Trial reportGenome research2020
Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region.
Abstract readClinical Trial
In one paragraph
Trial report in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
0numbers the graph read from it
0cells of the map it votes in
58citing papers in PubMed
–field-weighted citation impact
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.
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.
Who cites it
58 citing papers in PubMed.
- WEPP: Phylogenetic placement achieves near-haplotype resolution in wastewater-based epidemiology.PLoS computational biology · 2026Article
- Experimental evolution in an era of molecular manipulation.Nature reviews. Genetics · 2026Review
- Genomic Epidemiology of SARS-CoV-2 in Ukraine from May 2022 to March 2024 Reveals Omicron Variant Dynamics.Viruses · 2025Article
- Considerations for Severe Acute Respiratory Syndrome Coronavirus 2 Genomic Surveillance: A Joint Consensus Recommendation of the Association for Molecular Pathology and Association of Public Health Laboratories.The Journal of molecular diagnostics : JMD · 2025Review
- SARS-CoV-2 introductions to the island of Ireland: a phylogenetic and geospatiotemporal study of infection dynamics.Genome medicine · 2024Article
- Methods to Estimate the Between-Population Level Effective Reproductive Number for Infectious Disease Epidemics: Foot-And-Mouth Disease (FMD) in Vietnam.Transboundary and emerging diseases · 2024Article
- Estimating population infection rates from non-random testing data: Evidence from the COVID-19 pandemic.PloS one · 2024Article
- Variant-specific introduction and dispersal dynamics of SARS-CoV-2 in New York City - from Alpha to Omicron.PLoS pathogens · 2023Article
- Article
- Early Introduction and Community Transmission of SARS-CoV-2 Omicron Variant, New York, New York, USA.Emerging infectious diseases · 2023Article
- Wastewater-based monitoring of SARS-CoV-2 at UK airports and its potential role in international public health surveillance.PLOS global public health · 2023Article
- The role of multi-omics in the diagnosis of COVID-19 and the prediction of new therapeutic targets.Virulence · 2022Review
- The potential of genomics for infectious disease forecasting.Nature microbiology · 2022Review
- Public health genomics capacity assessment: readiness for large-scale pathogen genomic surveillance in Canada's public health laboratories.BMC public health · 2022Article
- Proficiency testing for SARS-CoV-2 whole genome sequencing.Pathology · 2022Article
- Genomic surveillance of SARS-CoV-2 during the first year of the pandemic in the Bronx enabled clinical and epidemiological inference.Cold Spring Harbor molecular case studies · 2022Article
- Statistical Challenges in Tracking the Evolution of SARS-CoV-2.Statistical science : a review journal of the Institute of Mathematical Statistics · 2022Article
- Virus-specific editing identification approach reveals the landscape of A-to-I editing and its impacts on SARS-CoV-2 characteristics and evolution.Nucleic acids research · 2022Article
- Genomic surveillance of SARS-CoV-2 during the first year of the pandemic in the Bronx enabled clinical and epidemiological inference.medRxiv : the preprint server for health sciences · 2022Article
- Mass Screening of SARS-CoV-2 Variants using Sanger Sequencing Strategy in Hiroshima, Japan.Scientific reports · 2022Article
Corrections and comments
- Update of
Authors and funding
45 authors.
Matthew T MauranoInstitute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.ORCID 0000-0002-2218-8628
Sitharam RamaswamiGenome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA.
Paul ZappileGenome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA.
Dacia DimartinoGenome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA.
Ludovic BoytardCenter for Biospecimen Research and Development, NYU Langone Health, New York, New York 10016, USA.
André M Ribeiro-Dos-SantosInstitute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.
Nicholas A VulpescuInstitute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.
Gael WestbyGenome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA.
Guomiao ShenDepartment of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
Xiaojun FengDepartment of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
Megan S HoganInstitute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.
Manon Ragonnet-CroninMRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, United Kingdom.ORCID 0000-0002-4879-2209
Lily GeidelbergMRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, United Kingdom.ORCID 0000-0002-8057-1844
Christian MarierGenome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA.
Peter MeynGenome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA.
Yutong ZhangGenome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA.
John CadleyInstitute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.
Raquel OrdoñezInstitute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.
Raven LutherInstitute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.
Emily HuangInstitute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.
Emily GuzmanGenome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA.
Carolina Arguelles-GrandeCenter for Biospecimen Research and Development, NYU Langone Health, New York, New York 10016, USA.ORCID 0000-0002-4835-1577
Kimon V ArgyropoulosDepartment of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
Margaret BlackDepartment of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
Antonio SerranoDepartment of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
Melissa E CallDepartment of Dermatology, NYU Grossman School of Medicine, New York, New York 10016, USA.ORCID 0000-0002-7327-485X
Min Jae KimDepartment of Dermatology, NYU Grossman School of Medicine, New York, New York 10016, USA.ORCID 0000-0003-3241-530X
Brendan BelovaracDepartment of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
Tatyana GindinDepartment of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
Andrew LytleDepartment of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
Jared PinnellDepartment of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
Theodore VougiouklakisDepartment of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
John ChenMedical Center IT, NYU Langone Health, New York, New York 10016, USA.
Lawrence H LinDepartment of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
Amy RapkiewiczDepartment of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
Vanessa RaabeDivision of Infectious Diseases and Immunology, Department of Medicine and NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, New York 10016, USA.
Marie I SamanovicDivision of Infectious Diseases and Immunology, Department of Medicine and NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, New York 10016, USA.
George JourDepartment of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
Iman OsmanCenter for Biospecimen Research and Development, NYU Langone Health, New York, New York 10016, USA.
Maria Aguero-RosenfeldDepartment of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
Mark J MulliganDivision of Infectious Diseases and Immunology, Department of Medicine and NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, New York 10016, USA.
Erik M VolzMRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, United Kingdom.ORCID 0000-0001-6268-8937
Paolo CotziaDepartment of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
Matija SnuderlDepartment of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.ORCID 0000-0003-0752-0917
Adriana HeguyDepartment of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.ORCID 0000-0002-2836-6683
Funding
Vaccine FacilityP30CA016087 · NCI · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI MARK Reid PHILIPS · 1985 to 2026
$83.1MEstablishment of the New York University Vaccine and Treatment Evaluation Unit (NYU VTEU) - DMID 21-0012UM1AI148574 · NIAID · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI Angelica Cifuentes Kottkamp, Anoma Nellore · 2020 to 2026
$23.9MSupplement for Center for Synthetic Regulatory Genomics: Building CACNA1C alleles associated with Neuropsychiatric DisordersRM1HG009491 · NHGRI · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI Jef D BOEKE · 2018 to 2026
$20.9MALABAMA/ZAMBIA HIV VACCINE CLINICAL TRIALS UNIT (HVTU)U01AI047996 · NIAID · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI GOEPFERT, PAUL A. · 2000 to 2006
$8.4MGenomic organization of long-distance gene regulationR35GM119703 · NIGMS · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI MAURANO, MATTHEW THOMAS · 2016 to 2020
$2.1MMedical Research Council MC_PC_19012Medical Research Council MR/R015600/1NCI NIH HHS P30 CA016087NHGRI NIH HHS RM1 HG009491NIAID NIH HHS U01 AI047996NIAID NIH HHS UM1 AI148574NIGMS NIH HHS R35 GM119703
Abstract
Effective public response to a pandemic relies upon accurate measurement of the extent and dynamics of an outbreak. Viral genome sequencing has emerged as a powerful approach to link seemingly unrelated cases, and large-scale sequencing surveillance can inform on critical epidemiological parameters. Here, we report the analysis of 864 SARS-CoV-2 sequences from cases in the New York City metropolitan area during the COVID-19 outbreak in spring 2020. The majority of cases had no recent travel history or known exposure, and genetically linked cases were spread throughout the region. Comparison to global viral sequences showed that early transmission was most linked to cases from Europe. Our data are consistent with numerous seeds from multiple sources and a prolonged period of unrecognized community spreading. This work highlights the complementary role of genomic surveillance in addition to traditional epidemiological indicators.
Indexed as
COVID-19Genome, ViralPandemicsPhylogenyWhole Genome SequencingFemaleHumansMaleNew York CitySARS-CoV-2
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Read underepoch 390
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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.