Introductions and early spread of SARS-CoV-2 in the New York City area

Gonzalez‐Reiche, Ana S.; Hernandez, Matthew M.; Sullivan, Mitchell J.; Ciferri, Brianne; Alshammary, Hala; Obla, Ajay; Fabre, Shelcie; Kleiner, Giulio; Polanco, Jose; Khan, Zenab; Alburquerque, Bremy; Guchte, Adriana van de; Dutta, Jayeeta; Francoeur, Nancy; Melo, Betsaida Salom; Oussenko, Irina; Deikus, Gintaras; Soto, Juan; Sridhar, Shwetha Hara; Wang, Ying-Chih; Twyman, Kathryn; Kasarskis, Andrew; Altman, Deena R.; Smith, Melissa; Sebra, Robert; Aberg, Judith A.; Krammer, Florian; Garcia-Sarstre, Adolfo; Łuksza, Marta; Patel, Gopi; Paniz‐Mondolfi, Alberto; Gitman, Melissa R.; Sordillo, Emilia Mia; Simon, Viviana; Bakel, Harm van

doi:10.1101/2020.04.08.20056929

Cited by 53 publications

(32 citation statements)

References 18 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The diversity present in our 320 viral genomes contrasts somewhat with data reported recently by Gonzalez-Reiche et al (30), who studied 84 SARS-CoV-2 isolates causing disease in patients in the New York City region. Those investigators concluded that the vast majority of disease was caused by progeny was not certified by peer review) is the author/funder.…”

Section: Discussioncontrasting

confidence: 96%

Molecular Architecture of Early Dissemination and Evolution of the SARS-CoV-2 Virus in Metropolitan Houston, Texas

Long

Olsen

Christensen

et al. 2020

Preprint

View full text Add to dashboard Cite

We sequenced the genomes of 320 SARS-CoV-2 strains from COVID-19 patients in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. These genomes were from the viruses causing infections in the earliest recognized phase of the pandemic affecting Houston. Substantial viral genomic diversity was identified, which we interpret to mean that the virus was introduced into Houston many times independently by individuals who had traveled from different parts of the country and the world. The majority of viruses are apparent progeny of strains derived from Europe and Asia. We found no significant evidence of more virulent viral types, stressing the linkage between severe disease, underlying medical conditions, and perhaps host genetics. We discovered a signal of selection acting on the spike protein, the primary target of massive vaccine efforts worldwide. The data provide a critical resource for assessing virus evolution, the origin of new outbreaks, and the effect of host immune response.SignificanceCOVID-19, the disease caused by the SARS-CoV-2 virus, is a global pandemic. To better understand the first phase of virus spread in metropolitan Houston, Texas, we sequenced the genomes of 320 SARS-CoV-2 strains recovered from COVID-19 patients early in the Houston viral arc. We identified no evidence that a particular strain or its progeny causes more severe disease, underscoring the connection between severe disease, underlying health conditions, and host genetics. Some amino acid replacements in the spike protein suggest positive immune selection is at work in shaping variation in this protein. Our analysis traces the early molecular architecture of SARS-CoV-2 in Houston, and will help us to understand the origin and trajectory of future infection spikes.

show abstract

Section: Discussioncontrasting

confidence: 96%

Molecular Architecture of Early Dissemination and Evolution of the SARS-CoV-2 Virus in Metropolitan Houston, Texas

Long

Olsen

Christensen

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…According to air transport statistics from the World Bank (https://data.worldbank.org) and the National Government We estimated these introductions could have occurred as early as mid-February, around 1 month before first cases were reported in Uruguay in March 13 th . This is in line with observations from other geographic regions, for example, in New York first cases were confirmed in March but a recent study suggested that initial virus introductions could be traced back to February 20 th [10]. Also, the virus was likely introduced in Europe by a traveler that arrived from Wuhan to France, but the recent identification of a group of ill Chinese tourists in France previous to this case supports earlier introductions [11].…”

Section: Discussionsupporting

confidence: 90%

Multiple introductions, regional spread and local differentiation during the first week of COVID-19 epidemic in Montevideo, Uruguay

Salazar

Díaz-Viraqué

Pereira-Gómez

et al. 2020

Preprint

View full text Add to dashboard Cite

Background. After its emergence in China in December 2019, the new coronavirus disease caused by SARS-CoV-2, has rapidly spread infecting more than 3 million people worldwide. South America is among the last regions hit by COVID-19 pandemic. In Uruguay, first cases were detected on March 13 th 2020 presumably imported by travelers returning from Europe. Methods.We performed whole-genome sequencing of 10 SARS-CoV-2 from patients diagnosed during the first week (March 16 th to 19 th ) of COVID-19 outbreak in Uruguay. Then, we applied genomic epidemiology using a global dataset to reconstruct the local spatio-temporal dynamics of SARS-CoV-2.Results. Our phylogeographic analysis showed three independent introductions of SARS-CoV-2 from different continents. Also, we evidenced regional circulation of viral strains originally detected in Spain.Introduction of SARS-CoV-2 in Uruguay could date back as early as Feb 20 th . Identification of specific mutations showed rapid local genetic differentiation.Conclusions. We evidenced early independent introductions of SARS-CoV-2 that likely occurred before first cases were detected. Our analysis set the bases for future genomic epidemiology studies to understand the dynamics of SARS-CoV-2 in Uruguay and the Latin America and the Caribbean region.

show abstract

“…Retrospective analysis could illuminate the degree of undetected community spreading on a per-region basis, to assess the efficacy of policy and behavioral changes, and prospectively to inform proactive management of an ongoing outbreak 15 . Two other groups have reported sequencing surveillance of nearby or overlapping regions 16,17 , and monitoring of a hospital system could be complemented by broader population studies 18 . Given the logistical and regulatory hurdles to establishing such surveillance, it is critical to have this infrastructure already in place for future waves of COVID-19 or other future pandemics.…”

Section: Discussionmentioning

confidence: 99%

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

Maurano

Ramaswami

Zappile

et al. 2020

Preprint

View full text Add to dashboard Cite

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 236 SARS-CoV2 sequences from cases in the New York City metropolitan area during the initial stages of the 2020 COVID-19 outbreak. The majority of cases throughout the region had no recent travel history or known exposure, and genetically linked cases were spread throughout the region. Comparison to global viral sequences showed that the majority were most related to cases from Europe. Our data are consistent with numerous seed transmissions from multiple sources and a prolonged period of unrecognized community spreading. This work highlights the complementary role of real-time genomic surveillance in addition to traditional epidemiological indicators.

show abstract

Introductions and early spread of SARS-CoV-2 in the New York City area

Cited by 53 publications

References 18 publications

Molecular Architecture of Early Dissemination and Evolution of the SARS-CoV-2 Virus in Metropolitan Houston, Texas

Molecular Architecture of Early Dissemination and Evolution of the SARS-CoV-2 Virus in Metropolitan Houston, Texas

Multiple introductions, regional spread and local differentiation during the first week of COVID-19 epidemic in Montevideo, Uruguay

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

Contact Info

Product

Resources

About