scholarly journals Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events

2020 ◽  
Author(s):  
Jacob Lemieux ◽  
Katherine J Siddle ◽  
Bennett M. Shaw ◽  
Christine Loreth ◽  
Stephen Schaffner ◽  
...  
Keyword(s):  
Genetic Data ◽  
The United States ◽  
Transmission Dynamics ◽  
Contact Tracing ◽  
Major Contributor ◽  
Nursing Facility ◽  
Rapid Spread ◽  
Community Transmission ◽  
New Mutations

SARS-CoV-2 has caused a severe, ongoing outbreak of COVID-19 in Massachusetts with 111,070 confirmed cases and 8,433 deaths as of August 1, 2020. To investigate the introduction, spread, and epidemiology of COVID-19 in the Boston area, we sequenced and analyzed 772 complete SARS-CoV-2 genomes from the region, including nearly all confirmed cases within the first week of the epidemic and hundreds of cases from major outbreaks at a conference, a nursing facility, and among homeless shelter guests and staff. The data reveal over 80 introductions into the Boston area, predominantly from elsewhere in the United States and Europe. We studied two superspreading events covered by the data, events that led to very different outcomes because of the timing and populations involved. One produced rapid spread in a vulnerable population but little onward transmission, while the other was a major contributor to sustained community transmission, including outbreaks in homeless populations, and was exported to several other domestic and international sites. The same two events differed significantly in the number of new mutations seen, raising the possibility that SARS-CoV-2 superspreading might encompass disparate transmission dynamics. Our results highlight the failure of measures to prevent importation into MA early in the outbreak, underscore the role of superspreading in amplifying an outbreak in a major urban area, and lay a foundation for contact tracing informed by genetic data.

scholarly journals A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage

2020 ◽  
Author(s):  
Xianding Deng ◽  
Wei Gu ◽  
Scot Federman ◽  
Louis du Plessis ◽  
Oliver G. Pybus ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
The United States ◽  
Contact Tracing ◽  
Northern California ◽  
Cruise Ship ◽  
Multiple Introductions ◽  
Genomic Epidemiology ◽  
The Usa ◽  
Community Transmission ◽  
Virus Genomes

AbstractThe COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has spread globally, resulting in >300,000 reported cases worldwide as of March 21st, 2020. Here we investigate the genetic diversity and genomic epidemiology of SARS-CoV-2 in Northern California using samples from returning travelers, cruise ship passengers, and cases of community transmission with unclear infection sources. Virus genomes were sampled from 29 patients diagnosed with COVID-19 infection from Feb 3rd through Mar 15th. Phylogenetic analyses revealed at least 8 different SARS-CoV-2 lineages, suggesting multiple independent introductions of the virus into the state. Virus genomes from passengers on two consecutive excursions of the Grand Princess cruise ship clustered with those from an established epidemic in Washington State, including the WA1 genome representing the first reported case in the United States on January 19th. We also detected evidence for presumptive transmission of SARS-CoV-2 lineages from one community to another. These findings suggest that cryptic transmission of SARS-CoV-2 in Northern California to date is characterized by multiple transmission chains that originate via distinct introductions from international and interstate travel, rather than widespread community transmission of a single predominant lineage. Rapid testing and contact tracing, social distancing, and travel restrictions are measures that will help to slow SARS-CoV-2 spread in California and other regions of the USA.

scholarly journals Political Ideology and the Outbreak of COVID-19 in the United States

2020 ◽  
Author(s):  
Daniel L. Rosenfeld
Keyword(s):  
United States ◽  
Political Ideology ◽  
State Level ◽  
The United States ◽  
The State ◽  
The Novel ◽  
Unique Role ◽  
Rapid Spread ◽  
Novel Coronavirus

At the state level within the United States, did political ideology predict the outbreak of the novel coronavirus (COVID-19)? Throughout March 2020, the United States became the epicenter of the COVID-19 pandemic, recording the most cases of any country worldwide. The current research found that, at the state level within the United States, more conservative political ideology predicted delayed implementation of stay-at-home orders and more rapid spread of COVID-19. Effects were significant across two distinct operationalizations of political ideology and held over and above relevant covariates, suggesting a potentially unique role of political ideology in the United States’ COVID-19 outbreak. Considering political ideological factors may offer valuable insights into epidemiological processes surrounding COVID-19.

scholarly journals COVID-19: Recent updates on SARS-CoV-2 and Preventing its Community Transmission in India by 21 Days Lockdown

2020 ◽  
Vol 14 (suppl 1) ◽  
pp. 921-929
Author(s):  
Satyajeet K. Pawar ◽  
Shivaji T. Mohite
Keyword(s):  
Hubei Province ◽  
Hand Washing ◽  
Contact Tracing ◽  
Wuhan City ◽  
Social Distancing ◽  
First Case ◽  
Rapid Spread ◽  
Community Transmission ◽  
Almost All

The current pandemic of COVID-19 has caused havoc all over world since its emergence and rapid spread. Within three months the virus SARS-CoV-2 which was isolated from pneumonia cases in Wuhan City, Hubei Province, China in late December 2019, has affected almost all countries. India reported its first case of COVID-19 from state of Kerala on January 30, 2020, a student returned from city of Wuhan. Till date in India the disease had affected 12759 patients with 420 deaths. With every passing day the mysterious virus is been uncovered with its unique characteristics enabling the researcher to unfold the various methods including hand washing and social distancing to curtail the pandemic. Measures like 21 days lockdown to certain extent are effective but considering asymptomatic spreaders, extended measured lockdowns will be useful in the long term war against COVID-19. Till the vaccine and therapeutic solutions are derived, answer to pandemic and SARS-CoV-2 lies in lockdown, social distancing, contact tracing and containment.

scholarly journals Introduction, Transmission Dynamics, and Fate of Early SARS-CoV-2 Lineages in Santa Clara County, California

2021 ◽  
Author(s):  
Elsa Villarino ◽  
Xianding Deng ◽  
Carol A Kemper ◽  
Michelle A Jorden ◽  
Brandon Bonin ◽  
...  
Keyword(s):  
Public Health ◽  
United States ◽  
Viral Genome ◽  
Public Health Intervention ◽  
The United States ◽  
Transmission Dynamics ◽  
Contact Tracing ◽  
Clinical Samples ◽  
Post Mortem ◽  
Santa Clara County

Abstract We combined viral genome sequencing with contact tracing to investigate introduction and evolution of SARS-CoV-2 lineages in Santa Clara County, California from January 27 to March 21, 2020. Of 558 persons with COVID-19, 101 genomes from 143 available clinical samples comprised 17 different lineages including SCC1 (n=41), WA1 (n=9, including the first 2 reported deaths in the United States, diagnosed post-mortem), D614G (n=4), ancestral Wuhan Hu-1 (n=21), and 13 others (n=26). Public health intervention may have curtailed the persistence of lineages that appeared transiently during February–March. By August, only D614G lineages introduced after March 21 were circulating in SCC.

scholarly journals Containing Covid-19 outbreaks with spatially targeted short-term lockdowns and mass-testing

2020 ◽  
Author(s):  
Justin Alsing ◽  
Thomas Kirk ◽  
Naïri Usher ◽  
Philip JD Crowley
Keyword(s):  
Process Model ◽  
Interaction Model ◽  
Transmission Dynamics ◽  
Contact Tracing ◽  
Moderate Increase ◽  
Mobility Patterns ◽  
Social Distancing ◽  
Targeted Interventions ◽  
Community Transmission ◽  
The Uk

ABSTRACTWe assess the efficacy of spatially targeted lockdown or mass-testing and case-isolation in individual communities, as a compliment to contact-tracing and social-distancing, for containing SARS-CoV-2 outbreaks. Using the UK as a case study, we construct a stochastic branching process model for the virus transmission, embedded on a network interaction model encoding mobility patterns in the UK. The network model is based on commuter data from the 2011 census, a catchment area model for schools, and a phenomenological model for mobility and interactions outside of work, school, and the home. We show that for outbreak scenarios where contact-tracing and moderate social distancing alone provide suppression but do not contain the spread, targeted lockdowns or mass-testing interventions at the level of individual communities (with just a few thousand inhabitants) can be effective at containing outbreaks. For spatially targeted mass-testing, a moderate increase in testing capacity would be required (typically < 40000 additional tests per day), while for local lockdowns we find that only a small fraction (typically < 0.1%) of the population needs to be locked down at any one time (assuming that one third of transmission occurs in the home, at work or school, and out in the wider community respectively). The efficacy of spatially targeted interventions is contingent on an appreciable fraction of transmission events occurring within (relative to across) communities. Confirming the efficacy of community-level interventions therefore calls for detailed investigation of spatial transmission patterns for SARS-CoV-2, accounting for sub-community-scale transmission dynamics, and changes in mobility patterns due to the presence of other containment measures (such as social distancing and travel restrictions).Disclaimer: We stress that this is a working paper where results are preliminary and subject to change. In particular, we note that the efficacy of spatially targeted interventions are sensitive to the relative proportions of intra-versus inter-community transmission (for a given definition of community boundaries), which in turn is sensitive to the assumptions about the transmission dynamics across different contexts. Whilst the assumptions made here about transmission across contexts are motivated, we are currently updating our model to make the estimated inter- and intra-community transmission rates as robust as possible, as well as running a comprehensive suite of sensitivity tests and different outbreak scenarios.

scholarly journals Using influenza surveillance networks to estimate state-specific prevalence of SARS-CoV-2 in the United States

2020 ◽  
Vol 12 (554) ◽  
pp. eabc1126 ◽  
Author(s):  
Justin D. Silverman ◽  
Nathaniel Hupert ◽  
Alex D. Washburne
Keyword(s):  
United States ◽  
False Negative ◽  
Emerging Infectious Diseases ◽  
The United States ◽  
Influenza Surveillance ◽  
Chain Reaction ◽  
Seroprevalence Data ◽  
Rapid Spread ◽  
Community Transmission ◽  
Polymerase Chain

Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections to date has relied heavily on reverse transcription polymerase chain reaction testing. However, limited test availability, high false-negative rates, and the existence of asymptomatic or subclinical infections have resulted in an undercounting of the true prevalence of SARS-CoV-2. Here, we show how influenza-like illness (ILI) outpatient surveillance data can be used to estimate the prevalence of SARS-CoV-2. We found a surge of non-influenza ILI above the seasonal average in March 2020 and showed that this surge correlated with coronavirus disease 2019 (COVID-19) case counts across states. If one-third of patients infected with SARS-CoV-2 in the United States sought care, this ILI surge would have corresponded to more than 8.7 million new SARS-CoV-2 infections across the United States during the 3-week period from 8 to 28 March 2020. Combining excess ILI counts with the date of onset of community transmission in the United States, we also show that the early epidemic in the United States was unlikely to have been doubling slower than every 4 days. Together, these results suggest a conceptual model for the COVID-19 epidemic in the United States characterized by rapid spread across the United States with more than 80% infected individuals remaining undetected. We emphasize the importance of testing these findings with seroprevalence data and discuss the broader potential to use syndromic surveillance for early detection and understanding of emerging infectious diseases.

scholarly journals Effectiveness of Intervention Strategies on MERS-CoV Transmission Dynamics in South Korea, 2015: Simulations on the Network Based on the Real-World Contact Data

2021 ◽  
Vol 18 (7) ◽  
pp. 3530
Author(s):  
Yunhwan Kim ◽  
Hohyung Ryu ◽  
Sunmi Lee
Keyword(s):  
South Korea ◽  
Real World ◽  
Intervention Strategies ◽  
Transmission Dynamics ◽  
Contact Tracing ◽  
Agent Based ◽  
The Real ◽  
Scale Free ◽  
Contact Data

The MERS-CoV spread in South Korea in 2015 was not only the largest outbreak of MERS-CoV in the region other than the Middle East but also a historic epidemic in South Korea. Thus, investigation of the MERS-CoV transmission dynamics, especially by agent-based modeling, would be meaningful for devising intervention strategies for novel infectious diseases. In this study, an agent-based model on MERS-CoV transmission in South Korea in 2015 was built and analyzed. The prominent characteristic of this model was that it built the simulation environment based on the real-world contact tracing network, which can be characterized as being scale-free. In the simulations, we explored the effectiveness of three possible intervention scenarios; mass quarantine, isolation, and isolation combined with acquaintance quarantine. The differences in MERS-CoV transmission dynamics by the number of links of the index case agent were examined. The simulation results indicate that isolation combined with acquaintance quarantine is more effective than others, and they also suggest the key role of super-spreaders in MERS-CoV transmission.

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

2020 ◽  
Author(s):  
Ana S. Gonzalez-Reiche ◽  
Matthew M. Hernandez ◽  
Mitchell Sullivan ◽  
Brianne Ciferri ◽  
Hala Alshammary ◽  
...  
Keyword(s):  
United States ◽  
New York ◽  
New York City ◽  
Phylogenetic Analysis ◽  
Metropolitan Area ◽  
York City ◽  
The United States ◽  
Rapid Spread ◽  
Community Transmission ◽  
The City

ABSTRACTNew York City (NYC) has emerged as one of the epicenters of the current SARS-CoV2 pandemic. To identify the early events underlying the rapid spread of the virus in the NYC metropolitan area, we sequenced the virus causing COVID19 in patients seeking care at the Mount Sinai Health System. Phylogenetic analysis of 84 distinct SARS-CoV2 genomes indicates multiple, independent but isolated introductions mainly from Europe and other parts of the United States. Moreover, we find evidence for community transmission of SARS-CoV2 as suggested by clusters of related viruses found in patients living in different neighborhoods of the city.

scholarly journals Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events

Science ◽  
2020 ◽  
pp. eabe3261 ◽  
Author(s):  
Jacob E. Lemieux ◽  
Katherine J. Siddle ◽  
Bennett M. Shaw ◽  
Christine Loreth ◽  
Stephen F. Schaffner ◽  
...  
Keyword(s):  
International Business ◽  
Skilled Nursing Facility ◽  
Transmission Dynamics ◽  
Nursing Facility ◽  
Skilled Nursing ◽  
Genomic Epidemiology ◽  
Community Transmission ◽  
Rapid Transmission ◽  
The Impact ◽  
Significant Mortality

Analysis of 772 complete SARS-CoV-2 genomes from early in the Boston area epidemic revealed numerous introductions of the virus, a small number of which led to most cases. The data revealed two superspreading events. One, in a skilled nursing facility, led to rapid transmission and significant mortality in this vulnerable population but little broader spread, while other introductions into the facility had little effect. The second, at an international business conference, produced sustained community transmission and was exported, resulting in extensive regional, national, and international spread. The two events also differed significantly in the genetic variation they generated, suggesting varying transmission dynamics in superspreading events. Our results show how genomic epidemiology can help understand the link between individual clusters and wider community spread.

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