Monitoring hand foot and mouth disease using long-term wastewater surveillance in Japan: Quantitative PCR assay development and application

Potential therapeutic substances for hand-foot-and-mouth disease in the interplay of enteroviruses and type I interferon

OBJECTIVES

Hand-foot-and-mouth disease (HFMD) is widespread in the world. Severe HFMD can lead to complications like pneumonia, encephalitis, myocarditis, transverse myelitis and even death. Since HFMD is caused by at least 20 types of enteroviruses, there is an urgent need for broad-spectrum antiviral drugs to help control the spread of HFMD outbreaks.

METHODS

Type I interferon (IFN), as an indispensable part of the immune response, plays a key role in the inhibition of the enterovirus replication cycle without species specificity, and regulation of the innate immune system by inducing the activation of the IFN-stimulated genes.

CONCLUSIONS

Here, the interplay of enteroviruses and type I IFN was systematically summarized, including pathways for the activation and evasion of type I IFN. Besides, we proposed promising anti-enterovirus agents with therapeutic potential.

Defining alarm thresholds for the load of pathogenic viruses in wastewater for decision making: An application to three French cities

Wastewater monitoring has the potential to complement infectious disease surveillance systems. However, the absence of predefined viral signal thresholds in wastewater is often presented as a limiting factor in triggering public health action. To overcome this issue, the feasibility of defining alarm threshold for viral loads in wastewater samples was assessed by quantifying genome fragments of SARS-CoV-2, influenza A virus (IAV), respiratory syncytial virus (RSV), norovirus (NoV), and rotavirus (RoV) by RT-digital PCR (dPCR) in untreated wastewater samples from three treatment plants. Cut-point values were calculated for periods with a high rate of visits to emergency rooms or at-home visits by SOS Médecins for the related diseases. ROC curves were constructed, and the values of alarm threshold in wastewater were defined using the Youden index. For each targeted virus, alarm thresholds were close to each other across the three WWTPs. As indicated by likelihood ratios, evidence to rule in the diagnosis of high rate of visits when the alarm threshold was exceeded ranged from weak to strong and was highest for RSV and SARS-CoV-2. Evidence to rule out the diagnosis when the alarm threshold was not exceeded was strong or moderate for IAV, SARS-CoV-2 and RSV. Diagnostic performance of the test was not as high for NoV and RoV. Positive predictive value was highest for SARS-CoV-2 and RSV. For SARS-CoV-2 and RSV, the definition of an alarm threshold in wastewater could substantially inform the diagnosis of a period with a high rate of medical visits for COVID-19 and bronchiolitis, respectively.

Optimization of a 6-plex Crystal Digital PCR® assay and its application to simultaneous surveillance of enteric and respiratory viruses in wastewater

Multiplex digital PCR (dPCR) approaches are commonly employed in wastewater-based epidemiology (WBE) studies. However, optimizing the dPCR workflow is a critical step to ensure its reliability and accuracy before application. In this study, a 6-plex Crystal Digital PCR® (cdPCR) workflow was optimized for the simultaneous detection of six epidemiologically important pathogens, including three enteric viruses, noroviruses of genogroups I and II (NoV-GI and GII) and enteroviruses (EnV), and three respiratory viruses, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), influenza A virus (InfA), and respiratory syncytial virus B (RSVB), in wastewater. Four cDNA input ratios (20 %-70 %) and two extraction kits were evaluated for optimization, with 30 % cDNA input and the AllPrep PowerViral DNA/RNA Kit (Qiagen) exhibiting optimal performance. The optimized 6-plex cdPCR assay was applied to a year-long wastewater surveillance study in Japan (n = 52), revealing distinct trends and prevalence ratios for enteric and respiratory viruses. NoV-GII was detected in 96 % of the samples with the highest mean concentration (6.1 ± 0.6 log10 copies/L), while SARS-CoV-2 and InfA were detected in 60 % and 50 % of the samples, respectively, which reflected the circulation of these pathogens within the community. Notably, RSVB was detected less frequently (25 %), in line with the fewer cases of RSVB reported during the study period. The wastewater concentrations of EnV and InfA showed significant positive correlations with hand foot and mouth disease and herpangina and influenza cases, respectively. However, no positive correlations were observed for RSV and COVID-19, possibly due to the testing of RSVB while RSVA was more prevalent and also due to cluster outbreaks. These findings demonstrated the utility of the 6-plex cdPCR assay in detecting pathogens and provided insights into community disease trends, representing an advancement in WBE.

Evaluation of the Enterovirus serotype monitoring approach for wastewater surveillance of hand foot and mouth disease using secondary epidemiological surveillance data

The serotypes of Enterovirus A (EVA) causing hand, foot, and mouth disease (HFMD) exhibit cyclical dominance, with the dominant serotypes being EVA71, Coxsackievirus A type 6 (CVA6), CVA10, and CVA16. In this study, a quadruplex digital polymerase chain reaction (dPCR) assay was developed for serotype-level monitoring in wastewater surveillance for HFMD. The quadruplex dPCR assay performance was comparable to that of the singleplex assays. Grab influent samples (n = 122) were collected weekly from a wastewater treatment plant in Yamanashi Prefecture, Japan, from March 2022 to July 2024. The dPCR results revealed that CVA6 had a lower prevalence in 2023 than in 2022 and 2024, while the detection ratio of EVA71 was significantly higher in 2023 than in 2022 (Chi-square test, P < 0.05). Triangulation of these results with a clinical report indicated the dominance of CVA6 in 2022 and 2024, but not in 2023, while EVA71 was found to be dominant in 2023. Secondary data revealed significantly higher HFMD cases in the catchment in the years when CVA6 was dominant and significantly lower in the years when EVA71 was dominant. The comparative analysis revealed a stronger correlation between CVA6 RNA concentrations and HFMD cases (r = 0.83) than that between a broad range of Enteroviruses, Pan-Enterovirus RNA concentrations (r = 0.47). Thus, serotype-level monitoring, particularly through quadruplex dPCR, provides valuable insights into EVA serotype dynamics, accurately reflects HFMD trends, and supports the monitoring of the cyclical patterns of EVA serotypes.

Prevalence of hepatitis A and E viruses in wastewater in Asian countries

Hepatitis A and E viruses (HAV and HEV, respectively) remain a significant global health concern despite advancements in healthcare and vaccination programs. Regular monitoring and vaccine efficacy of HAV are still lacking in different countries. This study aimed to investigate HAV and HEV prevalence in developed, developing, and least-developed Asian countries using wastewater as a surveillance tool. A total of 232 untreated wastewater samples were collected from six wastewater treatment plants, a sewage treatment plant, or an open drainage in six countries [Nepal (n = 51), Indonesia (n = 37), Thailand (n = 30), Vietnam (n = 27), the Philippines (n = 17), and Japan (n = 70)] between April and October 2022. Viruses in wastewater were concentrated by simple centrifugation or polyethylene glycol precipitation method, followed by viral RNA extraction and reverse transcription-quantitative polymerase chain reaction. HAV and HEV RNA were detected in the samples from Nepal (51 % for HAV and 2 % for HEV), Thailand (3 % for both viruses), and Japan (1 % for HAV and 24 % for HEV). Only HAV RNA was found in 11 % of the samples in Indonesia, whereas only HEV RNA was detected in Vietnam and the Philippines, with a positive ratio of 15 % and 12 %, respectively. These results highlighted the geographic variability in HAV and HEV prevalence, underscoring the need for localized public health strategies to address specific viral hepatitis challenges in each country.

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.

Optimization of the 5-plex digital PCR workflow for simultaneous monitoring of SARS-CoV-2 and other pathogenic viruses in wastewater

Wastewater-based epidemiology is a valuable tool for monitoring pathogenic viruses in the environment, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19). While quantitative polymerase chain reaction (qPCR) is widely used for pathogen surveillance in wastewater, it can be affected by inhibition and is limited to relative quantification. Digital PCR (dPCR) offers potential solutions to these limitations. In this study, a 5-plex dPCR workflow was optimized for the simultaneous detection of SARS-CoV-2, influenza A virus, enteroviruses (EnV), and noroviruses of genogroups I (NoV-GI) and GII (NoV-GII) in wastewater samples. Wastewater samples (n = 36) were collected from a wastewater treatment plant in Japan between August and October 2022. The optimization included the evaluation of singleplex and 5-plex dPCR assays, and two different concentration methods, extraction kits, and dPCR approaches. The performance of singleplex and 5-plex dPCR assays showed comparable linearity and reliability, with the 5-plex assays showing greater efficiency. The polyethylene glycol (PEG) precipitation method showed better performance over the centrifugation method, two-step reverse transcription (RT)-dPCR over the one-step RT-dPCR, and AllPrep PowerViral DNA/RNA Kit showed better performance than the QIAamp Viral RNA Mini Kit. The optimal workflow therefore included PEG precipitation, the AllPrep PowerViral DNA/RNA Kit, and two-step RT-dPCR. This workflow was selected to monitor the presence of SARS-CoV-2 and other pathogenic viruses in wastewater samples in a 5-plex dPCR approach, yielding promising results. SARS-CoV-2 RNA was detected in the majority of samples, with NoV-GI, NoV-GII, and EnV also being detected. The successful optimization and application of the 5-plex dPCR assay for pathogen surveillance in wastewater offers significant benefits, including enhanced community health assessment and more effective responses to public health threats.

Detection of enteroviruses related to hand foot and mouth disease in wastewater of Asian communities

Hand, foot, and mouth disease (HFMD) is contagious and predominantly affects children below the age of five. HFMD-associated serotypes of Enterovirus A (EVA) family include EVA71, Coxsackievirus A type 6 (CVA6), 10 (CVA10), and 16 (CVA16). Although prevalent in numerous Asian countries, studies on HFMD-causing agents in wastewater are scarce. This study aimed to conduct wastewater surveillance in various Asian communities to detect and quantify serotypes of EVA associated with HFMD. In total, 77 wastewater samples were collected from Indonesia, the Philippines, Thailand, and Vietnam from March 2022 to February 2023. The detection ratio for CVA6 RNA in samples from Vietnam was 40 % (8/20). The detection ratio for CVA6 and EVA71 RNA each was 25 % (5/20) for the Indonesian samples, indicating the need for clinical surveillance of CVA6, as clinical reports have been limited. For the Philippines, 12 % (2/17) of the samples were positive for CVA6 and EVA71 RNA each, with only one quantifiable sample each. Samples from Thailand had a lower detection ratio (1/20) for CVA6 RNA, and the concentration was unquantifiable. Conversely, CVA10 and CVA16 RNAs were not detected in any of the samples. The minimum and maximum concentrations of CVA6 RNA were 2.7 and 3.9 log10 copies/L and those for EVA71 RNA were 2.5 and 4.9 log10 copies/L, respectively. This study underscores the importance of wastewater surveillance in understanding the epidemiology of HFMD-associated EVA serotypes in Asian communities. Long-term wastewater surveillance is recommended to monitor changes in dominant serotypes, understand seasonality, and develop effective prevention and control strategies for HFMD.

Estimation of Norovirus infections in Japan: An application of wastewater-based epidemiology for enteric disease assessment

Noroviruses of genogroup I (NoV GI) and NoV GII are the primary causes of acute gastroenteritis (AGE) in developed countries. However, asymptomatic and untested NoV infections lead to an underestimation of AGE cases, and the lack of mandatory viral identification in clinical cases hinders precise estimation of NoV infections. Back estimation of NoV infections in the community using a wastewater-based epidemiology (WBE) approach can provide valuable insights into the disease's extent, progression, and epidemiology, aiding in developing effective control strategies. This study employed a one-step reverse transcription-quantitative PCR to quantify NoVs GI and GII in wastewater samples (n = 83) collected twice a week from June 2022 to March 2023 in Japan. All samples from the Winter-Spring (n = 27) tested positive for NoV GI and GII RNA, while 73 % and 88 % of samples from the Summer-Autumn (n = 56) were positive for NoV GI and NoV GII RNA, respectively. Significantly higher concentrations of NoV GI/GII RNA were found in the Winter-Spring season compared to the Summer-Autumn season. NoV RNA was consistently detected in wastewater throughout the year, demonstrating the persistence of AGE cases in the catchment, suggesting an endemic NoV infection. Estimates of NoV infection incorporated viral RNA concentrations, wastewater parameters, and signal persistence in a mass balance equation using Monte Carlo Simulation. The median estimated NoV GI infections per 100,000 population for Summer-Autumn was 133 and for the Winter-Spring season, it was 881. Estimated NoV GII infections were 1357 for Summer-Autumn and 11,997 for the Winter-Spring season per 100,000 population. The estimated NoV infections exceeded by 3.2 and 23.9 folds than the reported AGE cases in Summer-Autumn and Winter-Spring seasons, respectively. The seasonal trend of estimated NoV infections closely matched that of AGE cases, highlighting the utility of WBE in understanding the epidemiology of enteric infections.