2020, and an early expansion on 08 December 2019. Furthermore, phyloepidemiologic approaches have recovered specific directions of human-to-human transmissions and the potential sources for international infected cases.
新型冠状病毒肺炎的爆发始于 2019 年 12 月中旬。截至 2020 年 2 月 29 日，SARS-CoV-2 (HCoV-19 / 2019-nCoV) 已感染全球 85 000 多人。在这项研究中，我们使用了来自GISAID EpiFlu TM数据库的SARS-CoV-2 的 93 个完整基因组来调查爆发前两个月SARS-CoV-2 的进化和人传人情况。我们构建了SARS-CoV-2 基因组的单倍型，进行了系统基因组分析，并估计了病毒的潜在种群大小变化。根据扩展参数tau (τ)，使用公式t = τ/2 u计算种群扩展日期。在SARS-CoV-2 基因组的 8 个编码区共发现了 120 个具有 119 个密码子的替换位点，包括 79 个非同义替换和 40 个同义替换。40 个非同义替换与病毒适应潜在相关。未检测到组合。在研究中的 93 个病毒基因组中鉴定了 58 个单倍型 (在来自中国的样本中发现 31 个，来自中国以外的 31 个)，可以分为 5 组。通过应用已报道的蝙蝠冠状病毒基因组 (bat-RaTG13-CoV) 作为外群，我们发现单倍型H13 和H38 可能被认为是祖先单倍型，后来H1 来源于中间单倍型h3。据估计，SARS-CoV-2 的人口规模最近于 2020 年 1 月 6 日进行了扩大，并于 2019 年 12 月 8 日提前扩大。此外，系统流行病学方法已经恢复了人传人的特定方向和国际感染病例的潜在来源。
METHODS::Since mid-December of 2019, coronavirus disease 2019 (COVID-19) infection has been spreading from Wuhan, China. The confirmed COVID-19 patients in South Korea are those who came from or visited China. As secondary transmissions have occurred and the speed of transmission is accelerating, there are rising concerns about community infections. The 54-year old male is the third patient diagnosed with COVID-19 infection in Korea. He is a worker for a clothing business and had mild respiratory symptoms and intermittent fever in the beginning of hospitalization, and pneumonia symptoms on chest computerized tomography scan on day 6 of admission. This patient caused one case of secondary transmission and three cases of tertiary transmission. Hereby, we report the clinical findings of the index patient who was the first to cause tertiary transmission outside China. Interestingly, after lopinavir/ritonavir (Kaletra, AbbVie) was administered, β-coronavirus viral loads significantly decreased and no or little coronavirus titers were observed.
METHODS::In December 2019, a novel coronavirus (2019-nCoV) caused an outbreak in Wuhan, China, and soon spread to other parts of the world. It was believed that 2019-nCoV was transmitted through respiratory tract and then induced pneumonia, thus molecular diagnosis based on oral swabs was used for confirmation of this disease. Likewise, patient will be released upon two times of negative detection from oral swabs. However, many coronaviruses can also be transmitted through oral-fecal route by infecting intestines. Whether 2019-nCoV infected patients also carry virus in other organs like intestine need to be tested. We conducted investigation on patients in a local hospital who were infected with this virus. We found the presence of 2019-nCoV in anal swabs and blood as well, and more anal swab positives than oral swab positives in a later stage of infection, suggesting shedding and thereby transmitted through oral-fecal route. We also showed serology test can improve detection positive rate thus should be used in future epidemiology. Our report provides a cautionary warning that 2019-nCoV may be shed through multiple routes.
METHODS::There is a current worldwide outbreak of a new type of coronavirus (2019-nCoV), which originated from Wuhan in China and has now spread to 17 other countries. Governments are under increased pressure to stop the outbreak spiraling into a global health emergency. At this stage, preparedness, transparency, and sharing of information are crucial to risk assessments and beginning outbreak control activities. This information should include reports from outbreak sites and from laboratories supporting the investigation. This paper aggregates and consolidates the virology, epidemiology, clinical management strategies from both English and Chinese literature, official news channels, and other official government documents. In addition, by fitting the number of infections with a single-term exponential model, we report that the infection is spreading at an exponential rate, with a doubling period of 1.8 days.