Dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City

Dellicour, Simon; Hong, Samuel L.; Vrancken, Bram; Chaillon, Antoine; Gill, Mandev S.; Maurano, Matthew T.; Ramaswami, Sitharam; Zappile, Paul; Marier, Christian; Harkins, Gordon William; Baele, Guy; Duerr, Ralf; Heguy, Adriana

doi:10.1371/journal.ppat.1009571

Cited by 32 publications

(49 citation statements)

References 34 publications

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“…Some phylodynamic models allow for explicit modelling of sampling bias, and this has enhanced several SARS-CoV-2 studies 12 , 25 , 100 . In some cases, a single uniquely shared variant may be sufficient to determine the origin of a transmission chain 60 , 101 , and in studies in which one or several regions or periods were poorly sampled, unsampled individuals have been modelled and added to analyses 102 , or unobserved ancestral locations jointly inferred using phylogenies 103 . Delays between case detection 104 and genome sequence availability, as well as insufficiently dense sampling, can hinder outbreak analysis.…”

Section: Tackling Sampling Bias In Genomic Epidemiologymentioning

confidence: 99%

Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic

et al. 2022

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Determining the transmissibility, prevalence and patterns of movement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is central to our understanding of the impact of the pandemic and to the design of effective control strategies. Phylogenies (evolutionary trees) have provided key insights into the international spread of SARS-CoV-2 and enabled investigation of individual outbreaks and transmission chains in specific settings. Phylodynamic approaches combine evolutionary, demographic and epidemiological concepts and have helped track virus genetic changes, identify emerging variants and inform public health strategy. Here, we review and synthesize studies that illustrate how phylogenetic and phylodynamic techniques were applied during the first year of the pandemic, and summarize their contributions to our understanding of SARS-CoV-2 transmission and control.

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Section: Tackling Sampling Bias In Genomic Epidemiologymentioning

confidence: 99%

Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic

et al. 2022

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“…We modelled the phylogenetic diffusion and spread of these lineages within Brazil by analysing localized transmission (between Brazilian regions) using a flexible relaxed random walk (RRW) diffusion model 51,52 that accommodates branch-specific variation in rates of dispersal with a Cauchy distribution and a jitter window site of 0.01 52 . The choice of Cauchy distribution was based on recent studies demonstrating that it is successful for this kind of analyses based on genomes of SARS-CoV-2 and its variants 4,50,[54][55][56] . For each sequence, latitude and longitude coordinates were attributed.…”

Section: S7)mentioning

confidence: 99%

Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil

Giovanetti

Slavov

Fonseca

et al. 2021

Preprint

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Brazil has experienced some of the highest numbers of COVID-19 infections and deaths globally and made Latin America a pandemic epicenter from May 2021. Although SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, important gaps remain in our understanding of local virus transmission dynamics. Here, we describe the genomic epidemiology of SARS-CoV-2 using near-full genomes sampled from 27 Brazilian states and an adjacent country - Paraguay. We show that the early stage of the pandemic in Brazil was characterised by the co-circulation of multiple viral lineages, linked to multiple importations predominantly from Europe, and subsequently characterized by large local transmission clusters. As the epidemic progressed, the absence of effective restriction measures led to the local emergence and international spread of Variants of Concern (VOC) and under monitoring (VUM), including the Gamma (P.1) and Zeta (P.2) variants. In addition, we provide a preliminary genomic overview of the epidemic in Paraguay, showing evidence of importation from Brazil. These data reinforce the need for the implementation of widespread genomic surveillance in South America as a toolkit for pandemic monitoring and providing a means to follow the real-time spread of emerging SARS-CoV-2 variants with possible implications for public health and immunization strategies.

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“…While the outbreak in Italy has been traced phylogenetically to the Lombardy region, it remains unclear how exactly it started out and spread ( 62 ). A more recent phylogenetic study of viral samples from New York state during March–May 2020 confirmed the importance of Queens as a major transmission hub and provided supporting evidence of widespread geographic dispersion ( 63 ). Only 22% of the samples from New York City, however, were collected before the last week of March ( 64 ).…”

Section: Discussionmentioning

confidence: 87%

Critical Role of the Subways in the Initial Spread of SARS-CoV-2 in New York City

Harris

2021

Front. Public Health

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We studied the possible role of the subways in the spread of SARS-CoV-2 in New York City during late February and March 2020. Data on cases and hospitalizations, along with phylogenetic analyses of viral isolates, demonstrate rapid community transmission throughout all five boroughs within days. The near collapse of subway ridership during the second week of March was followed within 1–2 weeks by the flattening of COVID-19 incidence curve. We observed persistently high entry into stations located along the subway line serving a principal hotspot of infection in Queens. We used smartphone tracking data to estimate the volume of subway visits originating from each zip code tabulation area (ZCTA). Across ZCTAs, the estimated volume of subway visits on March 16 was strongly predictive of subsequent COVID-19 incidence during April 1–8. In a spatial analysis, we distinguished between the conventional notion of geographic contiguity and a novel notion of contiguity along subway lines. We found that the March 16 subway-visit volume in subway-contiguous ZCTAs had an increasing effect on COVID-19 incidence during April 1–8 as we enlarged the radius of influence up to 5 connected subway stops. By contrast, the March 31 cumulative incidence of COVID-19 in geographically-contiguous ZCTAs had an increasing effect on subsequent COVID-19 incidence as we expanded the radius up to three connected ZCTAs. The combined evidence points to the initial citywide dissemination of SARS-CoV-2 via a subway-based network, followed by percolation of new infections within local hotspots.

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Dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City

Cited by 32 publications

References 34 publications

Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic

Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic

Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil

Critical Role of the Subways in the Initial Spread of SARS-CoV-2 in New York City

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