The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing

The recent emergence of a coronavirus (SARS-CoV-2), first identified in the Chinese city of Wuhan in December 2019, has had major public health and economic consequences. Although 61,888 confirmed cases were reported in Brazil by 28 April 2020, little is known about the SARS-CoV-2 epidemic in this country. To better understand the recent epidemic in the second most populous state in southeast Brazil - Minas Gerais (MG) - we sequenced 40 complete SARS-CoV-2 genomes from MG cases and examined epidemiological data from three Brazilian states. Both the genome analyses and the geographical distribution of reported cases indicate for multiple independent introductions into MG. Epidemiological estimates of the reproductive number (R) using different data sources and theoretical assumptions suggest the potential for sustained virus transmission despite a reduction in R from the first reported case to the end of April 2020. The estimated date of SARS-CoV-2 introduction into Brazil was consistent with epidemiological data from the first case of a returned traveller from Lombardy, Italy. These findings highlight the nature of the COVID-19 epidemic in MG and reinforce the need for real-time and continued genomic surveillance strategies to better understand and prepare for the epidemic spread of emerging viral pathogens..

2019年12月在中国武汉首次发现的冠状病毒（SARS-CoV-2）的近期暴发，已对公共卫生与社会经济造成重大影响。截至2020年4月28日，巴西报告的确诊病例已达61888例，但学界对该国境内的SARS-CoV-2疫情认知仍十分有限。为深入了解巴西东南部第二大人口州——米纳斯吉拉斯州（Minas Gerais，MG）的近期疫情态势，本研究对来自该州的40株完整SARS-CoV-2基因组进行测序，并分析了巴西三个州的流行病学数据。基因组分析与报告病例的地理分布均显示，SARS-CoV-2曾多次独立传入米纳斯吉拉斯州。基于不同数据源与理论假设得出的再生数（R）流行病学估算结果显示，尽管自首例报告病例至2020年4月底，R值有所下降，但病毒仍存在持续传播的潜在风险。SARS-CoV-2传入巴西的估算时间，与意大利伦巴第大区返回旅行者的首例确诊病例的流行病学数据相吻合。本研究结果阐明了米纳斯吉拉斯州新冠肺炎（COVID-19）的流行特征，同时强调需开展实时持续的基因组监测策略，以更好地认识新兴病毒病原体的疫情传播态势并做好应对准备。