Combining individual and wastewater whole genome sequencing improves SARS-CoV-2 surveillance DOI
Evan P. Troendle, Andrew Lee, Marina Reyne

et al.

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 22, 2024

ABSTRACT Background Robust methods to track pathogens support public health surveillance. Both wastewater (WW) and individual whole genome sequencing (WGS) are used assess viral variant diversity spread. However, their relative performance the information provided by each approach have not been sufficiently quantified. Therefore, we conducted a comparative evaluation using extensive longitudinal SARS-CoV-2 WGS datasets in Northern Ireland (NI). Methods of was performed on >4k WW samples >23k individuals across NI from 14 th November 2021 11 March 2023. RNA amplified ARTIC nCov-2019 protocol sequenced an Illumina MiSeq. Wastewater data were analysed Freyja determine compositions, which compared through time series correlation analyses. Inter-programme agreements evaluated mean absolute error (MAE) calculations. treatment plant (WWTP) performances ranked MAE. Volatile periods identified numerical derivative Geospatial spreading patterns determined horizontal curve shifting. Findings Strong concordance observed between compositions distributions, influenced rate diversity. Overall derived sequences WWTP regionally clustered rather than dominated local population size. detected common nucleotide substitutions many variants complementary additional substitutions. Conserved both approaches. Interpretation effectively monitor dynamics. Combining these approaches enhances confidence predicting composition spread major variants, particularly with higher rates. Each method detects unique mutations, integration improves overall Funding Individual funded via Belfast Health Social Care Trust (Department for Ireland) COVID-19 Genomics UK (COG-UK) consortium, supported Medical Research Council (MRC), Innovation (UKRI), National Institute (NIHR), Department (DHSC), Wellcome Sanger Institute. The Surveillance Programme Ireland. EPT COG-UK Early Career Scheme.

Language: Английский

Wastewater-Based Surveillance of Respiratory Syncytial Virus Reveals a Temporal Disconnect in Disease Trajectory across an Active International Land Border DOI Creative Commons
Mackenzie Beach, Ryland Corchis-Scott, Qiudi Geng

et al.

Environment & Health, Journal Year: 2025, Volume and Issue: 3(4), P. 425 - 435

Published: Jan. 29, 2025

Conventional metrics for tracking infectious diseases, including case and outbreak data syndromic surveillance, can be resource-intensive, misleading, comparatively slow with prolonged collection, analysis authentication. This study examined the 2022–2023 Respiratory Syncytial Virus (RSV) season in a contiguous metropolitan area connected by an active international land border, affording opportunity comparison of respiratory virus spanning two independent public health jurisdictions. Time-lagged cross correlation qualitative examination wastewater signals showed that peak Detroit (MI, USA) RSV predated Windsor (ON, Canada) approximately 5 weeks. A strong positive relationship was observed between N-gene concentrations hospitalization rates Windsor-Essex (Kendall's τ = 0.539, p ≤ 0.001, Spearman's ρ 0.713, 0.001) as well 0.739, 0.888, 0.001). demonstrated surveillance reveal regional differences infection dynamics communities provide measure prevalence RSV, underreported disease. These findings support use cost-effective tool monitoring to enhance existing systems better inform disease mitigation strategies.

Language: Английский

Citations

0
Spatial and temporal variation in respiratory syncytial virus (RSV) subtype RNA in wastewater and relation to clinical specimens DOI Creative Commons

Winnie Zambrana,

ChunHong Huang,

D. Solis

et al.

mSphere, Journal Year: 2024, Volume and Issue: 9(7)

Published: June 27, 2024

Respiratory syncytial virus (RSV) causes a large burden of respiratory illness globally. It has two subtypes, RSV A and B, but little is known regarding the predominance these subtypes during different seasons their impact on morbidity mortality. Using molecular methods, we quantified B RNA in wastewater solids across multiple metropolitan areas to gain insight into subtypes. We determined predominant subtype for each group using proportion total (RSV + B) sample (

Language: Английский

Citations

3
Combining individual and wastewater whole genome sequencing improves SARS-CoV-2 surveillance DOI
Evan P. Troendle, Andrew Lee, Marina Reyne

et al.

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 22, 2024

ABSTRACT Background Robust methods to track pathogens support public health surveillance. Both wastewater (WW) and individual whole genome sequencing (WGS) are used assess viral variant diversity spread. However, their relative performance the information provided by each approach have not been sufficiently quantified. Therefore, we conducted a comparative evaluation using extensive longitudinal SARS-CoV-2 WGS datasets in Northern Ireland (NI). Methods of was performed on >4k WW samples >23k individuals across NI from 14 th November 2021 11 March 2023. RNA amplified ARTIC nCov-2019 protocol sequenced an Illumina MiSeq. Wastewater data were analysed Freyja determine compositions, which compared through time series correlation analyses. Inter-programme agreements evaluated mean absolute error (MAE) calculations. treatment plant (WWTP) performances ranked MAE. Volatile periods identified numerical derivative Geospatial spreading patterns determined horizontal curve shifting. Findings Strong concordance observed between compositions distributions, influenced rate diversity. Overall derived sequences WWTP regionally clustered rather than dominated local population size. detected common nucleotide substitutions many variants complementary additional substitutions. Conserved both approaches. Interpretation effectively monitor dynamics. Combining these approaches enhances confidence predicting composition spread major variants, particularly with higher rates. Each method detects unique mutations, integration improves overall Funding Individual funded via Belfast Health Social Care Trust (Department for Ireland) COVID-19 Genomics UK (COG-UK) consortium, supported Medical Research Council (MRC), Innovation (UKRI), National Institute (NIHR), Department (DHSC), Wellcome Sanger Institute. The Surveillance Programme Ireland. EPT COG-UK Early Career Scheme.

Language: Английский

Citations

0