Phylogenomic tracing of asymptomatic transmission in a COVID-19 outbreak

Ju Zhang; Nan Ding; Yangzi Song; Rui Song; Yang Pan; Linghang Wang; Shuo Yan; Qi Wang; Shanfang Ma; Lirong Wei; Fengting Yu; Lianhe Lu; Fujie Zhang; Chen Chen; Hui Zeng

doi:10.1016/j.xinn.2021.100099

Phylogenomic tracing of asymptomatic transmission in a COVID-19 outbreak

Innovation (Camb). 2021 May 28;2(2):100099. doi: 10.1016/j.xinn.2021.100099. Epub 2021 Mar 22.

Authors

Ju Zhang^{1

2}, Nan Ding^{1

2}, Yangzi Song^{1

2}, Rui Song¹, Yang Pan³, Linghang Wang^{1

2}, Shuo Yan¹, Qi Wang¹, Shanfang Ma¹, Lirong Wei¹, Fengting Yu^{1

2}, Lianhe Lu¹, Fujie Zhang^{1

2}, Chen Chen^{1

2}, Hui Zeng^{1

2}

Affiliations

¹ Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China.
² Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, China.
³ Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing 100013, China.

Abstract

SARS-CoV-2 has caused over 100 million deaths and continues to spread rapidly around the world. Asymptomatic transmission of SARS-CoV-2 is the Achilles' heel of COVID-19 public health control measures. Phylogenomic data on SARS-CoV-2 could provide more direct information about asymptomatic transmission. In this study, using a novel MINERVA sequencing technology, we traced asymptomatic transmission of COVID-19 patients in Beijing, China. One hundred and seventy-eight close contacts were quarantined, and 14 COVID-19 patients were laboratory confirmed by RT-PCR. We provide direct phylogenomic evidence of asymptomatic transmission by constructing the median joining network in the cluster. These data could help us to determine whether the current symptom-based screening should cover asymptomatic persons.

Keywords: COVID-19; SARS-CoV-2; asymptomatic transmission; outbreak; phylogenomic.