In New York City Sewage, a Mysterious Coronavirus Signal

Our work on detecting cryptic SARS-CoV-2 variants in NYC wastewater has been published in Nature Communciations. Emily Anthes of the NY Times wrote a great article abou the work.

Last January, a team of researchers searching for the coronavirus in New York City’s wastewater spotted something strange in their samples. The viral fragments they found had a unique constellation of mutations that had never been reported before in human patients — a potential sign of a new, previously undetected variant.

For the past year, these oddball sequences, or what the scientists call “cryptic lineages,” have continued to pop up in the city’s wastewater.

Lab Finds Earliest Evidence of Omicron Variant in the US

Omicron was probably in N.Y.C. well before the first U.S. case was detected, wastewater data suggest.

The samples suggest that someone in New York City may have had the Omicron variant as early as Nov. 21, four days before South African scientists first announced cases of the variant and ten days before the first U.S. case was reported. Researchers in California and Texas also found evidence of Omicron in wastewater samples from late November.

The article reports on a recent article published in the CDC’s Morbidity and Mortality Weekly Report .

The Lab has submitted a pair of preprints. In the first, we describe our protocol for quantifying SARS-CoV-2 in NYC wastewater. In the second, we used this protocol to sequence SARS-CoV-2 isolated from NYC wastewater. In our targeted sequencing assay, we find a high frequency of mutations associated with circulating Variants of Concern.

Protocol for Safe, Affordable, and Reproducible Isolation and Quantitation of SARS-CoV-2 RNA from Wastewater

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

Monitoring SARS-CoV-2 in Wastewater

Manuscript Published: Reproducibility and sensitivity of 36 methods to quantify the SARS-CoV-2 genetic signal in raw wastewater: findings from an interlaboratory methods evaluation in the U.S.

The Dennehy Lab participated in a nationwide consortial project comparing the best protocols for monitoring SARS-CoV-2 in wastewater. Our pasteurize, filter, PEG concentrate protocol was among the best performing methods for quantifying SARS-CoV-2 concentrations in wastewater. The results are published in Environmental Science: Water Research & Technology.

The Dennehy Lab receives funding from NIH for proposal “Novel Strategies for Treating Biofilm-Forming Pathogens with Phage Therapy”

The Dennehy Lab receives funding from NIH for proposal “Novel Strategies for Treating Biofilm-Forming Pathogens with Phage Therapy”

This project is a collaboration with Dr. Fabrizio Spagnolo. The aim of the proposed work is to assess the viability of a multi-pronged phage therapy approach to eliminate biofilm-associated bacteria. Specifically, we propose to induce prophages already contained within biofilm-associated bacteria to disrupt biofilms. Simultaneously, lytic phages will be applied to kill bacteria dispersing from the biofilm at the point of exit. This dual strategy may allow the eradication of intransigent infections resistant to traditional antibacterial therapy.

The Dennehy Laboratory receives funding from NSF for proposal titled “Metapopulation Modeling to Develop Strategies to Reduce COVID-19 Transmission in Public Spaces”

The Dennehy Laboratory receives funding from NSF for proposal titled “Metapopulation Modeling to Develop Strategies to Reduce COVID-19 Transmission in Public Spaces”

A recently developed computational model (the Ephemeral Island Metapopulation Model (EIMM) that applies metapopulation theory to explain how pathogens persist in hospital environments will be revised to address the spatial spread of SARS-CoV-2 within built environments. An enveloped bacteriophage phi6 will be used to validate model predictions as well as test control strategies. Recommendations resembling established building and fire codes, which regulate how space is allotted per occupant based upon design and usage requirements, will be generated. These recommendations are published at “COVID Code”.

Dr. Sherin Kannoly’s manuscript is published in iScience

In this manuscript, we show that noise in the timing of a cellular event, host cell lysis, follows a concave up curve. This finding suggests that lysis timing has an optimum value that minimizes noise. As such, lysis timing noise may be a target of natural selection. The manuscript is available here.

The Dennehy Lab