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1.
Cell ; 185(3): 485-492.e10, 2022 02 03.
Article in English | MEDLINE | ID: covidwho-1588148

ABSTRACT

An outbreak of over 1,000 COVID-19 cases in Provincetown, Massachusetts (MA), in July 2021-the first large outbreak mostly in vaccinated individuals in the US-prompted a comprehensive public health response, motivating changes to national masking recommendations and raising questions about infection and transmission among vaccinated individuals. To address these questions, we combined viral genomic and epidemiological data from 467 individuals, including 40% of outbreak-associated cases. The Delta variant accounted for 99% of cases in this dataset; it was introduced from at least 40 sources, but 83% of cases derived from a single source, likely through transmission across multiple settings over a short time rather than a single event. Genomic and epidemiological data supported multiple transmissions of Delta from and between fully vaccinated individuals. However, despite its magnitude, the outbreak had limited onward impact in MA and the US overall, likely due to high vaccination rates and a robust public health response.


Subject(s)
COVID-19/epidemiology , COVID-19/immunology , COVID-19/transmission , SARS-CoV-2/genetics , SARS-CoV-2/immunology , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/virology , Child , Child, Preschool , Contact Tracing/methods , Disease Outbreaks , Female , Genome, Viral , Humans , Infant , Infant, Newborn , Male , Massachusetts/epidemiology , Middle Aged , Molecular Epidemiology , Phylogeny , SARS-CoV-2/classification , Vaccination , Whole Genome Sequencing , Young Adult
2.
Science ; 371(6529)2021 02 05.
Article in English | MEDLINE | ID: covidwho-1388436

ABSTRACT

Analysis of 772 complete severe acute respiratory syndrome coronavirus 2 (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, whereas 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 substantially in the genetic variation they generated, suggesting varying transmission dynamics in superspreading events. Our results show how genomic epidemiology can help to understand the link between individual clusters and wider community spread.


Subject(s)
COVID-19/epidemiology , Genome, Viral , Phylogeny , SARS-CoV-2/genetics , Boston/epidemiology , COVID-19/transmission , Disease Outbreaks , Epidemiological Monitoring , Humans
3.
Viruses ; 13(8)2021 08 13.
Article in English | MEDLINE | ID: covidwho-1376992

ABSTRACT

While investigating a signal of adaptive evolution in humans at the gene LARGE, we encountered an intriguing finding by Dr. Stefan Kunz that the gene plays a critical role in Lassa virus binding and entry. This led us to pursue field work to test our hypothesis that natural selection acting on LARGE-detected in the Yoruba population of Nigeria-conferred resistance to Lassa Fever in some West African populations. As we delved further, we conjectured that the "emerging" nature of recently discovered diseases like Lassa fever is related to a newfound capacity for detection, rather than a novel viral presence, and that humans have in fact been exposed to the viruses that cause such diseases for much longer than previously suspected. Dr. Stefan Kunz's critical efforts not only laid the groundwork for this discovery, but also inspired and catalyzed a series of events that birthed Sentinel, an ambitious and large-scale pandemic prevention effort in West Africa. Sentinel aims to detect and characterize deadly pathogens before they spread across the globe, through implementation of its three fundamental pillars: Detect, Connect, and Empower. More specifically, Sentinel is designed to detect known and novel infections rapidly, connect and share information in real time to identify emerging threats, and empower the public health community to improve pandemic preparedness and response anywhere in the world. We are proud to dedicate this work to Stefan Kunz, and eagerly invite new collaborators, experts, and others to join us in our efforts.


Subject(s)
Disaster Planning , Lassa Fever/epidemiology , Lassa virus/physiology , Africa, Western/epidemiology , Disaster Planning/methods , Humans , Lassa Fever/genetics , Lassa Fever/prevention & control , Lassa Fever/virology , Lassa virus/genetics , N-Acetylglucosaminyltransferases/genetics , N-Acetylglucosaminyltransferases/immunology , Nigeria/epidemiology , Pandemics , Polymorphism, Genetic , Receptors, Virus/genetics , Receptors, Virus/immunology
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