ABSTRACT
The resurgence of coronavirus disease 2019 (COVID-19) has been seen in many counties where outbreaks appear to be leveling off. While China experienced a dramatic decline of COVID-19 at the outset of 2020, regional outbreaks continuously emerged in recent months. In Guangzhou, a small outbreak emerged in March and April involving less than 100 residents, and a comprehensive and near-real-time genomic surveillance of SARS-CoV-2 was conducted. When confirmed cases among overseas travelers increased, public health authorities enhanced measures as shifting self-quarantine to central quarantine and SARS-CoV-2 testing for all overseas travelers. From 109 imported cases we found diverse viral variants distributing in the global viral phylogeny, which were usually shared within households but not among passengers on the same flight. Nonetheless, local transmission was predominately attributed to two specific variants imported from Africa, including the local cases who reported no direct/indirect contact with imported cases. The introducing events of the virus were identified or deduced before enhanced measures were taken. These results show that the interventions are effective in containing the spread of SARS-CoV-2, and also rule out the possibility of cryptic transmission of viral variants from the first wave in January and February. Moreover, we found that intra-host viral diversity was usually different between close contacts, implying a transmission bottleneck of SARS-CoV-2. Our study provides evidence and emphasizes the importance of controls for oversea travelers in the context of the pandemic, and exemplifies how viral genomic data facilitates COVID-19 surveillance and prevention.Funding: This study was supported by National Natural Science Foundation of China (31870079, 91953122, 31871326), National Science and Technology Major Project of the Ministry of Science and Technology of China (2017ZX10103011, 2018ZX10305410, 2018ZX10201001), Guangdong Provincial Novel Coronavirus Scientific and Technological Project (2020111107001), Guangdong Basic and Applied Basic Research Foundation (2020A1515010776 and 2020B1515020057) and the Beijing Nova Program (Z181100006218114 and Z181100006218110) to M.N. and P.L..Conflict of Interest: The authors declare no competing interests.Ethical Approval: This study was approved by the ethics committee of the Center for Disease Control and Prevention (CDC) of Guangzhou (GZCDC-ECHR-2020P0002). Written informed consent was obtained from patients about the surveillance and data related to disease control and further analysis. All information regarding individual persons has been anonymized in this study.
Subject(s)
COVID-19ABSTRACT
In the middle of March, the World Health Organization declared the outbreak of COVID-19 caused by SARS-CoV-2 infection a global pandemic. While China experienced a dramatic decline in daily growth rate of COVID-19, multiple importations of new cases from other countries and their related local infections caused a rapid rise. Between March 12 and April 15, we collected nasopharyngeal samples from 109 imported cases from 25 countries and 69 local cases in Guangzhou, China. In order to characterize the transmission patterns and genetic evolution of this virus among different populations, we sequenced the genome of SARS-CoV-2. The imported viral strains were assigned to lineages distributed in Europe (33.0%), America (17.4%), Africa (25.7%), or Southeast/West Asia (23.9%). Importantly, 10 imported cases from Africa formed two novel sub-lineages not identified in global tree previously. A detailed analysis showed that the imported viral strains from Philippines and Pakistan were closely related and within the same sub-lineage, whereas Ethiopia had varied lineages in the African phylogenetic tree. In spite of the diversity of imported SARS-CoV-2, 60 of 69 local infections could be traced back to two specific small lineages imported from Africa. A combined genetic and epidemiological analysis revealed a high-resolution transmission network of the imported SARS-CoV-2 in local communities, which might help inform the public health response and genomic surveillance in other cities and regions. Finally, we observed in-frame deletions on seven loci of SARS-CoV-2 genome, some of which were intra-host mutations, and they exhibited no enrichment on the S protein. Our findings provide new insight into the viral phylodynamics of SARS-CoV-2 and beta coronavirus.