About: SARS-CoV-2 Community Transmission During Shelter-in-Place in San Francisco

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About: SARS-CoV-2 Community Transmission During Shelter-in-Place in San Francisco Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	SARS-CoV-2 Community Transmission During Shelter-in-Place in San Francisco
Creator	Hackett, John Chiu, Charles Havlir, Diane Phd, Gandhi, Monica Greenhouse, Bryan Jain, Vivek Kerkhoff, Andrew Marquez, Carina Appa, Ayesha Ba, Diane Ba, Francesco Ba, Jackie Batson Phd, Joshua Black Ba, Douglas Chamie, Gabriel Consortium, Cliahub Crawford Phd, Emily Derisi, Joe Dynerman Phd, David Gallardo-Brown, Tracy Hao Bs, Samantha Jacobo, Jon Kamm Phd, Jack Kistler Phd, Amy Peng, James Petersen Phd, Maya Rodgers Phd, Mary Rojas, Susana Schwab Phd, Daniel Schwab, Joshua Tulier-Laiwa, Valerie
Source	MedRxiv
abstract	ABSTRACT Background: We characterized SARS-CoV-2 infections in a densely-populated, majority Latinx San Francisco community six-weeks into the city's shelter-in-place order. Methods: We offered SARS-CoV-2 reverse transcription-PCR and antibody (Abbott ARCHITECT IgG) testing, regardless of symptoms, to all residents (>=4 years) and workers in a San Francisco census tract (population: 5,174) at outdoor, community-mobilized events over four days. We estimated SARS-CoV-2 point prevalence (PCR-positive) and cumulative incidence (antibody or PCR-positive) in the census tract and evaluated risk factors for recent (PCR-positive/antibody-negative) versus prior infection (antibody-positive/PCR-negative). SARS-CoV-2 genome recovery and phylogenetics were used to measure viral strain diversity, establish viral lineages present, and estimate number of introductions. Results: We tested 3,953 persons: 40% Latinx; 41% White; 9% Asian/Pacific Islander; and 2% Black. Overall, 2.1% (83/3,871) tested PCR-positive: 95% were Latinx and 52% asymptomatic when tested. 1.7% of residents and 6.0% of workers (non-census tract residents) were PCR-positive. Among 2,598 census tract residents, estimated point prevalence of PCR-positives was 2.3% (95%CI: 1.2-3.8%): 3.9% (95%CI: 2.0-6.4%) among Latinx vs. 0.2% (95%CI: 0.0-0.4%) among non-Latinx persons. Estimated cumulative incidence among residents was 6.1% (95%CI: 4.0-8.6%). Prior infections were 67% Latinx, 16% White, and 17% other ethnicities. Among recent infections, 96% were Latinx. Risk factors for recent infection were Latinx ethnicity, inability to shelter-in-place and maintain income, frontline service work, unemployment, and household income <$50,000/year. Five SARS-CoV-2 phylogenetic lineages were detected. Conclusion: SARS-CoV-2 infections from diverse lineages continued circulating among low-income, Latinx persons unable to work from home and maintain income during San Francisco's shelter-in-place ordinance.
has issue date	2020-06-17(xsd:dateTime)
bibo:doi	10.1101/2020.06.15.20132233
has license	medrxiv
sha1sum (hex)	13453a98fcc1d7e048f0fe6a2e347b026c393a40
schema:url	https://doi.org/10.1101/2020.06.15.20132233
resource representing a document's title	SARS-CoV-2 Community Transmission During Shelter-in-Place in San Francisco
resource representing a document's body	covid:13453a98fcc1d7e048f0fe6a2e347b026c393a40#body_text
is schema:about of	named entity 'PLACE' named entity 'Community Transmission' named entity 'SARS-CoV-2' named entity 'preprint' named entity 'Antibody' named entity 'symptom' named entity 'Latinx' named entity 'infection' named entity 'PCR' named entity 'sensitivity and specificity' named entity 'stay home' named entity 'confidence interval' named entity 'SARS-CoV-2' named entity 'Latinx' named entity 'census tract' named entity 'virus' named entity 'SARS-CoV-2' named entity 'medRxiv' named entity 'San Francisco' named entity 'preprint' named entity 'preprint' named entity 'preprint' named entity 'test sensitivity' named entity 'PCR' named entity 'SARS-CoV-2' named entity 'SARS-CoV-2' named entity 'preprint' named entity 'city block' named entity 'PCR' named entity 'UCSF' named entity 'June 17' named entity 'infection' named entity 'CC-BY-NC-ND 4.0' named entity 'contact tracing' named entity 'CC-BY-NC-ND 4.0' named entity 'medRxiv' named entity 'medRxiv' named entity 'PCR' named entity 'PCR' named entity 'cumulative incidence' named entity 'COVID-19' named entity 'PCR' named entity 'FDA' named entity 'linear interpolation' named entity 'medRxiv' named entity 'cumulative incidence' named entity 'medRxiv' named entity 'log10' named entity 'viral genome' named entity 'augur' named entity 'PCR' named entity 'antibody test' named entity 'preprint' named entity 'COVID'

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