scholarly journals Tracking Cryptic SARS-CoV-2 Lineages Detected in NYC Wastewater

2021 ◽  
Author(s):  
Davida S Smyth ◽  
Monica Trujillo ◽  
Devon A Gregory ◽  
Kristen Cheung ◽  
Anna Gao ◽  
...  
Keyword(s):  
New York ◽  
New York City ◽  
High Throughput Sequencing ◽  
Protein Gene ◽  
Wastewater Treatment Plants ◽  
Clinical Samples ◽  
Direct Inference ◽  
Animal Reservoir ◽  
Novel Variants ◽  
Induced Immunity

Tracking SARS-CoV-2 genetic diversity is strongly indicated because diversifying selection may lead to the emergence of novel variants resistant to naturally acquired or vaccine-induced immunity. To monitor New York City (NYC) for the presence of novel variants, we amplified regions of the SARS-CoV-2 Spike protein gene from RNA acquired from all 14 NYC wastewater treatment plants (WWTPs) and ascertained the diversity of lineages from these samples using high throughput sequencing. Here we report the detection and increasing frequencies of novel SARS-CoV-2 lineages not recognized in GISAIDs EpiCoV database. These lineages contain mutations rarely observed in clinical samples, including Q493K, Q498Y, H519N and T572N. Many of these mutations were found to expand the tropism of SARS-CoV-2 pseudoviruses by allowing infection of cells expressing the human, mouse, or rat ACE2 receptor. In addition, pseudoviruses containing the Spike amino acid sequence of these lineages were found to be resistant to many different classes of receptor binding domain (RBD) binding neutralizing monoclonal antibodies. We offer several hypotheses for the anomalous presence of these mutations, including the possibility of a non-human animal reservoir. Although wastewater sampling cannot provide direct inference of SARS-CoV-2 clinical sequences, our research revealed several lineages that could be relevant to public health and they would not have been discovered if not for wastewater surveillance.

scholarly journals Detection of Mutations Associated with Variants of Concern Via High Throughput Sequencing of SARS-CoV-2 Isolated from NYC Wastewater

2021 ◽  
Author(s):  
Davida S. Smyth ◽  
Monica Trujillo ◽  
Kristen Cheung ◽  
Anna Gao ◽  
Irene Hoxie ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Herd Immunity ◽  
Control Measures ◽  
Clinical Samples ◽  
Genetic Sequencing ◽  
Novel Variants ◽  
The World ◽  
Induced Immunity

ABSTRACTMonitoring SARS-CoV-2 genetic diversity is strongly indicated because diversifying selection may lead to the emergence of novel variants resistant to naturally acquired or vaccine-induced immunity. To date, most data on SARS-CoV-2 genetic diversity has come from the sequencing of clinical samples, but such studies may suffer limitations due to costs and throughput. Wastewater-based epidemiology may provide an alternative and complementary approach for monitoring communities for novel variants. Given that SARS-CoV-2 can infect the cells of the human gut and is found in high concentrations in feces, wastewater may be a valuable source of SARS-CoV-2 RNA, which can be deep sequenced to provide information on the circulating variants in a community. Here we describe a safe, affordable protocol for the sequencing of SARS-CoV-2 RNA using high-throughput Illumina sequencing technology. Our targeted sequencing approach revealed the presence of mutations associated with several Variants of Concern at appreciable frequencies. Our work demonstrates that wastewater-based SARS-CoV-2 sequencing can inform surveillance efforts monitoring the community spread of SARS-CoV-2 Variants of Concern and detect the appearance of novel emerging variants more cheaply, safely, and efficiently than the sequencing of individual clinical samples.IMPORTANCEThe SARS-CoV-2 pandemic has caused millions of deaths around the world as countries struggle to contain infections. The pandemic will not end until herd immunity is reached, that is, when most of the population has either recovered from SARS-CoV-2 infection or is vaccinated against SARS-CoV-2. However, the emergence of new SARS-CoV-2 variants of concern threatens to erase gains. Emerging new variants may re-infect persons who have recovered from COVID-19 or may evade vaccine-induced immunity. However, scaling up SARS-CoV-2 genetic sequencing to monitor Variants of Concern in communities around the world is challenging. Wastewater-based sequencing of SARS-CoV-2 RNA can be used to monitor the presence of emerging variants in large communities to enact control measures to minimize the spread of these variants. We describe here the identification of alleles associated with several variants of concern in wastewater obtained from NYC watersheds.

scholarly journals Initial Mapping of the New York City Wastewater Virome

mSystems ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
K. Gulino ◽  
J. Rahman ◽  
M. Badri ◽  
J. Morton ◽  
R. Bonneau ◽  
...  
Keyword(s):  
New York ◽  
New York City ◽  
York City ◽  
Wastewater Treatment Plants ◽  
Urban Environments ◽  
Metagenomic Data ◽  
Functional Importance ◽  
Wide Range ◽  
Viral Communities ◽  
Local Sampling

ABSTRACT Bacteriophages are abundant members of all microbiomes studied to date, influencing microbial communities through interactions with their bacterial hosts. Despite their functional importance and ubiquity, phages have been underexplored in urban environments compared to their bacterial counterparts. We profiled the viral communities in New York City (NYC) wastewater using metagenomic data collected in November 2014 from 14 wastewater treatment plants. We show that phages accounted for the largest viral component of the sewage samples and that specific virus communities were associated with local environmental conditions within boroughs. The vast majority of the virus sequences had no homology matches in public databases, forming an average of 1,700 unique virus clusters (putative genera). These new clusters contribute to elucidating the overwhelming proportion of data that frequently goes unidentified in viral metagenomic studies. We assigned potential hosts to these phages, which appear to infect a wide range of bacterial genera, often outside their presumed host. We determined that infection networks form a modular-nested pattern, indicating that phages include a range of host specificities, from generalists to specialists, with most interactions organized into distinct groups. We identified genes in viral contigs involved in carbon and sulfur cycling, suggesting functional importance of viruses in circulating pathways and gene functions in the wastewater environment. In addition, we identified virophage genes as well as a nearly complete novel virophage genome. These findings provide an understanding of phage abundance and diversity in NYC wastewater, previously uncharacterized, and further examine geographic patterns of phage-host association in urban environments. IMPORTANCE Wastewater is a rich source of microbial life and contains bacteria, viruses, and other microbes found in human waste as well as environmental runoff sources. As part of an effort to characterize the New York City wastewater metagenome, we profiled the viral community of sewage samples across all five boroughs of NYC and found that local sampling sites have unique sets of viruses. We focused on bacteriophages, or viruses of bacteria, to understand how they may influence the microbial ecology of this system. We identified several new clusters of phages and successfully associated them with bacterial hosts, providing insight into virus-host interactions in urban wastewater. This study provides a first look into the viral communities present across the wastewater system in NYC and points to their functional importance in this environment.

scholarly journals Uncertainty-based flood resiliency evaluation of wastewater treatment plants

2016 ◽  
Vol 18 (6) ◽  
pp. 990-1006 ◽  
Author(s):  
M. Karamouz ◽  
E. Rasoulnia ◽  
Z. Zahmatkesh ◽  
M. A. Olyaei ◽  
A. Baghvand
Keyword(s):  
New York ◽  
New York City ◽  
Wastewater Treatment ◽  
Flood Risk ◽  
Wastewater Treatment Plants ◽  
Urban Systems ◽  
Investment Strategies ◽  
New Perspective ◽  
Unified Index ◽  
Range Of Variation

Wastewater treatment plants (WWTPs) have a significant role in urban systems’ serviceability. These infrastructures, especially in coastal regions, are vulnerable to flooding. To minimize vulnerability, a better understanding of flood risk must be realized. To quantify the extent of efforts for flood risk management, a unified index is needed for evaluating resiliency as a key concept in understanding vulnerability. Here, a framework is developed to evaluate the resiliency of WWTPs in coastal areas of New York City. An analysis of the current understanding of vulnerability is performed and a new perspective utilizing different components including resourcefulness, robustness, rapidity, and redundancy is presented to quantify resiliency using a multi-criteria decision-making (MCDM) technique. To investigate the effect of certain factors of WWTPs on resiliency, uncertainty analysis is also incorporated in developing the framework. As a result, rather than a single value, a range of variation for each WWTP's resiliency is obtained. Finally, improvement of WWTPs’ performance is investigated by allocating financial resources. The results show the significant value of quantifying and improving resiliency that could be used in development of investment strategies. Consideration of uncertainty in the analysis is of great worth to estimate the potential room for improvement of resiliency of individual WWTPs.

scholarly journals Viral Diversity of House Mice in New York City

mBio ◽  
2018 ◽  
Vol 9 (2) ◽  
pp. e01354-17 ◽  
Author(s):  
Simon H. Williams ◽  
Xiaoyu Che ◽  
Joel A. Garcia ◽  
John D. Klena ◽  
Bohyun Lee ◽  
...  
Keyword(s):  
New York ◽  
New York City ◽  
York City ◽  
High Throughput Sequencing ◽  
Close Contact ◽  
Residential Buildings ◽  
Invasive Pest ◽  
House Mice ◽  
Human Pathogens ◽  
Wide Range

ABSTRACTThe microbiome of wildMus musculus(house mouse), a globally distributed invasive pest that resides in close contact with humans in urban centers, is largely unexplored. Here, we report analysis of the fecal virome of house mice in residential buildings in New York City, NY. Mice were collected at seven sites in Manhattan, Queens, Brooklyn, and the Bronx over a period of 1 year. Unbiased high-throughput sequencing of feces revealed 36 viruses from 18 families and 21 genera, including at least 6 novel viruses and 3 novel genera. A representative screen of 15 viruses by PCR confirmed the presence of 13 of these viruses in liver. We identified an uneven distribution of diversity, with several viruses being associated with specific locations. Higher mouse weight was associated with an increase in the number of viruses detected per mouse, after adjusting for site, sex, and length. We found neither genetic footprints to known human viral pathogens nor antibodies to lymphocytic choriomeningitis virus.IMPORTANCEMice carry a wide range of infectious agents with zoonotic potential. Their proximity to humans in the built environment is therefore a concern for public health. Laboratory mice are also the most common experimental model for investigating the pathobiology of infectious diseases. In this survey of mice trapped in multiple locations within New York City over a period of 1 year, we found a diverse collection of viruses that includes some previously not associated with house mice and others that appear to be novel. Although we found no known human pathogens, our findings provide insights into viral ecology and may yield models that have utility for clinical microbiology.

Critical modeling parameters identified for 3D CFD modeling of rectangular final settling tanks for New York City wastewater treatment plants

2012 ◽  
Vol 65 (6) ◽  
pp. 1087-1094 ◽  
Author(s):  
K. Ramalingam ◽  
S. Xanthos ◽  
M. Gong ◽  
J. Fillos ◽  
K. Beckmann ◽  
...  
Keyword(s):  
New York ◽  
New York City ◽  
Wastewater Treatment ◽  
York City ◽  
Wastewater Treatment Plants ◽  
Settling Tank ◽  
Cfd Modeling ◽  
Cfd Model ◽  
Conventional Activated Sludge ◽  
City College

New York City Environmental Protection is in the process of incorporating biological nitrogen removal (BNR) in its wastewater treatment plants (WWTPs) which entails operating the aeration tanks with higher levels of mixed liquor suspended solids (MLSS) than a conventional activated sludge process. The objective of this paper is to discuss two of the important parameters introduced in the 3D CFD model that has been developed by the City College of New York (CCNY) group: (a) the development of the ‘discrete particle’ measurement technique to carry out the fractionation of the solids in the final settling tank (FST) which has critical implications in the prediction of the effluent quality; and (b) the modification of the floc aggregation (KA) and floc break-up (KB) coefficients that are found in Parker's flocculation equation (Parker et al. 1970, 1971) used in the CFD model. The dependence of these parameters on the predictions of the CFD model will be illustrated with simulation results on one of the FSTs at the 26th Ward WWTP in Brooklyn, NY.

scholarly journals Spatiotemporal analyses illuminate the competitive advantage of a SARS-CoV-2 variant of concern over a variant of interest

2021 ◽  
Author(s):  
Alexis Russell ◽  
Collin O'Connor ◽  
Erica Lasek-Nesselquist ◽  
Jonathan Plitnick ◽  
John P Kelly ◽  
...  
Keyword(s):  
New York ◽  
New York City ◽  
Immune Evasion ◽  
York City ◽  
Scan Statistics ◽  
Competitive Advantages ◽  
Novel Variants ◽  
Spatiotemporal Analyses ◽  
Time Scan

The emergence of novel SARS-CoV-2 variants in late 2020 and early 2021 raised alarm worldwide and prompted reassessment of the management, surveillance, and projected future of COVID-19. Mutations that confer competitive advantages by increasing transmissibility or immune evasion have been associated with the localized dominance of single variants. Thus, elucidating the evolutionary and epidemiological dynamics among novel variants is essential for understanding the trajectory of the COVID-19 pandemic. Here we show the interplay between B.1.1.7 (Alpha) and B.1.526 (Iota) in New York (NY) from December 2020 to April 2021 through phylogeographic analyses, space-time scan statistics, and cartographic visualization. Our results indicate that B.1.526 likely evolved in the Bronx in late 2020, providing opportunity for an initial foothold in the heavily interconnected New York City (NYC) region, as evidenced by numerous exportations to surrounding locations. In contrast, B.1.1.7 became dominant in regions of upstate NY where B.1.526 had limited presence, suggesting that B.1.1.7 was able to spread more efficiently in the absence of B.1.526. Clusters discovered from the spatial-time scan analysis supported the role of competition between B.1.526 and B.1.1.7 in NYC in March 2021 and the outsized presence of B.1.1.7 in upstate NY in April 2021. Although B.1.526 likely delayed the rise of B.1.1.7 in NYC, B.1.1.7 became the dominant variant in the Metro region by the end of the study period. These results reveal the advantages endemicity may grant to a variant (founder effect), despite the higher fitness of an introduced lineage. Our research highlights the dynamics of inter-variant competition at a time when B.1.617.2 (Delta) is overtaking B.1.1.7 as the dominant lineage worldwide. We believe our combined spatiotemporal methodologies can disentangle the complexities of shifting SARS-CoV-2 variant landscapes at a time when the evolution of variants with additional fitness advantages is impending.

An Important Armenian MS. with Greek Miniatures

1942 ◽  
Vol 74 (3-4) ◽  
pp. 155-162
Author(s):  
H. Kurdian
Keyword(s):  
New York ◽  
New York City ◽  
York City ◽  
Christian Iconography

In 1941 while in New York City I was fortunate enough to purchase an Armenian MS. which I believe will be of interest to students of Eastern Christian iconography.

Hospitals: N.Y. Appellate Court Denies Move to Privatize Public Hospital

1999 ◽  
Vol 27 (2) ◽  
pp. 202-203
Author(s):  
Robert Chatham
Keyword(s):  
New York ◽  
New York City ◽  
York City ◽  
Public Health System ◽  
Municipal Hospital ◽  
The Public ◽  
Public Benefit ◽  
For Profit ◽  
Benefit Corporation ◽  
The City

The Court of Appeals of New York held, in Council of the City of New York u. Giuliani, slip op. 02634, 1999 WL 179257 (N.Y. Mar. 30, 1999), that New York City may not privatize a public city hospital without state statutory authorization. The court found invalid a sublease of a municipal hospital operated by a public benefit corporation to a private, for-profit entity. The court reasoned that the controlling statute prescribed the operation of a municipal hospital as a government function that must be fulfilled by the public benefit corporation as long as it exists, and nothing short of legislative action could put an end to the corporation's existence.In 1969, the New York State legislature enacted the Health and Hospitals Corporation Act (HHCA), establishing the New York City Health and Hospitals Corporation (HHC) as an attempt to improve the New York City public health system. Thirty years later, on a renewed perception that the public health system was once again lacking, the city administration approved a sublease of Coney Island Hospital from HHC to PHS New York, Inc. (PHS), a private, for-profit entity.

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