The emergence of SARS-CoV-2 in Europe and North America

Worobey, Michael; Pekar, Jonathan E.; Larsen, Brendan B.; Nelson, Martha I.; Hill, Verity; Joy, Jeffrey B.; Rambaut, Andrew; Suchard, Marc A.; Wertheim, Joel O.; Lemey, Philippe

doi:10.1126/science.abc8169

Cited by 356 publications

(400 citation statements)

References 33 publications

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“…Finally, we note that attribution of an Israeli sequence to a U.S. clade was normally based on two to four shared mutations, making it exceedingly unlikely that parallel independent substitutions occurred that could alternatively explain these patterns. However, we acknowledge that additional sequencing may change some of the inferences we make here, as has been shown elsewhere 20 .…”

Section: Resultsmentioning

confidence: 66%

Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel

et al. 2020

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Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequence 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. We find that travelers returning from the United States of America significantly contributed to viral spread in Israel, more than their proportion in incoming infected travelers. Using phylodynamic analysis, we estimate that the basic reproduction number of the virus was initially around 2.5, dropping by more than two-thirds following the implementation of social distancing measures. We further report high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 2-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings demonstrate the effectiveness of social distancing measures for reducing viral spread.

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Section: Resultsmentioning

confidence: 66%

Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel

et al. 2020

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“…Although phylogenetic trees are widely used for summarizing genealogies, a naive interpretation of results obtained from phylogenetic trees alone may not provide accurate conclusions. The low rate of SARS-CoV-2 evolution and the sampling bias of genomes can often lead to spurious conclusions (11), suggesting that it does not imply the direction of transmission from one to another.…”

Section: Resultsmentioning

confidence: 99%

A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan

Sekizuka

Itokawa

Hashino

et al. 2020

mSphere

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After the first case of coronavirus disease 2019 (COVID-19) in Japan on 15 January 2020, multiple nationwide COVID-19 clusters were identified by the end of February. The Japanese government focused on mitigating the emerging COVID-19 clusters by conducting active nationwide epidemiological surveillance. However, an increasing number of cases continued to appear until early April 2020, many with unclear infection routes and no recent history of travel outside Japan. We aimed to evaluate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequences from the COVID-19 cases that appeared until early April 2020 and to characterize their genealogical networks in order to demonstrate possible routes of spread in Japan. Nasopharyngeal specimens were collected from patients, and reverse transcription-quantitative PCR tests for SARS-CoV-2 were performed. Positive RNA samples were subjected to whole-genome sequencing, and a haplotype network analysis was performed. Some of the primary clusters identified during January and February 2020 in Japan descended directly from the Wuhan-Hu-1-related isolates from China and other distinct clusters. Clusters were almost contained until mid-March; the haplotype network analysis demonstrated that the COVID-19 cases from late March through early April may have created an additional large cluster related to the outbreak in Europe, leading to additional spread within Japan. In conclusion, genome surveillance has suggested that there were at least two distinct SARS-CoV-2 introductions into Japan from China and other countries. IMPORTANCE This study aimed to evaluate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequences from COVID-19 cases and to characterize their genealogical networks to demonstrate possible routes of spread in Japan. We found that there were at least two distinct SARS-CoV-2 introductions into Japan, initially from China and subsequently from other countries, including Europe. Our findings can help understand how SARS-CoV-2 entered Japan and contribute to increased knowledge of SARS-CoV-2 in Asia and its association with implemented stay-at-home/shelter-in-place/self-restraint/lockdown measures. This study suggested that it is necessary to formulate a more efficient containment strategy using real-time genome surveillance to support epidemiological field investigations in order to highlight potential infection linkages and mitigate the next wave of COVID-19 in Japan.

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“…Although our estimate of 109 introductions is thus likely to underestimate the total number of introductions, the genomic data are sufficient-ly informative to outline an unrecognized early spread in February which enabled rapid development of the outbreak in March. Further analysis (Worobey et al 2020) and sequencing of archival samples will be needed to refine assessments of the initial spread.…”

Section: Discussionmentioning

confidence: 99%

“…Collaborative development of targeted sequencing protocols (Quick et al 2017;ARTIC Network), open sharing of sequences through the GISAID (Global Initiative on Sharing All Influenza Data) repository (Shu and McCauley 2017), and rapid analysis and visualization of viral phylogenies using Nextstrain (Hadfield et al 2018) have provided unprecedented and timely insights into the spread of the pandemic. Notably, community transmission was identified using surveillance sequencing in the Seattle area in time to implement preventative measures (Bedford et al 2020;Worobey et al 2020).…”

Section: Introductionmentioning

confidence: 99%

Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region

et al. 2020

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Effective public response to a pandemic relies upon accurate measurement of the extent and dynamics of an outbreak. Viral genome sequencing has emerged as a powerful approach to link seemingly unrelated cases, and large-scale sequencing surveillance can inform on critical epidemiological parameters. Here, we report the analysis of 864 SARS-CoV-2 sequences from cases in the New York City metropolitan area during the COVID-19 outbreak in Spring 2020. The majority of cases had no recent travel history or known exposure, and genetically linked cases were spread throughout the region. Comparison to global viral sequences showed that early transmission was most linked to cases from Europe. Our data are consistent with numerous seeds from multiple sources and a prolonged period of unrecognized community spreading. This work highlights the complementary role of genomic surveillance in addition to traditional epidemiological indicators.

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The emergence of SARS-CoV-2 in Europe and North America

Cited by 356 publications

References 33 publications

Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel

Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel

A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan

Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region

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