A5080027419- SARS-CoV-2 and COVID-19 Research
- Animal Virus Infections Studies
- SARS-CoV-2 detection and testing
- COVID-19 epidemiological studies
- Reproductive tract infections research
- Viral Infections and Immunology Research
- Plant Virus Research Studies
- Viral gastroenteritis research and epidemiology
- Herpesvirus Infections and Treatments
- Virus-based gene therapy research
- COVID-19 Clinical Research Studies
- Pulsars and Gravitational Waves Research
- vaccines and immunoinformatics approaches
- Poxvirus research and outbreaks
- Reproductive System and Pregnancy
- Zoonotic diseases and public health
- Legionella and Acanthamoeba research
- COVID-19 Pandemic Impacts
- Bacillus and Francisella bacterial research
- Monoclonal and Polyclonal Antibodies Research
- Urinary Tract Infections Management
- Geophysics and Sensor Technology
- Respiratory viral infections research
- HIV Research and Treatment
- Viral Infections and Outbreaks Research
New York City Department of Health and Mental Hygiene
2015-2025
Centers for Disease Control and Prevention
2017
New York State Department of Health
2017
Wadsworth Center
2017
Rutgers, The State University of New Jersey
2005-2013
National Institutes of Health
1999-2004
Institute of Cellular and Intracellular Symbiosis
2004
Columbia University
2003
California Institute of Technology
2000
National Institute of Allergy and Infectious Diseases
1999-2000
Understanding the circumstances that lead to pandemics is important for their prevention. We analyzed genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in disease 2019 (COVID-19) pandemic. show SARS-CoV-2 before February 2020 likely comprised only two distinct viral lineages, denoted "A" and "B." Phylodynamic rooting methods, coupled with epidemic simulations, reveal these lineages were result at least separate cross-species transmission events into...
Abstract Wide-scale SARS-CoV-2 genome sequencing is critical to tracking viral evolution during the ongoing pandemic. We develop software tool, Variant Database (VDB), for quickly examining changing landscape of spike mutations. Using VDB, we detect an emerging lineage in New York region that shares mutations with previously reported variants. The most common sets this (now designated as B.1.526) are L5F, T95I, D253G, E484K or S477N, D614G, and A701V. This was first sequenced late November...
Abstract Wide-scale SARS-CoV-2 genome sequencing is critical to tracking viral evolution during the ongoing pandemic. Variants first detected in United Kingdom, South Africa, and Brazil have spread multiple countries. We developed software tool, Variant Database (VDB), for quickly examining changing landscape of spike mutations. Using VDB, we an emerging lineage New York region that shares mutations with previously reported variants. The most common sets this (now designated as B.1.526) are...
Recent studies have documented the emergence and rapid growth of B.1.526, a novel variant interest (VOI) SARS-CoV-2, virus that causes COVID-19, in New York City (NYC) area after its identification NYC November 2020.
Here we report the cloning and sequencing of a region chlamydiae chromosome termed "plasticity zone" from all human serovars <i>C. trachomatis</i> containing tryptophan biosynthesis genes. Our results show that this contains orthologues repressor as well α β subunits synthase. Results reverse transcription-PCR Western blot analyses indicate <i>trpBA</i> genes are transcribed, protein products expressed. The TrpB sequences highly conserved. In comparison with other synthase subunits,...
Objectives: Infections caused by Legionella are the leading cause of waterborne disease outbreaks in United States. We investigated a large outbreak Legionnaires’ New York City summer 2015 to characterize patients, risk factors for mortality, and environmental exposures. Methods: defined cases as patients with pneumonia laboratory evidence infection from July 2 through August 3, 2015, history residing or visiting 1 several South Bronx neighborhoods City. describe epidemiologic,...
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 only feasible when genetically distinct viruses contemporaneously infect the same host. Here, we identify instance SARS-CoV-2 superinfection, whereby individual was infected with two viral variants: Alpha (B.1.1.7) Epsilon (B.1.429). This superinfection first noted genome sequence...
Chlamydia trachomatis is a strict human pathogen producing infections that cause medically important chronic inflammatory diseases, such as blinding trachoma and tubal factor infertility. Isolates exist serotypes fall into distinct biologic pathological groups corresponding to differences in infection tissue tropism invasion properties. Paradoxically, genome sequencing of several diverse strains has revealed remarkable level genomic synteny, suggesting minor genetic determine the host-...
Abstract With the rapid spread and evolution of SARS-CoV-2, ability to monitor its transmission distinguish among viral lineages is critical for pandemic response efforts. The most commonly used software lineage assignment newly isolated SARS-CoV-2 genomes pangolin, which offers two methods assignment, pangoLEARN pUShER. PangoLEARN rapidly assigns using a machine-learning algorithm, while pUShER performs phylogenetic placement identify corresponding sequenced genome. In preliminary study, we...
Chlamydia trachomatis is a major cause of sexually transmitted disease (STD) worldwide. Antibiotics are effective in treating infection; however, reinfection common. This observation has led to the conclusion that infection fails elicit protective antichlamydial immune response. It was postulated high rates might be due early eradication organisms from genital tissue after antibiotic intervention, which could negatively influence development naturally acquired immunity. hypothesis tested by...
Abstract Resistance to the mouse pneumonitis (MoPn) strain of Chlamydia trachomatis has been mapped MHC class II-restricted, IL-12-dependent CD4+ T cells that secrete a type 1 profile proinflammatory cytokines, which includes IFN-γ and TNF-α. The relative contribution is controversial, however, due variation in results presented by different laboratories. To determine whether C. differences contributed this apparent conflict, resistance IFN-γ-deficient mice murine human strains was compared....
Abstract During the summer of 2015, New York, USA, had one largest and deadliest outbreaks Legionnaires' disease in history United States. A total 138 cases 16 deaths were linked to a single cooling tower South Bronx. Analysis environmental samples clinical isolates showed that sporadic legionellosis before, during, after outbreak could be traced slowly evolving, single-ancestor strain. Detection an ostensibly virulent Legionella strain endemic Bronx community suggests potential risk for...
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 adults. Methods Participants were recruited from 2020 Community Survey. We estimated citywide and stratified using hybrid design: serum tested with DiaSorin LIAISON...
Bivalent booster vaccination data were
Abstract Background The extent to which infections may have been undetected in an epicenter of the 2022 mpox outbreak is unknown. Methods A serosurvey (July and August 2022) assessed seroprevalence correlates infection among a diverse sample asymptomatic patients with no prior diagnoses known histories smallpox or vaccination. We present seropositivity stratified by participant characteristics collected via survey. Results Two-thirds 419 participants were cismen (281 419), whom 59.1% (166...
The 21.7-kb replicase locus of mouse hepatitis virus strain A59 (MHV-A59) encodes several putative functional domains, including three proteinase domains. Encoded closest to the 5' terminus this is first papain-like (PLP-1) (S. C. Baker et al., J. Virol. 67:6056-6063, 1993; H.-J. Lee Virology 180:567-582, 1991). This cysteine responsible for in vitro cleavage p28, a polypeptide that also present MHV-A59-infected cells. Cleavage at second site was recently reported (P. Bonilla 209:489-497,...
To characterize the epidemiological properties of B.1.526 SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) variant interest, here we used nine and population datasets model-inference methods to reconstruct transmission dynamics in New York City, where emerged. We estimated that had a moderate increase (15 25%) transmissibility, could escape immunity 0 10% previously infected individuals, substantially increased infection fatality risk (IFR) among adults 65 or older by >60%...
Chlamydia trachomatis inoculated by any mucosal route colonized multiple murine mucosae and, in most cases, the spleen, liver, and kidneys. Cell-to-cell transmission, systemic dissemination, autoinoculation of infectious fluids may have contributed to chlamydial spread. Intermucosal trafficking protective T cells cannot be accurately evaluated using live challenges.
The molecular mechanisms of resistance to genital infection with the mouse pneumonitis (MoPn) strain Chlamydia trachomatis are unknown. A role for major histocompatibility complex class II-restricted, interleukin-12-dependent CD4(+) T cells has been established, but functional activity these does not depend on secretion gamma interferon. Here we examined potential contribution T-cell-mediated cytotoxicity and apoptosis mucosal clearance MoPn by using mice deficient in mediators target cell...
From 2015 to 2017, 11 confirmed brucellosis cases were reported in New York City, leading 10 Brucella exposure risk events ( events) 7 clinical laboratories (CLs). Most patients had traveled countries where is endemic and presented with histories findings consistent brucellosis.
Surveillance systems that monitor pathogen genome sequences are critical for rapidly detecting the introduction and emergence of variants. To evaluate how interactions between surveillance capacity, variant properties, epidemiological context influence timeliness detection, we developed a geographically explicit stochastic compartmental model to simulate transmission novel SARS-CoV-2 in New York City. We measured impact (1) testing sequencing volume, (2) geographic targeting testing, (3)...