Tracing COVID-19 Trails in Wastewater: A Systematic Review of SARS-CoV-2 Surveillance with Viral Variants

Long-term surveillance of SARS-CoV-2 RNA in wastewater in Baltimore

This study was to determine the presence of SARS-CoV-2 RNA in wastewater samples from two wastewater treatment plants in Baltimore over a period of one year. The samples were concentrated by the Polyethylene Glycol 8000 (PEG) method, and RNA fragments were extracted using the QIAamp Viral RNA Mini Kit. RT-PCR and qPCR assays were performed, and Cq values below 40 were analyzed and presented as gene copies/L. N1 and N2 genes were detected in both WWTP samples, with N1 ranging from 1.38 to 3.34 log10 gc/l and N2 ranging from 1.88 to 3.20 log10 gc/l. COVID-19 hospitalization cases in Baltimore County and City were observed to be 40-42 % positively correlated with the copies of N-genes detected in the WWTP-A. On the contrary, the N-genes (N1 and N2) from both WWTPs exhibited a very weak positive and negative relationship with wastewater physical parameters such as pH, electrical conductivity, total dissolved solutes, salinity, and temperature. The reduction in positive correlation with hospitalization cases could be attributed to an increase in immunity amongst the population surveyed. There is a need to ascertain the effect of physical parameters changes from the sampling point to the processing point on the capture and detection of SARS-CoV-2 RNA in wastewater.

Evaluating Interlaboratory Variability in Wastewater-Based COVID-19 Surveillance

Wastewater-based environmental surveillance enables the monitoring of SARS-CoV-2 dynamics within populations, offering critical epidemiological insights. Numerous workflows for tracking SARS-CoV-2 have been developed globally, underscoring the need for interlaboratory comparisons to ensure data consistency and comparability. An inter-calibration test was conducted among laboratories within the network monitoring SARS-CoV-2 in wastewater samples across the Lombardy region (Italy). The test aimed to evaluate data reliability and identify potential sources of variability using robust statistical approaches. Three wastewater samples were analyzed in parallel by four laboratories using identical pre-analytical (PEG-8000-based centrifugation) and analytical processes (qPCR targeting N1/N3 and Orf-1ab). A two-way ANOVA framework within Generalized Linear Models was applied, and multiple pairwise comparisons among laboratories were performed using the Bonferroni post hoc test. The statistical analysis revealed that the primary source of variability in the results was associated with the analytical phase. This variability was likely influenced by differences in the standard curves used by the laboratories to quantify SARS-CoV-2 concentrations, as well as the size of the wastewater treatment plants. The findings of this study highlight the importance of interlaboratory testing in verifying the consistency of analytical determinations and in identifying the key sources of variation.

The Crucial Role of Laboratory Medicine in Addressing Future Public Health Infectious Threats: Insights Gained from the COVID-19 Pandemic

Laboratory testing has played a pivotal role throughout the coronavirus disease 2019 (COVID-19) pandemic, exemplifying the importance of in vitro diagnostics in addressing public health threats posed by outbreaks of infectious diseases. This article aims to present key insights from our expertise, derived from evidence gathered during the COVID-19 pandemic, to inform strategies for managing future infectious challenges. Current scientific evidence underscores that patient sample testing not only allows to diagnose an acute severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but also supports outbreak prediction, improved control measures, anticipation of pressure on the healthcare system, mitigation of adverse clinical outcomes, and early detection of emerging SARS-CoV-2 variants. Additionally, wastewater monitoring has emerged as a powerful tool for forecasting disease burden, including both prevalence and severity. Collectively, these findings underscore the value of diagnostic testing and wastewater surveillance in guiding healthcare planning and optimizing resource allocation during the COVID-19 pandemic, offering a valid framework to be applied to future public health threats, especially to any potential outbreak of "Disease X" that may emerge in the future.

Therapeutic Potential of Neutralizing Monoclonal Antibodies (nMAbs) against SARS-CoV-2 Omicron Variant

BACKGROUND

The COVID-19 pandemic has spurred significant endeavors to devise treatments to combat SARS-CoV-2. A limited array of small-molecule antiviral drugs, specifically monoclonal antibodies and interferon therapy, have been sanctioned to treat COVID-19. These treatments typically necessitate administration within ten days of symptom onset. There have been reported reductions in the effectiveness of these medications due to mutations in non-structural protein genes, particularly against Omicron subvariants. This underscores the pressing requirement for healthcare systems to continually monitor pathogen variability and its impact on the efficacy of prevention and treatments.

AIM

This review aimed to comprehend the therapeutic benefits and recent progress of nMAbs for preventing and treating the Omicron variant of SARS-CoV-2.

RESULTS AND DISCUSSION

Neutralizing monoclonal antibodies (nMAbs) provide a treatment avenue for severely affected individuals, especially those at high risk for whom vaccination is not viable. With their specific epitope affinity, they pose no significant risk of severe adverse effects. The degree of reduction in neutralization varies significantly across different monoclonal antibodies and variant combinations. For instance, Sotrovimab maintained its neutralization effectiveness against Omicron BA.1, but exhibited diminished efficacy against BA.2, BA.4, BA.5, and BA.2.12.1.

CONCLUSION

Bebtelovimab has been observed to preserve its efficacy against all subtypes of the Omicron variant. Subsequently, WKS13, mAb-39, 19n01, F61-d2 cocktail, etc., have become effective. This review has highlighted the therapeutic implications of nMAbs in SARS-CoV-2 Omicron treatment and the progress of COVID-19 drug discovery.

Assessment of environmental factors influencing SARS-CoV-2 in Vietnam's surface water across two years of clinical data

Wastewater-based epidemiology (WBE) is an effective, non-invasive method for monitoring the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by tracking viral prevalence in water. This study aimed to investigate the presence of SARS-CoV-2 in surface water in Vietnam over two years. One-step quantitative reverse transcription polymerase chain reaction (qRT-PCR) assays were employed to quantify SARS-CoV-2 and its variant-specific mutation sites (G339D/E484A) and pepper mild mottle virus (PMMoV) from a total of 315 samples (105 samples per site) to compare with reported Coronavirus disease 2019 (COVID-19) cases and environmental factors. SARS-CoV-2 was detected in 38 % (40/105), 43 % (45/105), and 39 % (41/105) of water samples from Sites A, B, and C, respectively, with concentrations of 3.0-5.6 log10 copies/L. PMMoV concentrations were 5.1-8.9 log10 copies/L. SARS-CoV-2 levels were higher in winter compared with summer. There was a strong positive association between the mutant type and SARS-CoV-2 concentrations (Spearman's rho = 0.77, p < 0.01). The mean concentrations of mutant and nonmutant types were 2.3 and 1.8 log10 copies/L, respectively. Peaks in SARS-CoV-2 concentrations preceded reported COVID-19 cases by 2-4 weeks, with the highest association observed at a 4-week delay (Pearson's correlation coefficient: 0.46-0.53). Environmental factors, including temperature, pH, and electrical conductivity, correlated negatively with SARS-CoV-2 (Spearman's rho = -0.21, -0.28, and -0.21, respectively, p < 0.05), whereas average rainfall, humidity, and dissolved oxygen correlated positively (Spearman's rho = 0.20, 0.27, and 0.51, respectively, p < 0.05). These correlations highlight the significance of environmental variables in understanding viral prevalence in water. Our findings confirmed the utility of WBE as an early warning system for long-term monitoring. Future research should incorporate environmental factors to improve prediction accuracy for clinical cases and other waterborne diseases.

Tracking the Spread of the BA.2.86 Lineage in Italy Through Wastewater Analysis

The emergence of new SARS-CoV-2 variants poses challenges to global surveillance efforts, necessitating swift actions in their detection, evaluation, and management. Among the most recent variants, Omicron BA.2.86 and its sub-lineages have gained attention due to their potential immune evasion properties. This study describes the development of a digital PCR assay for the rapid detection of BA.2.86 and its descendant lineages, in wastewater samples. By using this assay, we analyzed wastewater samples collected in Italy from September 2023 to January 2024. Our analysis revealed the presence of BA.2.86 lineages already in October 2023 with a minimal detection rate of 2% which then rapidly increased, becoming dominant by January 2024, accounting for a prevalence of 62%. The findings emphasize the significance of wastewater-based surveillance in tracking emerging variants and underscore the efficacy of targeted digital PCR assays for environmental monitoring.

Long-term longitudinal monitoring of SARS CoV-2 in urban rivers and sewers of Nepal

In regions without adequate centralized wastewater treatment plants, sample collection from rivers and sewers can be an alternative sampling strategy for wastewater surveillance. This study aimed to assess the feasibility of alternative sampling strategies by testing samples collected from rivers (n = 246) and sewers (n = 244) in the Kathmandu Valley between March 2021 and February 2022. All samples were concentrated using the skimmed-milk flocculation method and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA was quantified using the nucleocapsid (N) and envelope (E) genes qPCR assays. Of the total, 75 % (371/490) of the samples tested positive using at least one qPCR assay, with concentrations ranging from 3.0 to 8.3 log10 gene copies/L. No significant correlation between concentrations of SARS-CoV-2 from both sewers and river with the number of confirmed coronavirus disease 2019 (COVID-19) cases in the Kathmandu valley was observed (p > 0.05). Despite the high concentration of SARS-CoV-2 in rivers and sewers, we hypothesize this finding to be a result of inaccurate number of clinical cases possibly due to inadequate clinical testing. This longitudinal study further supports the statement to consider sampling strategies from sewers and rivers for WBS in Nepal and other low and middle-income countries.

Comparative analysis of membrane filter diameters for detection of selected viruses in wastewater samples

Wastewater serves as a valuable source of information as it contains biological markers that have been shed by infected individuals and from other biological organisms such as plants and animals. Wastewater has been proven to indicate the presence of emerging pathogens in a community before the manifestation of clinical symptoms. Several methods of concentration and nucleic acid extraction have been employed all around the world without a unified method. One such method involves the use of the adsorption extraction method (AE-method), which involves the use of electronegative membrane filters of different pore sizes. The membrane filters also differ by diameter, but no study has been reported on the effect of diameter on capture efficiency. This study was aimed at evaluating the comparative capture efficiency of two different membrane filter diameters of 45 and 90 mm with pore sizes of 0.45 μm for the detection of indicator and pathogenic viruses. Primary influent samples were obtained from two wastewater treatment plants in Baltimore, Maryland, between April 27 and June 29, 2023. A total of twenty samples were processed using 45- and 90-mm membrane filters. Nucleic acids were extracted from the filters using the QIAmp Viral RNA Mini Kit and assayed for four different targets: PMMoV, Norovirus (GI and GII), and CrAssphage by RT-qPCR. The result showed that 45 mm membrane filters had a higher combined mean capture efficiency in log10 gene copies per liter (gc/l) for crAssphage (7.40) than 90 mm membrane filters (7.10). Similarly, the 45-mm filter had higher mean capture efficiency for Norovirus GI (4.67) than the 90-mm filter (1.84) and likewise for Norovirus GII (2.14, 1.04). On the contrary, 90-mm membrane filters were observed to have better capture of PMMoV (6.84) compared to 45-mm membrane filters (6.69). This result therefore implies that 45-mm membrane filters could be more efficient for wastewater surveillance studies through the AE method for indicator viruses like CrAssphage and human disease-causing viruses like Norovirus.

Integration of Whole-Genome Sequencing with ddPCR Kit for Detection of Omicron Subvariants in Wastewater in the Upper Peninsula of Michigan

This study explores the integration of genome sequencing and digital droplet polymerase chain reaction (ddPCR)-based methods for tracking the diversity of COVID-19 variants in wastewater. The research focuses on monitoring various Omicron subvariants during a period of significant viral evolution. Genome sequencing, particularly using Oxford Nanopore Technology (ONT), provides a detailed view of emerging variants, surpassing the limitations of PCR-based detection kits that rely on known sequences. Of the 43 samples analyzed, 39.5% showed matching results between the GT Molecular ddPCR kits and sequencing, though only 4% were exact matches. Some mismatches occurred due to newer subvariants like XBB and BQ.1, which the ddPCR kits could not detect. This emphasized the limitations of ddPCR kits, which rely on known variant sequences, while sequencing provides real-time data on emerging variants, offering a more comprehensive view of circulating strains. This study highlights the effectiveness of combining these methodologies to enhance early detection and inform public health strategies, especially in regions with limited clinical sequencing capabilities.

Key considerations for pathogen surveillance in wastewater

Wastewater surveillance (WWS) has received significant attention as a rapid, sensitive, and cost-effective tool for monitoring various pathogens in a community. WWS is employed to assess the spatial and temporal trends of diseases and identify their early appearances and reappearances, as well as to detect novel and mutated variants. However, the shedding rates of pathogens vary significantly depending on factors such as disease severity, the physiology of affected individuals, and the characteristics of pathogen. Furthermore, pathogens may exhibit differential fate and decay kinetics in the sewerage system. Variable shedding rates and decay kinetics may affect the detection of pathogens in wastewater. This may influence the interpretation of results and the conclusions of WWS studies. When selecting a pathogen for WWS, it is essential to consider it's specific characteristics. If data are not readily available, factors such as fate, decay, and shedding rates should be assessed before conducting surveillance. Alternatively, these factors can be compared to those of similar pathogens for which such data are available.

Avian Influenza outbreaks: Human infection risks for beach users - One health concern and environmental surveillance implications

Despite its popularity for water activities, such as swimming, surfing, fishing, and rafting, inland and coastal bathing areas occasionally experience outbreaks of highly pathogenic avian influenza virus (HPAI), including A(H5N1) clade 2.3.4.4b. Asymptomatic infections and symptomatic outbreaks often impact many aquatic birds, which increase chances of spill-over events to mammals and pose concerns for public health. This review examined the existing literature to assess avian influenza virus (AIV) transmission risks to beachgoers and the general population. A comprehensive understanding of factors governing such crossing of the AIV host range is currently lacking. There is limited knowledge on key factors affecting risk, such as species-specific interactions with host cells (including binding, entry, and replication via viral proteins hemagglutinin, neuraminidase, nucleoprotein, and polymerase basic protein 2), overcoming host restrictions, and innate immune response. AIV efficiently transmits between birds and to some extent between marine scavenger mammals in aquatic environments via consumption of infected birds. However, the current literature lacks evidence of zoonotic AIV transmission via contact with the aquatic environment or consumption of contaminated water. The zoonotic transmission risk of the circulating A(H5N1) clade 2.3.4.4b virus to the general population and beachgoers is currently low. Nevertheless, it is recommended to avoid direct contact with sick or dead birds and to refrain from bathing in locations where mass bird mortalities are reported. Increasing reports of AIVs spilling over to non-human mammals have raised valid concerns about possible virus mutations that lead to crossing the species barrier and subsequent risk of human infections and outbreaks.

SARS-CoV-2 RNA Detection in Wastewater and Its Effective Correlation with Clinical Data during the Outbreak of COVID-19 in Salamanca

Wastewater treatment plants (WWTPs) are the final stage of the anthropogenic water cycle where a wide range of chemical and biological markers of human activity can be found. In COVID-19 disease contexts, wastewater surveillance has been used to infer community trends based on viral abundance and SARS-CoV-2 RNA variant composition, which has served to anticipate and establish appropriate protocols to prevent potential viral outbreaks. Numerous studies worldwide have provided reliable and robust tools to detect and quantify SARS-CoV-2 RNA in wastewater, although due to the high dilution and degradation rate of the viral RNA in such samples, the detection limit of the pathogen has been a bottleneck for the proposed protocols so far. The current work provides a comprehensive and systematic study of the different parameters that may affect the detection of SARS-CoV-2 RNA in wastewater and hinder its quantification. The results obtained using synthetic viral RNA as a template allow us to consider that 10 genome copies per µL is the minimum RNA concentration that provides reliable and consistent values for the quantification of SARS-CoV-2 RNA. RT-qPCR analysis of wastewater samples collected at the WWTP in Salamanca (western Spain) and at six pumping stations in the city showed that below this threshold, positive results must be confirmed by sequencing to identify the specific viral sequence. This allowed us to find correlations between the SARS-CoV-2 RNA levels found in wastewater and the COVID-19 clinical data reported by health authorities. The close match between environmental and clinical data from the Salamanca case study has been confirmed by similar experimental approaches in four other cities in the same region. The present methodological approach reinforces the usefulness of wastewater-based epidemiology (WBE) studies in the face of future pandemic outbreaks.

EU surveys insights: analytical tools, future directions, and the essential requirement for reference materials in wastewater monitoring of SARS-CoV-2, antimicrobial resistance and beyond

BACKGROUND

Wastewater surveillance (WWS) acts as a vigilant sentinel system for communities, analysing sewage to protect public health by detecting outbreaks and monitoring trends in pathogens and contaminants. To achieve a thorough comprehension of present and upcoming practices and to identify challenges and opportunities for standardisation and improvement in WWS methodologies, two EU surveys were conducted targeting over 750 WWS laboratories across Europe and other regions. The first survey explored a diverse range of activities currently undertaken or planned by laboratories. The second survey specifically targeted methods and quality controls utilised for SARS-CoV-2 surveillance.

RESULTS

The findings of the two surveys provide a comprehensive insight into the procedures and methodologies applied in WWS. In Europe, WWS primarily focuses on SARS-CoV-2 with 99% of the survey participants dedicated to this virus. However, the responses highlighted a lack of standardisation in the methodologies employed for monitoring SARS-CoV-2. The surveillance of other pathogens, including antimicrobial resistance, is currently fragmented and conducted by only a limited number of laboratories. Notably, these activities are anticipated to expand in the future. Survey replies emphasise the collective recognition of the need to enhance the accuracy of results in WWS practices, reflecting a shared commitment to advancing precision and effectiveness in WWS methodologies.

CONCLUSIONS

These surveys identified a lack of standardised common procedures in WWS practices and the need for quality standards and reference materials to enhance the accuracy and reliability of WWS methods in the future. In addition, it is important to broaden surveillance efforts beyond SARS-CoV-2 to include other emerging pathogens and antimicrobial resistance to ensure a comprehensive approach to protecting public health.

Leveraging wastewater surveillance to detect viral diseases in livestock settings

Wastewater surveillance has evolved into a powerful tool for monitoring public health-relevant analytes. Recent applications in tracking severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection highlight its potential. Beyond humans, it can be extended to livestock settings where there is increasing demand for livestock products, posing risks of disease emergence. Wastewater surveillance may offer non-invasive, cost-effective means to detect potential outbreaks among animals. This approach aligns with the "One Health" paradigm, emphasizing the interconnectedness of animal, human, and ecosystem health. By monitoring viruses in livestock wastewater, early detection, prevention, and control strategies can be employed, safeguarding both animal and human health, economic stability, and international trade. This integrated "One Health" approach enhances collaboration and a comprehensive understanding of disease dynamics, supporting proactive measures in the Anthropocene era where animal and human diseases are on the rise.

Developing wastewater-based surveillance schemes for multiple pathogens: The WastPan project in Finland

Wastewater comprises multiple pathogens and offers a potential for wastewater-based surveillance (WBS) to track the prevalence of communicable diseases. The Finnish WastPan project aimed to establish wastewater-based pandemic preparedness for multiple pathogens (viruses, bacteria, parasites, fungi), including antimicrobial resistance (AMR). This article outlines WastPan's experiences in this project, including the criteria for target selection, sampling locations, frequency, analysis methods, and results communication. Target selection relied on epidemiological and microbiological evidence and practical feasibility. Within the WastPan framework, wastewater samples were collected between 2021 and 2023 from 10 wastewater treatment plants (WWTPs) covering 40 % of Finland's population. WWTP selection was validated for reported cases of Extended Spectrum Beta-lactamase-producing bacterial pathogens (Escherichia coli and Klebsiella pneumoniae) from the National Infectious Disease Register. The workflow included 24-h composite influent samples, with one fraction for culture-based analysis (bacteria and fungi) and the rest of the sample was reserved for molecular analysis (viruses, bacteria, antibiotic resistance genes, and parasites). The reproducibility of the monitoring workflow was assessed for SARS-CoV-2 through inter-laboratory comparisons using the N2 and N1 assays. Identical protocols were applied to same-day samples, yielding similar positivity trends in the two laboratories, but the N2 assay achieved a significantly higher detection rate (Laboratory 1: 91.5 %; Laboratory 2: 87.4 %) than the N1 assay (76.6 %) monitored only in Laboratory 2 (McNemar, p < 0.001 Lab 1, = 0.006 Lab 2). This result indicates that the selection of monitoring primers and assays may impact monitoring sensitivity in WBS. Overall, the current study recommends that the selection of sampling frequencies and population coverage of the monitoring should be based on pathogen-specific epidemiological characteristics. For example, pathogens that are stable over time may need less frequent annual sampling, while those that are occurring across regions may require reduced sample coverage. Here, WastPan successfully piloted WBS for monitoring multiple pathogens, highlighting the significance of one-litre community composite wastewater samples for assessing community health. The infrastructure established for COVID-19 WBS is valuable for monitoring various pathogens. The prioritization of the monitoring targets optimizes resource utilization. In the future legislative support in target selection, coverage determination, and sustained funding for WBS is recomended.

De novo design of potential peptide analogs against the main protease of Omicron variant using in silico studies

SARS-CoV-2 and its variants are crossing the immunity barrier induced through vaccination. Recent Omicron sub-variants are highly transmissible and have a low mortality rate. Despite the low severity of Omicron variants, these new variants are known to cause acute post-infectious syndromes. Nowadays, novel strategies to develop new potential inhibitors for SARS-CoV-2 and other Omicron variants have gained prominence. For viral replication and survival the main protease of SARS-CoV-2 plays a vital role. Peptide-like inhibitors that mimic the substrate peptide have already proved to be effective in inhibiting the Mpro of SARS-CoV-2 variants. Our systematic canonical amino acid point mutation analysis on the native peptide has revealed various ways to improve the native peptide of the main protease. Multi mutation analysis has led us to identify and design potent peptide-analog inhibitors that act against the Mpro of the Omicron sub-variants. Our in-depth analysis of all-atom molecular dynamics studies has paved the way to characterize the atomistic behavior of Mpro in Omicron variants. Our goal is to develop potent peptide-analogs that could be therapeutically effective against Omicron and its sub-variants.

Detection of SARS-COV-2 variants and their proportions in wastewater samples using next-generation sequencing in Finland

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants may have different characteristics, e.g., in transmission, mortality, and the effectiveness of vaccines, indicating the importance of variant detection at the population level. Wastewater-based surveillance of SARS-CoV-2 RNA fragments has been shown to be an effective way to monitor the COVID-19 pandemic at the population level. Wastewater is a complex sample matrix affected by environmental factors and PCR inhibitors, causing insufficient coverage in sequencing, for example. Subsequently, results where part of the genome does not have sufficient coverage are not uncommon. To identify variants and their proportions in wastewater over time, we utilized next-generation sequencing with the ARTIC Network's primer set and bioinformatics pipeline to evaluate the presence of variants in partial genome data. Based on the wastewater data from November 2021 to February 2022, the Delta variant was dominant until mid-December in Helsinki, Finland's capital, and thereafter in late December 2022 Omicron became the most common variant. At the same time, the Omicron variant of SARS-CoV-2 outcompeted the previous Delta variant in Finland in new COVID-19 cases. The SARS-CoV-2 variant findings from wastewater are in agreement with the variant information obtained from the patient samples when visually comparing trends in the sewerage network area. This indicates that the sequencing of wastewater is an effective way to monitor temporal and spatial trends of SARS-CoV-2 variants at the population level.

Antibiotic resistance monitoring in wastewater in the Nordic countries: A systematic review

The Nordic countries (Denmark, Finland, Iceland, Norway, and Sweden) have effectively kept lower antibiotic-resistant bacterial (ARB) pathogen rates than many other countries. However, in recent years, these five countries have encountered a rise in ARB cases and challenges in treating infections due to the growing prevalence of ARB pathogens. Wastewater-based surveillance (WBS) is a valuable supplement to clinical methods for ARB surveillance, but there is a lack of comprehensive understanding of WBS application for ARB in the Nordic countries. This review aims to compile the latest state-of-the-art developments in WBS for ARB monitoring in the Nordic countries and compare them with clinical surveillance practices. After reviewing 1480 papers from the primary search, 54 were found relevant, and 15 additional WBS-related papers were included. Among 69 studies analyzed, 42 dedicated clinical epidemiology, while 27 focused on wastewater monitoring. The PRISMA review of the literature revealed that Nordic countries focus on four major WBS objectives of ARB: assessing ARB in the human population, identifying ARB evading wastewater treatment, quantifying removal rates, and evaluating potential ARB evolution during the treatment process. In both clinical and wastewater contexts, the most studied targets were pathogens producing carbapenemase and extended-spectrum beta-lactamase (ESBL), primarily Escherichia coli and Klebsiella spp. However, vancomycin-resistant Enterococcus (VRE) and methicillin-resistant Staphylococcus aureus (MRSA) have received more attention in clinical epidemiology than in wastewater studies, probably due to their lower detection rates in wastewater. Clinical surveillance has mostly used culturing, antibiotic susceptibility testing, and genotyping, but WBS employed PCR-based and metagenomics alongside culture-based techniques. Imported cases resulting from international travel and hospitalization abroad appear to have frequently contributed to the rise in ARB pathogen cases in these countries. The many similarities between the Nordic countries (e.g., knowledge exchange practices, antibiotic usage patterns, and the current ARB landscape) could facilitate collaborative efforts in developing and implementing WBS for ARB in population-level screening.

Detection of SARS-CoV-2 and Omicron variant RNA in wastewater samples from Manila, Philippines

Manila, a highly urbanized city, is listed as one of the top cities with the highest recorded number of coronavirus disease 2019 (COVID-19) cases in the Philippines. This study aimed to detect and quantify the RNA of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the Omicron variant in 51 wastewater samples collected from three locations in Manila, namely Estero de Santa Clara, Estero de Pandacan, which are open drainages, and a sewage treatment plant (STP) at De La Salle University-Manila, between July 2022 and February 2023. Using one-step reverse transcription-quantitative polymerase chain reaction, SARS-CoV-2 and Omicron variant RNA were detected in 78 % (40/51; 4.9 ± 0.5 log10 copies/L) and 60 % (24/40; 4.4 ± 0.3 log10 copies/L) of wastewater samples collected from all sampling sites, respectively. SARS-CoV-2 RNA was detected frequently at Estero de Santa Clara (88 %, 15/17); its highest concentration was at the STP (6.3 log10 copies/L). The Omicron variant RNA was present in the samples collected (4.4 ± 0.3 log10 copies/L) from all sampling sites, with the highest concentration at the STP (4.9 log10 copies/L). Regardless of normalization, using concentrations of pepper mild mottle virus RNA, SARS-CoV-2 RNA concentrations exhibited the highest positive correlation with COVID-19 reported cases in Manila 5 days after the clinical report. These findings revealed that wastewater-based epidemiology may aid in identifying and monitoring of the presence of pathogens in open drainages and STPs in the Philippines. This paper provides the first documentation on SARS-CoV-2 and the Omicron variant in wastewater from Manila.

Real-time evaluation of signal accuracy in wastewater surveillance of pathogens with high rates of mutation

Wastewater surveillance of coronavirus disease 2019 (COVID-19) commonly applies reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to quantify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concentrations in wastewater over time. In most applications worldwide, maximal sensitivity and specificity of RT-qPCR has been achieved, in part, by monitoring two or more genomic loci of SARS-CoV-2. In Ontario, Canada, the provincial Wastewater Surveillance Initiative reports the average copies of the CDC N1 and N2 loci normalized to the fecal biomarker pepper mild mottle virus. In November 2021, the emergence of the Omicron variant of concern, harboring a C28311T mutation within the CDC N1 probe region, challenged the accuracy of the consensus between the RT-qPCR measurements of the N1 and N2 loci of SARS-CoV-2. In this study, we developed and applied a novel real-time dual loci quality assurance and control framework based on the relative difference between the loci measurements to the City of Ottawa dataset to identify a loss of sensitivity of the N1 assay in the period from July 10, 2022 to January 31, 2023. Further analysis via sequencing and allele-specific RT-qPCR revealed a high proportion of mutations C28312T and A28330G during the study period, both in the City of Ottawa and across the province. It is hypothesized that nucleotide mutations in the probe region, especially A28330G, led to inefficient annealing, resulting in reduction in sensitivity and accuracy of the N1 assay. This study highlights the importance of implementing quality assurance and control criteria to continually evaluate, in near real-time, the accuracy of the signal produced in wastewater surveillance applications that rely on detection of pathogens whose genomes undergo high rates of mutation.

Potential transmission of SARS-CoV-2 through microplastics in sewage: A wastewater-based epidemiological review

In light of the current COVID-19 pandemic caused by the virus SARS-CoV-2, there is an urgent need to identify and investigate the various pathways of transmission. In addition to contact and aerosol transmission of the virus, this review investigated the possibility of its transmission via microplastics found in sewage. Wastewater-based epidemiological studies on the virus have confirmed its presence and persistence in both influent sewage as well as treated ones. The hypothesis behind the study is that the huge amount of microplastics, especially Polyvinyl Chloride and Polyethylene particles released into the open waters from sewage can become a good substrate and vector for microbes, especially Polyvinyl Chloride and Polyethylene particles, imparting stability to microbes and aiding the "plastisphere" formation. A bibliometric analysis highlights the negligence of research toward plastispheres and their presence in sewage. The ubiquity of microplastics and their release along with the virus into the open waters increases the risk of viral plastispheres. These plastispheres may be ingested by aquatic organisms facilitating reverse zoonosis and the commercial organisms already reported with accumulating microplastics through the food chain poses a risk to human populations as well. Reliance of high population density areas on open waters served by untreated sewage in economically less developed countries might bring back viral transmission.

Monitoring Monkeypox: Safeguarding Global Health through Rapid Response and Global Surveillance

Monkeypox, a viral zoonotic disease, has emerged as a significant global threat in recent years. This review focuses on the importance of global monitoring and rapid response to monkeypox outbreaks. The unpredictable nature of monkeypox transmissions, its potential for human-to-human spread, and its high morbidity rate underscore the necessity for proactive surveillance systems. By analyzing the existing literature, including recent outbreaks, this review highlights the critical role of global surveillance in detecting, containing, and preventing the further spread of monkeypox. It also emphasizes the need for enhanced international collaboration, data sharing, and real-time information exchange to effectively respond to monkeypox outbreaks as a global health concern. Furthermore, this review discusses the challenges and opportunities of implementing robust surveillance strategies, including the use of advanced diagnostic tools and technologies. Ultimately, these findings underscore the urgency of establishing a comprehensive global monitoring framework for monkeypox, enabling early detection, prompt response, and effective control measures to protect public health worldwide.

Evaluation of the pilot wastewater surveillance for SARS-CoV-2 in Norway, June 2022 - March 2023

BACKGROUND

During the COVID-19 pandemic, wastewater-based surveillance gained great international interest as an additional tool to monitor SARS-CoV-2. In autumn 2021, the Norwegian Institute of Public Health decided to pilot a national wastewater surveillance (WWS) system for SARS-CoV-2 and its variants between June 2022 and March 2023. We evaluated the system to assess if it met its objectives and its attribute-based performance.

METHODS

We adapted the available guidelines for evaluation of surveillance systems. The evaluation was carried out as a descriptive analysis and consisted of the following three steps: (i) description of the WWS system, (ii) identification of users and stakeholders, and (iii) analysis of the system's attributes and performance including sensitivity, specificity, timeliness, usefulness, representativeness, simplicity, flexibility, stability, and communication. Cross-correlation analysis was performed to assess the system's ability to provide early warning signal of new wave of infections.

RESULTS

The pilot WWS system was a national surveillance system using existing wastewater infrastructures from the largest Norwegian municipalities. We found that the system was sensitive, timely, useful, representative, simple, flexible, acceptable, and stable to follow the general trend of infection. Preliminary results indicate that the system could provide an early signal of changes in variant distribution. However, challenges may arise with: (i) specificity due to temporary fluctuations of RNA levels in wastewater, (ii) representativeness when downscaling, and (iii) flexibility and acceptability when upscaling the system due to limited resources and/or capacity.

CONCLUSIONS

Our results showed that the pilot WWS system met most of its surveillance objectives. The system was able to provide an early warning signal of 1-2 weeks, and the system was useful to monitor infections at population level and complement routine surveillance when individual testing activity was low. However, temporary fluctuations of WWS values need to be carefully interpreted. To improve quality and efficiency, we recommend to standardise and validate methods for assessing trends of new waves of infection and variants, evaluate the WWS system using a longer operational period particularly for new variants, and conduct prevalence studies in the population to calibrate the system and improve data interpretation.

An improved method for determining frequency of multiple variants of SARS-CoV-2 in wastewater using qPCR assays

Wastewater-based surveillance has become an effective tool around the globe for indirect monitoring of COVID-19 in communities. Variants of Concern (VOCs) have been detected in wastewater by use of reverse transcription polymerase chain reaction (RT-PCR) or whole genome sequencing (WGS). Rapid, reliable RT-PCR assays continue to be needed to determine the relative frequencies of VOCs and sub-lineages in wastewater-based surveillance programs. The presence of multiple mutations in a single region of the N-gene allowed for the design of a single amplicon, multiple probe assay, that can distinguish among several VOCs in wastewater RNA extracts. This approach which multiplexes probes designed to target mutations associated with specific VOC's along with an intra-amplicon universal probe (non-mutated region) was validated in singleplex and multiplex. The prevalence of each mutation (i.e. VOC) is estimated by comparing the abundance of the targeted mutation with a non-mutated and highly conserved region within the same amplicon. This is advantageous for the accurate and rapid estimation of variant frequencies in wastewater. The N200 assay was applied to monitor frequencies of VOCs in wastewater extracts from several communities in Ontario, Canada in near real time from November 28, 2021 to January 4, 2022. This includes the period of the rapid replacement of the Delta variant with the introduction of the Omicron variant in these Ontario communities in early December 2021. The frequency estimates using this assay were highly reflective of clinical WGS estimates for the same communities. This style of qPCR assay, which simultaneously measures signal from a non-mutated comparator probe and multiple mutation-specific probes contained within a single qPCR amplicon, can be applied to future assay development for rapid and accurate estimations of variant frequencies.