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1.
Science ; : eabp8337, 2022 Jul 26.
Article in English | MEDLINE | ID: covidwho-1962060

ABSTRACT

Understanding the circumstances that lead to pandemics is important for their prevention. Here, we analyze the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the coronavirus disease 2019 (COVID-19) pandemic. We show that SARS-CoV-2 genomic diversity before February 2020 likely comprised only two distinct viral lineages, denoted A and B. Phylodynamic rooting methods, coupled with epidemic simulations, reveal that these lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses around 18 November 2019 (23 October-8 December), while the separate introduction of lineage A likely occurred within weeks of this event. These findings indicate that it is unlikely that SARS-CoV-2 circulated widely in humans prior to November 2019 and define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported. As with other coronaviruses, SARS-CoV-2 emergence likely resulted from multiple zoonotic events.

2.
Nat Commun ; 13(1): 3645, 2022 06 25.
Article in English | MEDLINE | ID: covidwho-1908172

ABSTRACT

Recombination is an evolutionary process by which many pathogens generate diversity and acquire novel functions. Although a common occurrence during coronavirus replication, detection of recombination is only feasible when genetically distinct viruses contemporaneously infect the same host. Here, we identify an instance of SARS-CoV-2 superinfection, whereby an individual was infected with two distinct viral variants: Alpha (B.1.1.7) and Epsilon (B.1.429). This superinfection was first noted when an Alpha genome sequence failed to exhibit the classic S gene target failure behavior used to track this variant. Full genome sequencing from four independent extracts reveals that Alpha variant alleles comprise around 75% of the genomes, whereas the Epsilon variant alleles comprise around 20% of the sample. Further investigation reveals the presence of numerous recombinant haplotypes spanning the genome, specifically in the spike, nucleocapsid, and ORF 8 coding regions. These findings support the potential for recombination to reshape SARS-CoV-2 genetic diversity.


Subject(s)
COVID-19 , Superinfection , Genome, Viral/genetics , Humans , New York City/epidemiology , Recombination, Genetic , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics
3.
J Infect Dis ; 2022 Jun 30.
Article in English | MEDLINE | ID: covidwho-1908839

ABSTRACT

BACKGROUND: Monitoring the emergence and spread of SARS-CoV-2 variants is an important public health objective. We investigated how the Gamma variant was established in New York City (NYC) in early 2021 in the presence of travel restrictions that aimed to prevent viral spread from Brazil, the country where the variant was first identified. METHODS: We performed phylogeographic analysis on 15,967 Gamma sequences sampled between March 10th through May 1st, 2021, to identify geographic sources of Gamma lineages introduced into NYC. We identified locally circulating Gamma transmission clusters and inferred the timing of their establishment in NYC. RESULTS: We identified 16 phylogenetically-distinct Gamma clusters established in NYC (cluster sizes ranged 2-108 genomes); most of them were introduced from Florida and Illinois and only one directly from Brazil. By the time the first Gamma case was reported by genomic surveillance in NYC on March 10th, the majority (57%) of circulating Gamma lineages had already been established in the city for at least two weeks. CONCLUSIONS: Although travel from Brazil to the US was restricted from May 2020 through the end of the study period, this restriction did not prevent Gamma from becoming established in NYC as most introductions occurred from domestic locations.

4.
Epidemiol Infect ; 150: e105, 2022 05 18.
Article in English | MEDLINE | ID: covidwho-1852325

ABSTRACT

Repeated serosurveys are an important tool for understanding trends in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and vaccination. During 1 September 2020-20 March 2021, the NYC Health Department conducted a population-based SARS-CoV-2 antibody prevalence survey of 2096 NYC adults who either provided a blood specimen or self-reported the results of a previous antibody test. The serosurvey, the second in a series of surveys conducted by the NYC Health Department, aimed to estimate SARS-CoV-2 antibody prevalence across the city and for different groups at higher risk for adverse health outcomes. Weighted citywide prevalence was 23.5% overall (95% confidence interval (CI) 20.1-27.4) and increased from 19.2% (95% CI 14.7-24.6) before coronavirus disease 2019 vaccines were available to 31.3% (95% CI 24.5-39.0) during the early phases of vaccine roll-out. We found no differences in antibody prevalence by age, race/ethnicity, borough, education, marital status, sex, health insurance coverage, self-reported general health or neighbourhood poverty. These results show an overall increase in population-level seropositivity in NYC following the introduction of SARS-CoV-2 vaccines and highlight the importance of repeated serosurveys in understanding the pandemic's progression.


Subject(s)
COVID-19 , SARS-CoV-2 , Adult , Antibodies, Viral , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19 Vaccines , Humans , New York City/epidemiology , Prevalence , Vaccination
5.
Nat Commun ; 12(1): 4886, 2021 08 09.
Article in English | MEDLINE | ID: covidwho-1349666

ABSTRACT

Wide-scale SARS-CoV-2 genome sequencing is critical to tracking viral evolution during the ongoing pandemic. We develop the software tool, Variant Database (VDB), for quickly examining the changing landscape of spike mutations. Using VDB, we detect an emerging lineage of SARS-CoV-2 in the New York region that shares mutations with previously reported variants. The most common sets of spike mutations in this lineage (now designated as B.1.526) are L5F, T95I, D253G, E484K or S477N, D614G, and A701V. This lineage was first sequenced in late November 2020. Phylodynamic inference confirmed the rapid growth of the B.1.526 lineage. In concert with other variants, like B.1.1.7, the rise of B.1.526 appears to have extended the duration of the second wave of COVID-19 cases in NYC in early 2021. Pseudovirus neutralization experiments demonstrated that B.1.526 spike mutations adversely affect the neutralization titer of convalescent and vaccinee plasma, supporting the public health relevance of this lineage.


Subject(s)
COVID-19/virology , SARS-CoV-2/classification , SARS-CoV-2/isolation & purification , COVID-19/epidemiology , Genome, Viral , Humans , Models, Molecular , Mutation , New York/epidemiology , Phylogeny , SARS-CoV-2/genetics , Software , Spike Glycoprotein, Coronavirus/genetics
6.
Am J Clin Pathol ; 156(3): 370-380, 2021 08 04.
Article in English | MEDLINE | ID: covidwho-1322609

ABSTRACT

OBJECTIVES: The Abbot ID NOW COVID-19 assay and Quidel Sofia 2 SARS Antigen FIA are point-of-care assays that offer rapid testing for severe acute respiratory syndrome coronavirus 2 viral RNA and nucleocapsid protein, respectively. Given the utility of these devices in the field, we investigated the feasibility and safety of using the ID NOW and Sofia assays in the public health response to the coronavirus disease 2019 pandemic and in future public health emergencies. METHODS: A combination of utilization and contamination testing in addition to a review of instrument workflows was conducted. RESULTS: Utilization testing demonstrated that both tests are intuitive, associated with high user test success (85%) in our study, and could be implemented by staff after minimal training. Contamination tests revealed potential biosafety concerns due to the open design of the ID NOW instrument and the transfer mechanisms with the Sofia. When comparing the workflow of the ID NOW and the Sofia, we found that the ID NOW was more user-friendly and that the transfer technology reduces the chance of contamination. CONCLUSIONS: The ID NOW, Sofia, and other emerging point-of-care tests should be used only after careful consideration of testing workflow, biosafety risk mitigations, and appropriate staff training.


Subject(s)
Antigens, Viral/analysis , COVID-19 Testing , COVID-19/diagnosis , Pandemics , Point-of-Care Testing , SARS-CoV-2/immunology , COVID-19/epidemiology , COVID-19/virology , Containment of Biohazards , Equipment Safety , Feasibility Studies , Humans , Risk Assessment , SARS-CoV-2/isolation & purification
7.
Diagn Microbiol Infect Dis ; 101(3): 115468, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1293712

ABSTRACT

Nasal and nasopharyngeal swab specimens tested by the Cepheid Xpert Xpress SARS-CoV-2 were analyzed by whole-genome sequencing based on impaired detection of the N2 target. Each viral genome had at least one mutation in the N gene, which likely arose independently in the New York City and Pittsburgh study sites.


Subject(s)
COVID-19/epidemiology , COVID-19/virology , Coronavirus Nucleocapsid Proteins/genetics , SARS-CoV-2/genetics , Cities/epidemiology , Databases, Genetic , Genome, Viral , Humans , Mutation , Phosphoproteins/genetics , United States/epidemiology
8.
J Infect Dis ; 224(2): 188-195, 2021 07 15.
Article in English | MEDLINE | ID: covidwho-1258779

ABSTRACT

BACKGROUND: Serosurveys help to ascertain burden of infection. Prior severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serosurveys in New York City (NYC) used nonrandom samples. During June-October 2020, the NYC Health Department conducted a population-based survey estimating SARS-CoV-2 antibody prevalence in NYC adults. METHODS: Participants were recruited from the NYC 2020 Community Health Survey. We estimated citywide and stratified antibody prevalence using a hybrid design: serum tested with the DiaSorin LIAISON SARS-CoV-2 S1/S2 IgG assay and self-reported antibody test results were used together. We estimated univariate frequencies and 95% confidence intervals (CI), accounting for complex survey design. Two-sided P values ≤ .05 were statistically significant. RESULTS: There were 1074 respondents; 497 provided blood and 577 provided only a self-reported antibody test result. Weighted prevalence was 24.3% overall (95% CI, 20.7%-28.3%). Latino (30.7%; 95% CI, 24.1%-38.2%; P < .01) and black (30.7%; 95% CI, 21.9%-41.2%; P = .02) respondents had a higher weighted prevalence compared with white respondents (17.4%; 95% CI, 12.5%-23.7%). CONCLUSIONS: By October 2020, nearly 1 in 3 black and 1 in 3 Latino NYC adults had SARS-CoV-2 antibodies, highlighting unequal impacts of the coronavirus disease 2019 (COVID-19) pandemic on black and Latino NYC adults.


Subject(s)
Antibodies, Viral/blood , SARS-CoV-2/immunology , Adolescent , Adult , Aged , COVID-19/epidemiology , Female , Humans , Male , Middle Aged , New York City/epidemiology , Prevalence , Seroepidemiologic Studies , Young Adult
9.
MMWR Morb Mortal Wkly Rep ; 70(19): 712-716, 2021 May 14.
Article in English | MEDLINE | ID: covidwho-1227231

ABSTRACT

Recent studies have documented the emergence and rapid growth of B.1.526, a novel variant of interest (VOI) of SARS-CoV-2, the virus that causes COVID-19, in the New York City (NYC) area after its identification in NYC in November 2020 (1-3). Two predominant subclades within the B.1.526 lineage have been identified, one containing the E484K mutation in the receptor-binding domain (1,2), which attenuates in vitro neutralization by multiple SARS-CoV-2 antibodies and is present in variants of concern (VOCs) first identified in South Africa (B.1.351) (4) and Brazil (P.1).* The NYC Department of Health and Mental Hygiene (DOHMH) analyzed laboratory and epidemiologic data to characterize cases of B.1.526 infection, including illness severity, transmission to close contacts, rates of possible reinfection, and laboratory-diagnosed breakthrough infections among vaccinated persons. Preliminary data suggest that the B.1.526 variant does not lead to more severe disease and is not associated with increased risk for infection after vaccination (breakthrough infection) or reinfection. Because relatively few specimens were sequenced over the study period, the statistical power might have been insufficient to detect modest differences in rates of uncommon outcomes such as breakthrough infection or reinfection. Collection of timely viral genomic data for a larger proportion of citywide cases and rapid integration with population-based surveillance data would enable improved understanding of the impact of emerging SARS-CoV-2 variants and specific mutations to help guide public health intervention efforts.


Subject(s)
COVID-19/epidemiology , COVID-19/virology , SARS-CoV-2/genetics , Adolescent , Adult , Aged , COVID-19 Nucleic Acid Testing , Child , Child, Preschool , Female , Humans , Infant , Infant, Newborn , Male , Middle Aged , New York City/epidemiology , Young Adult
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