Detection of Six Different Human Enteric Viruses Contaminating Environmental Water in Chiang Mai, Thailand

The impact of signal variability on COVID-19 epidemic growth rate estimation from wastewater surveillance data

Testing samples of wastewater for markers of infectious disease became a widespread method of surveillance during the COVID-19 pandemic. While these data generally correlate well with other indicators of national prevalence, samples that cover localised regions tend to be highly variable over short time scales. Here we introduce a procedure for estimating the real-time growth rate of pathogen prevalence using time series data from wastewater sampling. The number of copies of a target gene found in a sample is modelled as time-dependent random variable whose distribution is estimated using maximum likelihood. The output depends on a hyperparameter that controls the sensitivity to variability in the underlying data. We apply this procedure to data reporting the number of copies of the N1 gene of SARS-CoV-2 collected at water treatment works across Scotland between February 2021 and February 2023. The real-time growth rate of the SARS-CoV-2 prevalence is estimated at all 121 wastewater sampling sites covering a diverse range of locations and population sizes. We find that the sensitivity of the fitting procedure to natural variability determines its reliability in detecting the early stages of an epidemic wave. Applying the same procedure to hospital admissions data, we find that changes in the growth rate are detected an average of 2 days earlier in wastewater than in hospital admissions. In conclusion, this paper provides a robust method to generate reliable estimates of epidemic growth from highly variable data. Applying this method to samples collected at wastewater treatment works provides highly responsive situational awareness to inform public health.

Molecular detection of SARS-CoV-2 and medically important respiratory and gastrointestinal virus pathogens on Thai currency

Fomite-mediated viral transmission through using cash might be a potential risk to human health. Persistence of SARS-CoV-2, and other medically important viruses was investigated. A total of 300 samples (i.e., 150 banknotes and 150 coins) were randomly collected from nineteen fresh markets distributed across seventeen districts of Bangkok, Thailand. Every banknote or coin was entirely swabbed and generated a total of 100 pool samples. Total viral nucleic acid was extracted and subjected for multiplex real-time qRT-PCR using Allplex™ SARS-CoV-2/FluA/FluB/RSV assay and Allplex™ GI-virus assay. The results revealed detection rate of 4% (4/100), and they were only detected in banknote pooled samples. Two samples collected from fish shops tested positive for SARS-CoV-2 (2%, 2/100); meanwhile, two samples (2%, 2/100) from pork and chicken shops tested positive for rotavirus A. None of pool samples were detected for influenza A and B viruses, respiratory syncytial virus, norovirus genogroup I and II, adenovirus, astrovirus, and sapovirus. Phylogenetic analysis demonstrated that rotavirus A belonged to genotype G8; meanwhile, SARS-CoV-2 resembled omicron GRA JN.1 sub variant. Our finding is the first report for demonstrating the presence of SARS-CoV-2 and rotavirus A in Thai banknotes on real-world situation, implying the potential risk to human health and safety.

A highly prevalent and specific cryptic plasmid pBI143 for human fecal pollution tracking in a subtropical urban river

Microbial source tracking (MST) is a critical tool for identifying sources of human and animal fecal pollution in aquatic environments. To enhance human fecal pollution tracking, this study evaluated the performance characteristics of pBI143, a cryptic plasmid recently identified for potential MST applications. Nucleic acid samples from ten animal species were screened for pBI143, revealing its presence in a small number of pigs, cows, dogs, cats, and flying fox fecal samples. Despite minor cross-detection with non-human fecal samples, pBI143 exhibited a high specificity value (up to 0.93). In untreated urban wastewater, pBI143 was consistently detected in all samples, exhibiting higher concentrations than the well-established human Bacteroides HF183 marker gene. Following a wastewater discharge event, pBI143 concentrations were monitored in an urban river and correlated well with both HF183 and enterococci 23S rRNA marker genes. Using conditional probability analysis, the likelihood of human fecal pollution was estimated to be 89.3 % when pBI143 was detected in 50 % of the river water samples. This study demonstrates that pBI143 is a highly abundant and specific human fecal marker for tracking human fecal pollution in environmental waters. Monitoring of pBI143 could significantly improve the accuracy of human fecal source identification in environmental waters, offering valuable insights for public health risk management and pollution mitigation strategies.

Capsid Integrity Detection of Enteric Viruses in Reclaimed Waters

Climate change, unpredictable weather patterns, and droughts are depleting water resources in some parts of the globe, where recycling and reusing wastewater is a strategy for different purposes. To counteract this, the EU regulation for water reuse sets minimum requirements for the use of reclaimed water for agricultural irrigation, including a reduction in human enteric viruses. In the present study, the occurrence of several human enteric viruses, including the human norovirus genogroup I (HuNoV GI), HuNoV GII, and rotavirus (RV), along with viral fecal contamination indicator crAssphage was monitored by using (RT)-qPCR methods on influent wastewater and reclaimed water samples. Moreover, the level of somatic coliphages was also determined as a culturable viral indicator. To assess the potential viral infectivity, an optimization of a capsid integrity PMAxx-RT-qPCR method was performed on sewage samples. Somatic coliphages were present in 60% of the reclaimed water samples, indicating inefficient virus inactivation. Following PMAxx-RT-qPCR optimization, 66% of the samples tested positive for at least one of the analyzed enteric viruses, with concentrations ranging from 2.79 to 7.30 Log10 genome copies (gc)/L. Overall, most of the analyzed reclaimed water samples did not comply with current EU legislation and contained potential infectious viral particles.

Biosensors for waterborne virus detection: Challenges and strategies

Waterborne viruses that can be harmful to human health pose significant challenges globally, affecting health care systems and the economy. Identifying these waterborne pathogens is essential for preventing diseases and protecting public health. However, handling complex samples such as human and wastewater can be challenging due to their dynamic and complex composition and the ultralow concentration of target analytes. This review presents a comprehensive overview of the latest breakthroughs in waterborne virus biosensors. It begins by highlighting several promising strategies that enhance the sensing performance of optical and electrochemical biosensors in human samples. These strategies include optimizing bioreceptor selection, transduction elements, signal amplification, and integrated sensing systems. Furthermore, the insights gained from biosensing waterborne viruses in human samples are applied to improve biosensing in wastewater, with a particular focus on sampling and sample pretreatment due to the dispersion characteristics of waterborne viruses in wastewater. This review suggests that implementing a comprehensive system that integrates the entire waterborne virus detection process with high-accuracy analysis could enhance virus monitoring. These findings provide valuable insights for improving the effectiveness of waterborne virus detection, which could have significant implications for public health and environmental management.