Dataset Information

Genetic Adaptation in New York City Rats.

ABSTRACT: Brown rats (Rattus norvegicus) thrive in urban environments by navigating the anthropocentric environment and taking advantage of human resources and by-products. From the human perspective, rats are a chronic problem that causes billions of dollars in damage to agriculture, health and infrastructure. Did genetic adaptation play a role in the spread of rats in cities? To approach this question, we collected whole-genome sequences from 29 brown rats from New York City (NYC) and scanned for genetic signatures of adaptation. We tested for (i) high-frequency, extended haplotypes that could indicate selective sweeps and (ii) loci of extreme genetic differentiation between the NYC sample and a sample from the presumed ancestral range of brown rats in northeast China. We found candidate selective sweeps near or inside genes associated with metabolism, diet, the nervous system and locomotory behavior. Patterns of differentiation between NYC and Chinese rats at putative sweep loci suggest that many sweeps began after the split from the ancestral population. Together, our results suggest several hypotheses on adaptation in rats living in close proximity to humans.

SUBMITTER: Harpak A

PROVIDER: S-EPMC7851592 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Genetic Adaptation in New York City Rats.

Harpak Arbel A Garud Nandita N Rosenberg Noah A NA Petrov Dmitri A DA Combs Matthew M Pennings Pleuni S PS Munshi-South Jason J

Genome biology and evolution 20210101 1

Brown rats (Rattus norvegicus) thrive in urban environments by navigating the anthropocentric environment and taking advantage of human resources and by-products. From the human perspective, rats are a chronic problem that causes billions of dollars in damage to agriculture, health, and infrastructure. Did genetic adaptation play a role in the spread of rats in cities? To approach this question, we collected whole-genome sequences from 29 brown rats from New York City (NYC) and scanned for genet ...[more]

PMID: 33211096

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Project description:Millions of Norway rats (Rattus norvegicus) inhabit New York City (NYC), presenting the potential for transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from humans to rats. We evaluated SARS-CoV-2 exposure among 79 rats captured from NYC during the fall of 2021. Our results showed that 13 of the 79 rats (16.5%) tested IgG- or IgM-positive, and partial SARS-CoV-2 genomes were recovered from all 4 rats that were qRT-PCR (reverse transcription-quantitative PCR)-positive. Genomic analyses suggest these viruses were associated with genetic lineage B, which was predominant in NYC in the spring of 2020 during the early pandemic period. To further investigate rat susceptibility to SARS-CoV-2 variants, we conducted a virus challenge study and showed that Alpha, Delta, and Omicron variants can cause infections in wild-type Sprague Dawley (SD) rats, including high replication levels in the upper and lower respiratory tracts and induction of both innate and adaptive immune responses. Additionally, the Delta variant resulted in the highest infectivity. In summary, our results indicate that rats are susceptible to infection with Alpha, Delta, and Omicron variants, and wild Norway rats in the NYC municipal sewer systems have been exposed to SARS-CoV-2. Our findings highlight the need for further monitoring of SARS-CoV-2 in urban rat populations and for evaluating the potential risk of secondary zoonotic transmission from these rat populations back to humans. IMPORTANCE The host tropism expansion of SARS-CoV-2 raises concern for the potential risk of reverse-zoonotic transmission of emerging variants into rodent species, including wild rat species. In this study, we present both genetic and serological evidence for SARS-CoV-2 exposure to the New York City wild rat population, and these viruses may be linked to the viruses that were circulating during the early stages of the pandemic. We also demonstrated that rats are susceptible to additional variants (i.e., Alpha, Delta, and Omicron) that have been predominant in humans and that susceptibility to infection varies by variant. Our findings highlight the reverse zoonosis of SARS-CoV-2 to urban rats and the need for further monitoring of SARS-CoV-2 in rat populations for potential secondary zoonotic transmission to humans.

Project description:BackgroundSexually transmitted infections spread across contact networks. Partner elicitation and notification are commonly used public health tools to identify, notify, and offer testing to persons linked in these contact networks. For HIV-1, a rapidly evolving pathogen with low per-contact transmission rates, viral genetic sequences are an additional source of data that can be used to infer or refine transmission networks.Methods and findingsThe New York City Department of Health and Mental Hygiene interviews individuals newly diagnosed with HIV and elicits names of sexual and injection drug using partners. By law, the Department of Health also receives HIV sequences when these individuals enter healthcare and their physicians order resistance testing. Our study used both HIV sequence and partner naming data from 1342 HIV-infected persons in New York City between 2006 and 2012 to infer and compare sexual/drug-use named partner and genetic transmission networks. Using these networks, we determined a range of genetic distance thresholds suitable for identifying potential transmission partners. In 48% of cases, named partners were infected with genetically closely related viruses, compatible with but not necessarily representing or implying, direct transmission. Partner pairs linked through the genetic similarity of their HIV sequences were also linked by naming in 53% of cases. Persons who reported high-risk heterosexual contact were more likely to name at least one partner with a genetically similar virus than those reporting their risk as injection drug use or men who have sex with men.ConclusionsWe analyzed an unprecedentedly large and detailed partner tracing and HIV sequence dataset and determined an empirically justified range of genetic distance thresholds for identifying potential transmission partners. We conclude that genetic linkage provides more reliable evidence for identifying potential transmission partners than partner naming, highlighting the importance and complementarity of both epidemiological and molecular genetic surveillance for characterizing regional HIV-1 epidemics.

Project description:ImportanceMore evidence on associations between mandated paid sick leave and health service utilization among low-income adults is needed to guide health policy and legislation nationwide.ObjectiveTo evaluate the association between New York City's 2014 paid sick leave mandate and health care utilization among Medicaid-enrolled adults.Design setting and participantsThis retrospective cohort study used New York State Medicaid administrative data for adults 18 to 64 years old continuously enrolled in Medicaid from August 1, 2011, through July 31, 2017. A difference-in-differences approach with entropy balancing weights was used to compare New York City with the rest of New York State to assess the association of the paid sick leave mandate with health care utilization, and for those 40 to 64 years old, with preventive care utilization. The data analysis was performed from June through August 2020.ExposuresTemporal and spatial variation in exposure to the mandate.Main outcomes and measuresAnnual health care utilization (emergency care, specialist visits, and primary care clinician visits) per Medicaid-enrolled adult. Secondary outcomes include categories of emergency utilization and utilization of 5 preventive services.ResultsOf 552 857 individuals (mean [SD] age, 43 [12] years; 351 130 [64%] women) who met inclusion criteria, 99 181 (18%) were White, 162 492 (29%) Black, and 138 061 (25%) Hispanic. Paid sick leave was significantly associated with a reduction in the probability of emergency care (-0.6 percentage points [pp]; 95% CI, -0.7 to -0.5 pp; P < .001), including a 0.3 pp reduction (95% CI, -0.4 to -0.2; P < .001) in care for conditions treatable in a primary care setting and an increase in annual outpatient visits (0.124 pp; 95% CI, 0.040 to 0.208 pp; P < .001). Among those 40 to 64 years old, the mandate was significantly associated with increased probabilities of glycated hemoglobin A1c level testing (2.9 pp; 95% CI, 2.5-3.3 pp; P < .001), blood cholesterol testing (2.7 pp; 95% CI, 2.5-2.9 pp; P < .001), and colon cancer screening (0.4 pp; 95% CI, 0.2-0.6 pp; P < .001).Conclusions and relevanceThis retrospective cohort study of nonelderly adults enrolled in Medicaid New York State showed that mandated paid sick leave in New York City was significantly associated with differences in several dimensions of health care services use.

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Genetic Adaptation in New York City Rats.

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Genetic Adaptation in New York City Rats.

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