scholarly journals Genomic surveillance of SARS-CoV-2 in the Bronx enables clinical and epidemiological inference

2021 ◽  
Author(s):  
J. Maximilian Fels ◽  
Saad Khan ◽  
Ryan Forster ◽  
Karin A. Skalina ◽  
Surksha Sirichand ◽  
...  
Keyword(s):  
New York ◽  
Persistent Infection ◽  
New York State ◽  
Late Summer ◽  
Genomic Diversity ◽  
Temporal Sampling ◽  
Novel Variants ◽  
The Usa ◽  
Early Fall ◽  
Viral Isolates

AbstractThe Bronx was an early epicenter of the COVID-19 pandemic in the USA. We conducted temporal genomic surveillance of SARS-CoV-2 genomes across the Bronx from March-October 2020. Although the local structure of SARS-CoV-2 lineages mirrored those of New York City and New York State, temporal sampling revealed a dynamic and changing landscape of SARS-CoV-2 genomic diversity. Mapping the trajectories of variants, we found that while some have become ‘endemic’ to the Bronx, other, novel variants rose in prevalence in the late summer/early fall. Geographically resolved genomes enabled us to distinguish between a case of reinfection and a case of persistent infection. We propose that limited, targeted, temporal genomic surveillance has clinical and epidemiological utility in managing the ongoing COVID pandemic.SignificanceThe ongoing emergence of novel SARS-CoV-2 variants has highlighted the need for continual genomic surveillance in order to track their spread and limit introductions into new areas. An understanding of circulating viral strains also provides a powerful tool that can be used to make clinical inferences. Here, we employ temporally and geographically resolved sequencing of SARS-CoV-2 samples in order to describe the local landscape of viral variants in the Bronx and to differentiate between cases of re-infection and persistent infection. We propose that local and targeted sequencing of viral isolates is an underutilized approach for managing the COVID pandemic.

scholarly journals Three months of informational trends in COVID-19 across New York City

2020 ◽  
Vol 42 (3) ◽  
pp. 448-450
Author(s):  
Wil Lieberman-Cribbin ◽  
Naomi Alpert ◽  
Adam Gonzalez ◽  
Rebecca M Schwartz ◽  
Emanuela Taioli
Keyword(s):  
New York ◽  
New York City ◽  
York City ◽  
Information Seeking ◽  
New York State ◽  
Search Term ◽  
Multiple Sources ◽  
The Usa ◽  
Trend Data ◽  
Over Time

Abstract In the midst of widespread community transmission of coronavirus disease 2019 (COVID-19) in New York, residents have sought information about COVID-19. We analyzed trends in New York State (NYS) and New York City (NYC) data to quantify the extent of COVID-19-related queries. Data on the number of 311 calls in NYC, Google Trend data on the search term ‘Coronavirus’ and information about trends in COVID-19 cases in NYS and the USA were compiled from multiple sources. There were 1228 994 total calls to 311 between 22 January 2020 and 22 April 2020, with 50 845 calls specific to COVID-19 in the study period. The proportion of 311 calls related to COVID-19 increased over time, while the ‘interest over time’ of the search term ‘Coronavirus’ has exponentially increased since the end of February 2020. It is vital that public health officials provide clear and up-to-date information about protective measures and crucial communications to respond to information-seeking behavior across NYC.

scholarly journals The Impact of Pharmacist Vaccination Privilege during a Nation-Wide Measles Outbreak

Pharmacy ◽  
2020 ◽  
Vol 8 (1) ◽  
pp. 7 ◽  
Author(s):  
Tanya Singh ◽  
Renae L. Smith-Ray ◽  
Michael Taitel
Keyword(s):  
New York ◽  
New York State ◽  
Operating Conditions ◽  
Susceptible Population ◽  
Maximum Capacity ◽  
The Public ◽  
Health Value ◽  
Measles Outbreak ◽  
The Usa ◽  
The Impact

The 2019 measles outbreak was the worst since the USA eliminated measles in 2000. This paper presents the vaccination trends for a large chain-pharmacy, Walgreens, and examines the estimated vaccination capacity and impact of pharmacist privilege policies across states. Specifically, we estimated the number of people who could have been vaccinated in eight states with reduced or no measles, mumps, and rubella (MMR) vaccination privilege during the study period January–June, 2019. During the study period, Walgreens pharmacists administered MMR vaccines to 62,526 patients, a 231.9% increase. If pharmacists had been permitted to vaccinate against measles in the eight states investigated, Walgreens pharmacies would have administered between 12,404 and 36,551 additional vaccinations during that time. We also estimated all chain pharmacies’ capacity to vaccinate in one state that was severely impacted by the measles outbreak, New York, using a range from normal pharmacy operating conditions to maximum capacity. Assuming sufficient demand, it was estimated that chain pharmacies in New York State would have the capacity to vaccinate between 47,688 and 174,856 patients daily, achieving MMR vaccination (first dose) of the measles-susceptible population within 8–28 days. Overall, this study demonstrates the public health value of pharmacist vaccination privilege during a nation-wide outbreak of measles.

scholarly journals Hurricane Irene and Tropical Storm Lee: How Unusual Were They in the Catskill Mountains?

2017 ◽  
Vol 04 (02) ◽  
pp. 1750009 ◽  
Author(s):  
Allan Frei ◽  
Petra Kelly-Voicu
Keyword(s):  
New York ◽  
New York State ◽  
Historical Context ◽  
Late Summer ◽  
Careful Analysis ◽  
Tropical Storm ◽  
Catskill Mountains ◽  
South Central ◽  
Hurricane Irene ◽  
History Of

During the late summer and early autumn of 2011, the Catskill Mountains in south-central New York State experienced devastating flooding associated with former Hurricane Irene and former Tropical Storm Lee. Even in this particularly flood-prone region, the events of fall 2011 are perceived to be unique in the known history of the region and marked a turning point in the perceptions of residents about climate change. Here, precipitation and stream gage records are analyzed to determine just how unusual this season was. The historical precipitation gage record requires careful analysis due to the changing availability of stations. After a set of stations is developed that is appropriate for this analysis, events of lengths 1 day, 5 days, and 60 days are analyzed to identify regionally significant events (as opposed to events localized to one basin) since the early 20th century and to evaluate Irene and Lee in that historical context. Gage record results corroborate the perceptions of local residents that the period between 1996 and 2011, and in particular the events of fall 2011, were unprecedented in the last 100 years and as inferred from analyses of regional tree rings, probably in the last 500 years.

scholarly journals How well does Predictive Soil Mapping represent soil geography? An investigation from the USA

2021 ◽  
Author(s):  
David G. Rossiter ◽  
Laura Poggio ◽  
Dylan Beaudette ◽  
Zamir Libohova
Keyword(s):  
New York ◽  
Soil Properties ◽  
Spatial Patterns ◽  
Landscape Metrics ◽  
New York State ◽  
Histogram Equalization ◽  
Soil Mapping ◽  
Partial Replacement ◽  
Field Surveys ◽  
The Usa

Abstract. We present methods to evaluate the spatial patterns of the geographic distribution of soil properties in the USA, as shown in gridded maps produced by Predictive Soil Mapping (PSM) at global (SoilGrids v2), national (Soil Properties and Class 100 m Grids of the USA), and regional (POLARIS soil properties) scales, and compare them to spatial patterns known from detailed field surveys (gSSURGO). The methods are illustrated with an example: topsoil pH for an area in central New York State. A companion report examines other areas, soil properties, and depth slices. A set of R Markdown scripts is referenced so that readers can apply the analysis for areas of their interest. For the test case we discover and discuss substan- tial discrepancies between PSM products, as well as large differences between the PSM products and legacy field surveys. These differences are in whole-map statistics, visually-identifiable landscape features, level of detail, range and strength of spatial autocorrelation, landscape metrics (Shannon diversity and evenness, shape, aggregation, mean fractal dimension, co-occurence vectors), and spatial patterns of property maps classified by histogram equalization. Histograms and variogram analysis revealed the smoothing effect of machine-learning models. Property class maps made by histogram equalization were substantially different, but there was no consistent trend in their landscape metrics. The model using only national points and covariates was not better than the global model, and in some cases introduced artefacts from a lithology covariate. Uncertainty (5–95% confidence intervals) provided by SoilGrids and POLARIS were unrealistically wide compared to gSSURGO low and high estimated values and show substantially different spatial patterns. We discuss the potential use of the PSM products as a (partial) replacement for field-based soil surveys.

scholarly journals Local persistence of novel regional variants of La Crosse virus in the Northeast USA

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Gillian Eastwood ◽  
John J. Shepard ◽  
Michael J. Misencik ◽  
Theodore G. Andreadis ◽  
Philip M. Armstrong
Keyword(s):  
New York ◽  
New York State ◽  
La Crosse Virus ◽  
The Usa ◽  
Distinct Lineage ◽  
Northeast Usa ◽  
Multiple Species ◽  
Relationship Of ◽  
Virus Isolates

Abstract Background La Crosse virus (LACV) (genus Orthobunyavirus, family Peribunyaviridae) is a mosquito-borne virus that causes pediatric encephalitis and accounts for 50–150 human cases annually in the USA. Human cases occur primarily in the Midwest and Appalachian regions whereas documented human cases occur very rarely in the northeastern USA. Methods Following detection of a LACV isolate from a field-collected mosquito in Connecticut during 2005, we evaluated the prevalence of LACV infection in local mosquito populations and genetically characterized virus isolates to determine whether the virus is maintained focally in this region. Results During 2018, we detected LACV in multiple species of mosquitoes, including those not previously associated with the virus. We also evaluated the phylogenetic relationship of LACV strains isolated from 2005–2018 in Connecticut and found that they formed a genetically homogeneous clade that was most similar to strains from New York State. Conclusion Our analysis argues for local isolation and long-term persistence of a genetically distinct lineage of LACV within this region. We highlight the need to determine more about the phenotypic behavior of these isolates, and whether this virus lineage poses a threat to public health.

Measuring the results of a workshop on installing anaerobic digesters on smaller livestock farms

2018 ◽  
Vol 34 (6) ◽  
pp. 487-491 ◽  
Author(s):  
Rick Welsh ◽  
Michaele E. Webb ◽  
Stefan Grimberg ◽  
Shane Rogers
Keyword(s):  
New York ◽  
New York State ◽  
Ease Of Use ◽  
Small Scale ◽  
Odor Control ◽  
Anaerobic Digesters ◽  
The Usa ◽  
Potential Benefits ◽  
Livestock Farmers ◽  
Livestock Farms

AbstractIt is accepted generally that anaerobic digesters (AD) are efficacious technologies for reducing greenhouse gas emissions from livestock operations (Pronto and Gooch, 2009). In addition, AD technology has a number of other potential benefits including: energy production for use on the farm and for sale, separation of manure solids for ease of use or export off-farm, pathogen reduction leading to healthier labor and herd outcomes and odor control. It is also clear that in the USA, research and extension efforts, including public financing of AD technology installations, have disproportionally been focused on larger farms- e.g., dairy farms with at least 500 milking cows. The latter has begun to change as more resources are being invested in AD technology for smaller livestock farms. We present the results of a pre and post survey implemented at four workshops on small-scale AD technology for livestock farmers in northeastern New York State. Results indicate that information presented shifted farmers’ attitudes such that they viewed AD technology as not overly complex; and, they became less interested in selling generated surplus power off-farm.

Human resource risk and succession planning

2015 ◽  
Vol 75 (1) ◽  
pp. 133-139
Author(s):  
A Edward Staehr
Keyword(s):  
New York ◽  
Human Resource ◽  
Succession Planning ◽  
Business Performance ◽  
New York State ◽  
Management Tools ◽  
Content Type ◽  
York State ◽  
The Usa ◽  
Financial Consultants

Purpose – The purpose of this paper is to illustrate the benefits of utilizing teams of personal and financial consultants to work with farm families in New York State on issues affecting farm business performance. Design/methodology/approach – Program experience in implementing an integrated consulting model provides a framework for illustrating how such a model may be utilized on farms and other family businesses for succession planning. Findings – An integrated personal and financial consulting model is effective in producing lasting business results such as business growth, improved profitability, and reduced interpersonal conflict on farms in New York State. Originality/value – Farmers employ a multitude of risk management tools, such as crop insurance, to reduce various types of risk affecting their farm businesses in New York State, but an area often overlooked by farmers is managing human resource risk, namely succession risk. As the average age of farmers in the USA continues to increase, employing new tools and strategies is critical when developing an effective business succession plan for farmers.

scholarly journals Analysis of SARS-CoV-2 Genomes from Southern California Reveals Community Transmission Pathways in the Early Stage of the US COVID-19 Pandemic

2020 ◽  
Author(s):  
Wenjuan Zhang ◽  
John Paul Govindavari ◽  
Brian Davis ◽  
Stephanie Chen ◽  
Jong Taek Kim ◽  
...  
Keyword(s):  
New York ◽  
Los Angeles ◽  
Local Community ◽  
Early Stage ◽  
Medical Center ◽  
New York State ◽  
The United States ◽  
Genomic Diversity ◽  
York State ◽  
The Us

AbstractGiven the higher mortality rate and widespread phenomenon of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2) within the United States (US) population, understanding the mutational pattern of SARS CoV-2 has global implications for detection and therapy to prevent further escalation. Los Angeles has become an epicenter of the SARS-CoV-2 pandemic in the US. Efforts to contain the spread of SARS-CoV-2 require identifying its genetic and geographic variation and understanding the drivers of these differences. For the first time, we report genetic characterization of SARS-CoV-2 genome isolates in the Los Angeles population using targeted next generation sequencing (NGS). Samples collected at Cedars Sinai Medical Center were collected from patients with confirmed SARS-CoV-2 infection. We identified and diagnosed 192 patients by our in-house qPCR assay. In this population, the highest frequency variants were in known mutations in the 5’UTR, AA193 protein, RdRp and the spike glycoprotein. SARS-CoV-2 transmission within the local community was tracked by integrating mutation data with patient postal codes with two predominant community spread clusters being identified. Notably, significant viral genomic diversity was identified. Less than 10% of the Los Angeles community samples resembled published mutational profiles of SARS-CoV-2 genomes from China, while >50% of the isolates shared closely similarities to those from New York State. Based on these findings we conclude SARS-CoV-2 was likely introduced into the Los Angeles community predominantly from New York State but also via multiple other independent transmission routes including but not limited to Washington State and China.

Vincetoxicum rossicum (European swallowwort).

2021 ◽  
Author(s):  
André Gassmann
Keyword(s):  
New York ◽  
Negative Impact ◽  
New York State ◽  
Danaus Plexippus ◽  
Monarch Butterfly ◽  
Microbial Composition ◽  
Rare And Endangered Species ◽  
Vincetoxicum Rossicum ◽  
The Usa ◽  
Rare And Endangered

Abstract V. rossicum is a herbaceous perennial climbing vine native to Ukraine and southwestern European Russia. It was introduced into North America for ornamental purposes and has spread extensively throughout the lower Great Lakes Basin, particularly Lake Ontario, including New York State, USA and Ontario, Canada. Self-fertility and large numbers of wind-borne seeds ensure rapid dispersal of V. rossicum to new sites. Small patches of V. rossicum can coalesce to form very large, monospecific stands which can outcompete native vegetation resulting in a change in habitats and a decrease in biodiversity. V. rossicum is allelopathic and can alter the microbial composition in the rhizosphere preventing the growth of sensitive plant species. In the USA, competition from V. rossicum is putting pressure on the rare and endangered species Asplenium scolopendrium var. americanum. In addition to this, V. rossicum has been shown to decrease insect biodiversity and may have negative impact on the reproduction of the Monarch butterfly, Danaus plexippus.

scholarly journals State-by-State estimates of R0 at the start of COVID-19 outbreaks in the USA

2020 ◽  
Author(s):  
Anthony R Ives ◽  
Claudio Bozzuto
Keyword(s):  
Public Health ◽  
New York ◽  
New York State ◽  
State Space Model ◽  
Strongly Correlated ◽  
Public Health Policies ◽  
Health Measures ◽  
Rate Of Spread ◽  
The Usa ◽  
Death Count

We estimated the initial rate of spread (r0) and basic reproduction number (R0) for States in the USA experiencing COVID-19 epidemics by analyzing death data time series using a time-varying autoregressive state-space model. The initial spread varied greatly among States, with the highest r0 = 0.31 [0.23, 0.39] (95% CI) in New York State, corresponding to R0 = 6.4 [4.3, 9.0] (95% CI). The variation in initial R0 was strongly correlated with the peak daily death count among States, showing that the initial R0 anticipates subsequent challenges in controlling epidemics. Furthermore, the variation in initial R0 implies different needs for public health measures. Finally, the States that relaxed public health measures early were not those with the lowest risks of resurgence, highlighting the need for science to guide public health policies.

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