Dataset Information

Cryptic transmission of SARS-CoV-2 in Washington State.

ABSTRACT: Following its emergence in Wuhan, China, in late November or early December 2019, the SARS-CoV-2 virus has rapidly spread throughout the world. On March 11, 2020, the World Health Organization declared Coronavirus Disease 2019 (COVID-19) a pandemic. Genome sequencing of SARS-CoV-2 strains allows for the reconstruction of transmission history connecting these infections. Here, we analyze 346 SARS-CoV-2 genomes from samples collected between 20 February and 15 March 2020 from infected patients in Washington State, USA. We found that the large majority of SARS-CoV-2 infections sampled during this time frame appeared to have derived from a single introduction event into the state in late January or early February 2020 and subsequent local spread, strongly suggesting cryptic spread of COVID-19 during the months of January and February 2020, before active community surveillance was implemented. We estimate a common ancestor of this outbreak clade as occurring between 18 January and 9 February 2020. From genomic data, we estimate an exponential doubling between 2.4 and 5.1 days. These results highlight the need for large-scale community surveillance for SARS-CoV-2 introductions and spread and the power of pathogen genomics to inform epidemiological understanding.

SUBMITTER: Bedford T

PROVIDER: S-EPMC7276023 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Cryptic transmission of SARS-CoV-2 in Washington State.

Bedford Trevor T Greninger Alexander L AL Roychoudhury Pavitra P Starita Lea M LM Famulare Michael M Huang Meei-Li ML Nalla Arun A Pepper Gregory G Reinhardt Adam A Xie Hong H Shrestha Lasata L Nguyen Truong N TN Adler Amanda A Brandstetter Elisabeth E Cho Shari S Giroux Danielle D Han Peter D PD Fay Kairsten K Frazar Chris D CD Ilcisin Misja M Lacombe Kirsten K Lee Jover J Kiavand Anahita A Richardson Matthew M Sibley Thomas R TR Truong Melissa M Wolf Caitlin R CR Nickerson Deborah A DA Rieder Mark J MJ Englund Janet A JA Hadfield James J Hodcroft Emma B EB Huddleston John J Moncla Louise H LH Müller Nicola F NF Neher Richard A RA Deng Xianding X Gu Wei W Federman Scot S Chiu Charles C Duchin Jeff J Gautom Romesh R Melly Geoff G Hiatt Brian B Dykema Philip P Lindquist Scott S Queen Krista K Tao Ying Y Uehara Anna A Tong Suxiang S MacCannell Duncan D Armstrong Gregory L GL Baird Geoffrey S GS Chu Helen Y HY Shendure Jay J Jerome Keith R KR

medRxiv : the preprint server for health sciences 20200406

Following its emergence in Wuhan, China, in late November or early December 2019, the SARS-CoV-2 virus has rapidly spread throughout the world. On March 11, 2020, the World Health Organization declared Coronavirus Disease 2019 (COVID-19) a pandemic. Genome sequencing of SARS-CoV-2 strains allows for the reconstruction of transmission history connecting these infections. Here, we analyze 346 SARS-CoV-2 genomes from samples collected between 20 February and 15 March 2020 from infected patients in ...[more]

PMID: 32511596

Similar Datasets

Project description:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that was first reported in Wuhan, China in December of 2019 and has since caused a global pandemic resulting in millions of deaths and tens of millions of patients testing positive for infection. Analysis of different viral strains has identified a D614G change in the spike protein that is correlated with the virus becoming more transmissible. While studies have shown G614 viruses to be more transmissible, the effects of this mutation on the host response, especially on the cellular level, are yet to be fully elucidated. In this experiment we infected NHBE cells with the Washington (D614) strain or the New York (G614) strains of SARS-CoV-2. We generated RNA sequencing data at three different time points to improve our understanding of how the intracellular host response differs between infections with these two strains. We analyzed these data with a bioinformatics pipeline that identifies differentially expressed genes, enriched Gene Ontology terms and dysregulated signaling pathways. We detected over 2,000 differentially expressed genes, over 600 Gene Ontology terms, and 29 affected pathways between the two treatments. Many of these entities play a role in immune signaling and response. When comparing the different strains and different time points we found more overall similarities between matched time points than across different time points with the same strain. When specifically comparing the affected pathways, we saw that the 24hr time point of the New York strain was more similar to the 12hr time point of the Washington strain with a large number of pathways related to translation being inhibited in both strains at these time points. These results suggest that D614G substitution in the spike protein, combined with other nonsynonymous changes in the viral gene products cause distinct responses in infected host cells, especially relating to how quickly translation is dysregulated after infection. These observed differences in the intracellular host response to infection could play a role in driving the increase in pathogenicity and mortality seen in the New York outbreaks versus the Washington outbreaks at the beginning of the SARS-CoV-2 pandemic.

Dataset Information

Cryptic transmission of SARS-CoV-2 in Washington State.

Publications

Cryptic transmission of SARS-CoV-2 in Washington State.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure