Springer eBooks, Год журнала: 2024, Номер unknown, С. 65 - 77
Опубликована: Янв. 1, 2024
Язык: Английский
BMC Genomics, Год журнала: 2025, Номер 26(1)
Опубликована: Янв. 29, 2025
Abstract The COVID-19 pandemic has underscored the importance of virus surveillance in public health and wastewater-based epidemiology (WBE) emerged as a non-invasive, cost-effective method for monitoring SARS-CoV-2 its variants at community level. Unfortunately, current variant methods depend heavily on updated genomic databases with data derived from clinical samples, which can become less sensitive representative testing sequencing efforts decline. In this paper, we introduce HERCULES ( H igh-throughput E pidemiological R econstruction C lustering U ncovering L ineages nvironmental S ARS-CoV-2), an unsupervised that uses long-read single 1 Kb fragment Spike gene. identifies quantifies mutations lineages without requiring database-guided deconvolution, enhancing detection novel variants. We evaluated Norwegian wastewater samples collected July 2022 to October 2023 part national pilot WBE SARS-CoV-2. Strong correlations were observed between sample terms prevalence lineages. Furthermore, found trends identified one week earlier than data. Our results demonstrate HERCULES’ capability identify new before their providing early warnings potential outbreaks. methodology described paper is easily adaptable other pathogens, offering versatile tool environmental emerging pathogens.
Язык: Английский
Процитировано
0
PLoS ONE, Год журнала: 2025, Номер 20(1), С. e0317105 - e0317105
Опубликована: Янв. 30, 2025
Estimating the trend of new infections was crucial for monitoring risk and evaluating strategies interventions during COVID-19 pandemic. The pandemic revealed utility data sources highlighted challenges in interpreting surveillance indicators when changes disease severity, testing practices or reporting occur. Our study aims to estimate underlying by combining estimates growth rates from all available Norway. We estimated using a negative binomial regression method aligned time hospital admissions maximising correlations. Using meta-analysis framework, we calculated overall reproduction numbers including assessments heterogeneity between indicators. find that reached maximum 25% per day March 2020, but afterwards they were -10% 10% day. correlations different 0.5 1.0. Growth based on wastewater, panel cohort can give up 14 days earlier signals trends compared admissions, while positive lab tests 7 earlier. Combining multiple provides useful description This is powerful technique holistic understanding easily be adapted situations.
Язык: Английский
Процитировано
0
PLOS Global Public Health, Год журнала: 2025, Номер 5(4), С. e0004397 - e0004397
Опубликована: Апрель 9, 2025
By tracking infectious diseases through sewage, municipal-scale wastewater surveillance has provided early warnings of future COVID-19 hospitalisations, identified biases in diagnostic testing, and is rapidly expanding to a broader array pathogens. Despite applications the targeted delivery local interventions, near-source received less attention we know little about time series dynamics contrasting To address this, conducted at five sites for SARS-CoV-2 two norovirus GI, GII, influenza A virus, B human respiratory syncytial virus (RSV RSV B). Sites were selected functions: an office, charity centre, museum, university, care home. The key findings are (1) detections linked events (staff sickness, enhanced cleaning, changing populations); (2) decreased order GII > GI ≈ B; (3) correlation between data national increases as function catchment size viral prevalence (examples include BA.4/BA.5 variant peak museum winter season); (4) strong weekday periodicity detections, with against case numbers increasing when modelling variable lag times faecal shedding onset clinical diagnosis (R 2 = 0.45 0.84-0.86); (5) log-linear relationship frequency detection log(catchment size⋅viral prevalence) 0.6914-0.9066). Finally, propose use cases. Firstly, rare or high-risk pathogens, sentinel systems provide warning outbreaks, achieving high community coverage without behaviour change low cost versus testing. Secondly, endemic reveals long-term patterns trends, effectiveness policies, vulnerabilities.
Язык: Английский
Процитировано
0
NEJM Evidence, Год журнала: 2024, Номер 3(5)
Опубликована: Апрель 23, 2024
Accurate diagnostics are critical in public health to ensure successful disease tracking, prevention, and control. Many of the same characteristics desirable for diagnostic procedures both medicine health: example, low cost, high speed, invasiveness, ease use interpretation, day-to-day consistency, accuracy. This review lays out five principles that salient when goal diagnosis is improve overall a population rather than particular patient, it applies them two important cases: pandemic infectious antimicrobial resistance.
Язык: Английский
Процитировано
2
Future Microbiology, Год журнала: 2024, Номер 19(9), С. 761 - 769
Опубликована: Май 23, 2024
Aim: Wastewater-based epidemiology (WBE) is increasingly used to monitor pandemics. In this manuscript, we review methods and limitations of WBE, as well their online dashboards. Materials & methods: Online dashboards were retrieved using PubMed search engines, annotated for timeliness, availability English version, details on SARS-CoV-2 sublineages, normalization by population PPMoV load, case/hospitalization count charts raw data export. Results: We 51 web portals, half them from Europe. Africa represented South only, only seven portals are available Asia. Conclusion: WBS provides near-real-time cost-effective monitoring analytes across space time in populations. However, tremendous heterogeneity still persists the WBE literature.
Язык: Английский
Процитировано
2
Опубликована: Июнь 26, 2024
Wastewater-based surveillance has emerged as an important method for monitoring SARS-CoV-2. This study investigated the presence of SARS-CoV-2 in wastewater Zambia. We conducted a longitudinal Copperbelt and Eastern provinces Zambia from October 2023 to December during which 155 samples were collected. The subjected three different concentration methods, namely bag-mediated filtration, skimmed milk flocculation, polythene glycol-based assays. Molecular detection nucleic acid was using real-time PCR. Whole genome sequencing Illumina COVIDSEQ assay. Of samples, 62 (40%) tested positive these, 13 sequences sufficient length determine lineages obtained two phylogenetically analyzed. Various Omicron subvariants detected including BA.5, XBB.1.45, BA.2.86, JN.1. Some these have been clinical cases Interestingly, phylogenetic analysis positioned sequence Province B.1.1.529 clade, suggesting that earlier variants late 2021 could still be circulating may not wholly replaced by newer subvariants. stresses need integrating into mainstream strategies circulation
Язык: Английский
Процитировано
1
Eurosurveillance, Год журнала: 2024, Номер 29(33)
Опубликована: Авг. 15, 2024
Wastewater-based surveillance (WBS) has become a widespread method to monitor transmission of SARS-CoV-2 and other human pathogens in Europe. We conducted survey about WBS systems’ objectives, approaches, representativeness usefulness 10 invited European countries 2023, i.e. Austria, Belgium, Denmark, Finland, Greece, Hungary, Italy, Luxembourg, the Netherlands Norway. All completed study questionnaire their systems, shared information as deemed relevant. systems primarily monitored national subnational trends (population coverage: 25–99%), majority (8/10) also tracked variant distribution. Nine reported that were representative population all remarked findings valuable for public health decision-making. Results with relevant authorities published via dedicated websites and/or dashboards. mostly early stages, some implementing pilots. Notable exceptions well-established poliovirus Italy Netherlands. This brings understanding diverse landscape Europe, offering insights future developments collaborations. Furthermore, it highlights need further integration into systems.
Язык: Английский
Процитировано
1
Frontiers in Public Health, Год журнала: 2024, Номер 12
Опубликована: Ноя. 19, 2024
Prisons are high-risk settings for the transmission of communicable disease. Robust surveillance systems required to identify and control outbreaks. Wastewater SARS-CoV-2 was introduced in four prisons Wales March 2022. We investigated its contribution COVID-19 programme.
Язык: Английский
Процитировано
0
International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(16), С. 8839 - 8839
Опубликована: Авг. 14, 2024
Wastewater-based surveillance has emerged as an important method for monitoring the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). This study investigated presence of SARS-CoV-2 in wastewater Zambia. We conducted a longitudinal Copperbelt and Eastern provinces Zambia from October 2023 to December during which 155 samples were collected. The subjected three different concentration methods, namely bag-mediated filtration, skimmed milk flocculation, polythene glycol-based assays. Molecular detection nucleic acid was using real-time Polymerase Chain Reaction (PCR). Whole genome sequencing Illumina COVIDSEQ assay. Of samples, 62 (40%) tested positive SARS-CoV-2. these, 13 sequences sufficient length determine lineages obtained phylogenetically analyzed. Various Omicron subvariants detected including BA.5, XBB.1.45, BA.2.86, JN.1. Some these have been clinical cases Interestingly, phylogenetic analysis positioned sequence Province B.1.1.529 clade, suggesting that earlier variants late 2021 could still be circulating may not wholly replaced by newer subvariants. stresses need integrating into mainstream strategies circulation
Язык: Английский
Процитировано
0
PLoS ONE, Год журнала: 2024, Номер 19(8), С. e0308978 - e0308978
Опубликована: Авг. 15, 2024
During the COVID-19 pandemic in Norway, testing criteria and capacity changed numerous times. In this study, we aim to assess consequences of changes for infectious disease surveillance. We plotted proportion positive PCR tests total number different periods Norway. fitted regression models probability tests, with time weekday as explanatory variables. The analysis focuses on period until 2021, i.e. before Norway started vaccination. There were clear over time. particular, there was a marked difference regime after introduction self-testing, drastic increase self-tests. test being higher weekends public holidays than Mondays-Fridays. lowest Mondays. This implies that and/or test-seeking behaviour weekdays. Though clearly time, cannot general conclude occurred direct consequence policies. It is natural change during pandemic. smaller do not seem have large, abrupt surveillance, larger like massive use self-tests makes data less useful
Язык: Английский
Процитировано
0