Evidence map›Paper›PMID 33893501›Full record

ArticleThe Journal of infectious diseases2021

Introduction, Transmission Dynamics, and Fate of Early Severe Acute Respiratory Syndrome Coronavirus 2 Lineages in Santa Clara County, California.

Elsa Villarino, Xianding Deng, Carol A Kemper, Michelle A Jorden, Brandon Bonin, Sarah L Rudman, George S Han, Guixia Yu, Candace Wang, Scot Federman and 11 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in The Journal of infectious diseases, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

21 authors.

Elsa VillarinoCounty of Santa Clara Public Health Department, San Jose, California, USA.
Xianding DengDepartment of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA.
Carol A KemperEl Camino Hospital, Mountain View and Los Gatos, California, USA.
Michelle A JordenOffice of the Medical Examiner-Coroner, County of Santa Clara, San Jose, California, USA.
Brandon BoninCounty of Santa Clara Public Health Department, San Jose, California, USA.
Sarah L RudmanCounty of Santa Clara Public Health Department, San Jose, California, USA.
George S HanCounty of Santa Clara Public Health Department, San Jose, California, USA.
Guixia YuDepartment of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA.
Candace WangDepartment of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA.
Scot FedermanDepartment of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA.
Brian BushnellLawrence Berkeley National Laboratory, Berkeley, California, USA.
CZB COVIDTracker Consortium
Debra A WadfordViral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California, USA.
Wen LinCounty of Santa Clara Public Health Department, San Jose, California, USA.
Ying TaoCenters for Disease Control and Prevention, Atlanta, Georgia, USA.
Clinton R PadenCenters for Disease Control and Prevention, Atlanta, Georgia, USA.
Julu BhatnagarCenters for Disease Control and Prevention, Atlanta, Georgia, USA.
Tara MacCannellCounty of Santa Clara Public Health Department, San Jose, California, USA.
Suxiang TongCenters for Disease Control and Prevention, Atlanta, Georgia, USA.
Joshua BatsonChan Zuckerberg Biohub, San Francisco, California, USA.
Charles Y ChiuDepartment of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA.

Funding

Identification of diagnostic and prognostic host biomarkers of Zika virus infection by transcriptome profilingR21AI129455 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHIU, CHARLES YEN · 2017 to 2018
$436k
CIHRInnovative Genomics InstituteNIAID NIH HHS R21 AI129455NIH HHS R33-AI129455
6 · The paper itself

Abstract

We combined viral genome sequencing with contact tracing to investigate introduction and evolution of severe acute respiratory syndrome coronavirus 2 lineages in Santa Clara County, California, from 27 January to 21 March 2020. From 558 persons with coronavirus disease 2019, 101 genomes from 143 available clinical samples comprised 17 lineages, including SCC1 (n = 41), WA1 (n = 9; including the first 2 reported deaths in the United States, with postmortem diagnosis), 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 and March. By August, only D614G lineages introduced after 21 March were circulating in Santa Clara County.

Indexed as

AdultAgedCaliforniaContact TracingCOVID-19FemaleGenetic VariationGenome, ViralGenotypeHumansMaleMiddle AgedPhylogenyRisk FactorsSARS-CoV-2TravelCOVID-19D614G lineageepidemiologypublic health surveillanceSARS-CoV-2viral evolutionviral whole-genome sequencing

Identifiers

PMID33893501
PMCPMC8135363

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.