Occurrence of noroviruses in recycled water and sewage sludge: emergence of recombinant norovirus strains

Recovery and Quantification of Norovirus in Air Samples from Experimentally Produced Aerosols

Norovirus is the leading cause of acute gastroenteritis in humans across all age groups worldwide. Norovirus-infected patients can produce aerosolized droplets which play a role in gastroenteritis transmission. The study aimed to assess bioaerosol sampling in combination with a virus concentrating procedure to facilitate molecular detection of norovirus genogroup (G) II from experimentally contaminated aerosols. Using a nebulizer within an experimental chamber, aerosols of norovirus GII were generated at known concentrations. Air samples were then collected in both 5 mL and 20 mL water using the SKC BioSampler at a flow rate of 12.5 L/min, 15 min. Subsequently, the virus in collected water was concentrated using speedVac centrifugation and quantified by RT-qPCR. The optimal distances between the nebulizer and the SKC BioSampler yielded high recoveries of the virus for both 5 and 20 mL collections. Following nebulization, norovirus GII RNA was detectable up to 120 min in 5 mL and up to 240 min in 20 mL collection. The concentrations of norovirus GII RNA recovered from air samples in the aerosol chamber ranged from 102 to 105 genome copies/mL, with average recoveries of 25 ± 12% for 5 mL and 22 ± 19% for 20 mL collections. These findings provide quantitative data on norovirus GII in aerosols and introduce a novel virus concentrating method for aerosol collection in water, thus enhancing surveillance of this virus.

Diverse genotypes of norovirus genogroup I and II contamination in environmental water in Thailand during the COVID-19 outbreak from 2020 to 2022

Noroviruses (NoVs) are the most significant viral pathogens associated with waterborne and foodborne outbreaks of nonbacterial acute gastroenteritis in humans worldwide. This study aimed to investigate the prevalence and diversity of NoVs contaminated in the environmental water in Chiang Mai, Thailand. A total of 600 environmental water samples were collected from ten sampling sites in Chiang Mai from July 2020 to December 2022. The presence of NoV genogroups I (GI), GII, and GIV were examined using real-time RT-PCR assay. The genotype of the virus was determined by nucleotide sequencing and phylogenetic analysis. The results showed that NoV GI and GII were detected at 8.5% (51/600) and 11.7% (70/600) of the samples tested, respectively. However, NoV GIV was not detected in this study. NoV circulated throughout the year, with a higher detection rate during the winter season. Six NoV GI genotypes (GI.1-GI.6) and eight NoV GII genotypes (GII.2, GII.3, GII.7, GII.8, GII.10, GII.13, GII.17, and GII.21) were identified. Among 121 NoV strains detected, GII.17 was the most predominant genotype (24.8%, 30 strains), followed by GII.2 (21.5%, 26 strains), GI.3 (17.4%, 21 strains), and GI.4 (16.5%, 20 strains). Notably, NoV GII.3, GII.7, GII.8, and GII.10 were detected for the first time in water samples in this area. This study provides insight into the occurrence and seasonal pattern of NoV along with novel findings of NoV strains in environmental water in Thailand during the COVID-19 outbreak. Our findings emphasize the importance of further surveillance studies to monitor viral contamination in environmental water.

Multiple Novel Human Norovirus Recombinants Identified in Wastewater in Pretoria, South Africa by Next-Generation Sequencing

The genogroup II genotype 4 (GII.4) noroviruses are a major cause of viral gastroenteritis. Since the emergence of the Sydney_2012 variant, no novel norovirus GII.4 variants have been reported. The high diversity of noroviruses and periodic emergence of novel strains necessitates continuous global surveillance. The aim of this study was to assess the diversity of noroviruses in selected wastewater samples from Pretoria, South Africa (SA) using amplicon-based next-generation sequencing (NGS). Between June 2018 and August 2020, 200 raw sewage and final effluent samples were collected fortnightly from two wastewater treatment plants in Pretoria. Viruses were recovered using skimmed milk flocculation and glass wool adsorption-elution virus recovery methods and screened for noroviruses using a one-step real-time reverse-transcription PCR (RT-PCR). The norovirus BC genotyping region (570-579 bp) was amplified from detected norovirus strains and subjected to Illumina MiSeq NGS. Noroviruses were detected in 81% (162/200) of samples. The majority (89%, 89/100) of raw sewage samples were positive for at least one norovirus, compared with 73% (73/100) of final effluent samples. Overall, a total of 89 different GI and GII RdRp-capsid combinations were identified, including 51 putative novel recombinants, 34 previously reported RdRp-capsid combinations, one emerging novel recombinant and three Sanger-sequencing confirmed novel recombinants.

A probabilistic assessment of microbial infection risks due to occupational exposure to wastewater in a conventional activated sludge wastewater treatment plant

Exposure to pathogens during wastewater treatment could result in significant health risks. In this paper, a probabilistic approach for assessing the risks of microbial infection for workers in an activated sludge wastewater treatment plant is presented. A number of exposure routes were modelled, including hand-to-mouth and droplet ingestion of untreated wastewater, droplet ingestion and inhalation of aerosols after secondary treatment, and ingestion of sludge during drying. Almost all workers exposed to untreated wastewater could be infected with the three selected potential pathogens of pathogenic E. coli, Norovirus and Cryptosporidium spp. Hand-to-mouth ingestion is the single most significant route of exposure at the head of works. There is also a risk of infections resulting from ingestion of droplets or inhalation of aerosols at the aeration tanks or contaminated hands at the clarifiers during secondary wastewater treatment. For sludge, the risks of infection with Norovirus was found to be the highest due to accidental ingestion (median risks of 2.2 × 10^-2(±3.3 × 10^-3)). Regardless of the point and route of exposure, Norovirus and Cryptosporidium spp. presented the highest risks. The study finds that occupational exposure to wastewater at wastewater treatment plants can result in significant viral and protozoan infections. This risk assessment framework can be used to establish and measure the success of risk reduction measures in wastewater treatment plants. These measures could include the use of personal protective equipment and adherence to strict personal hygiene.

Global public health implications of human exposure to viral contaminated water

Enteric viruses are common waterborne pathogens found in environmental water bodies contaminated with either raw or partially treated sewage discharge. Examples of these viruses include adenovirus, rotavirus, noroviruses, and other caliciviruses and enteroviruses like coxsackievirus and polioviruses. They have been linked with gastroenteritis, while some enteric viruses have also been implicated in more severe infections such as encephalitis, meningitis, hepatitis (hepatitis A and E viruses), cancer (polyomavirus), and myocarditis (enteroviruses). Therefore, this review presents information on the occurrence of enteric viruses of public health importance, diseases associated with human exposure to enteric viruses, assessment of their presence in contaminated water, and their removal in water and wastewater sources. In order to prevent illnesses associated with human exposure to viral contaminated water, we suggest the regular viral monitoring of treated wastewater before discharging it into the environment. Furthermore, we highlight the need for more research to focus on the development of more holistic disinfection methods that will inactivate waterborne viruses in municipal wastewater discharges, as this is highly needed to curtail the public health effects of human exposure to contaminated water. Moreover, such a method must be devoid of disinfection by-products that have mutagenic and carcinogenic potential.

Occurrence of viruses in sewage sludge: A systematic review

Enteric viruses are of great importance in wastewater due to their high excretion from infected individuals, low removal in wastewater treatment processes, long-time survival in the environment, and low infectious dose. Among the other viruses, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surveillance in wastewater systems has received particular attention as a result of the current COVID-19 epidemic. Viruses adhering to solid particles in wastewater treatment processes will end up as sewage sludge, and therefore insufficient sludge treatment may result in viral particles dissemination into the environment. Here, we review data on viruses' presence in sewage sludge, their detection and concentration methods, and information on human health issues associated with sewage sludge land application. We used combinations of the following keywords in the Scopus, Web of Science (WOS), and PubMed databases, which were published between 2010 and January 21th, 2022: sludge (sewage sludge, biosolids, sewage solids, wastewater solids) and virus (enteric virus, viral particles, viral contamination, SARS-CoV-2, coronavirus). The sources were searched twice, once with and then without the common enteric virus names (adenovirus, rotavirus, norovirus, enterovirus, hepatitis A virus). Studies suggest adenovirus and norovirus as the most prevalent enteric viruses in sewage sludge. Indeed, other viruses include rotavirus, hepatitis A virus, and enterovirus were frequently found in sewage sludge samples. Untreated biological sludge and thickened sludge showed more viral contamination level than digested sludge and the lowest prevalence of viruses was reported in lime stabilized sludge. The review reveals that land application of sewage sludge may pose viral infection risks to people due to accidently ingestion of sludge or intake of crops grown in biosolids amended soil. Moreover, contamination of groundwater and/or surface water may occur due to land application of sewage sludge.

Molecular characterization of human bocavirus in recycled water and sewage sludge in Thailand

The study aimed to assess the presence and molecular characterization of human bocavirus (HBoV) in recycled water and sewage sludge samples in Thailand. One hundred and two recycled water and eighty-six sewage sludge samples collected from a wastewater treatment plant were tested for the presence of HBoV using nested PCR with broad-range primer pairs targeting the capsid proteins VP1 and VP2. HBoV DNA was detected in recycled water of 9/102 (8.8%) samples and sewage sludge of 27/86 (31.4%) samples. Based on DNA sequencing and phylogenetic analysis, the HBoV DNA sequences had 98.8-100.0% nucleotide identity to the sequences from HBoV reported globally. Thirty-five HBoV-positive samples were identified to genotypes as the predominant HBoV2; 26 followed by HBoV3; 8 and the rare HBoV4; 1 sample. Concerning recycled water, HBoV2 was detected in 3 (2.9%) and HBoV3 was detected in 5 (4.9%) of all samples. The sewage sludge samples were characterized as HBoV2 in 23 (26.7%), HBoV3 in 3 (3.5%) and HBoV4 in 1 (1.2%) of all samples. The frequency of HBoV detected in recycled water and sewage sludge samples significantly differed in sample type (p-value = 0.007). The findings of three HBoV genotypes in recycled water and sewage sludge emphasized the circulation of the virus in the environment and the potential source of transmission to the community.

Detection of Norovirus Recombinant GII.2[P16] Strains in Oysters in Thailand

Human norovirus causes sporadic and epidemic acute gastroenteritis worldwide, and the predominant strains are genotype GII.4 variants. Recently, a novel GII.17[P17] and a recombinant GII.2[P16] strain have been reported as the causes of gastroenteritis outbreaks. Outbreaks of norovirus are frequently associated with foodborne illness. In this study, each of 75 oyster samples processed by a proteinase K extraction method and an adsorption-elution method were examined for noroviruses using RT-nested PCR with capsid primers. Thirteen (17.3%) samples processed by either method tested positive for norovirus genogroup II (GII). PCR amplicons were characterized by DNA sequencing and phylogenetic analysis as GII.2 (n = 6), GII.4 (n = 1), GII.17 (n = 3), and GII.unclassified (n = 3). Norovirus-positive samples were further amplified by semi-nested RT-PCR targeting the polymerase-capsid genes. One nucleotide sequence revealed GII.17[P17] Kawasaki strain. Five nucleotide sequences were identified as belonging to the recombinant GII.2[P16] strains by recombination analysis. The collected oyster samples were quantified for norovirus GII genome copy number by RT-quantitative PCR. Using the proteinase K method, GII was found in 13/75 (17.3%) of samples with a range of 8.83-1.85 × 10⁴ genome copies/g of oyster. One sample (1/75, 1.3%) processed by the adsorption-elution method was positive for GII at 5.00 × 10¹ genome copies/g. These findings indicate the circulation of a new variant GII.17 Kawasaki strain and the recombinant GII.2[P16] in oyster samples corresponding to the circulating strains reported at a global scale during the same period of time. The detection of the recombinant strains in oysters emphasizes the need for continuing systematic surveillance for control and prevention of norovirus gastroenteritis.

Application of Lab-on-Chip for Detection of Microbial Nucleic Acid in Food and Environment

Various diseases caused by food-borne or environmental pathogenic microorganisms have been a persistent threat to public health and global economies. It is necessary to regularly detect microorganisms in food and environment to prevent infection of pathogenic microorganisms. However, most traditional detection methods are expensive, time-consuming, and unfeasible in practice in the absence of sophisticated instruments and trained operators. Point-of-care testing (POCT) can be used to detect microorganisms rapidly on site and greatly improve the efficiency of microbial detection. Lab-on-chip (LOC) is an emerging POCT technology with great potential by integrating most of the experimental steps carried out in the laboratory into a single monolithic device. This review will primarily focus on principles and techniques of LOC for detection of microbial nucleic acid in food and environment, including sample preparation, nucleic acid amplification and sample detection.

Recovery of polymeric substances from excess sludge: Surfactant-enhanced ultrasonic extraction and properties analysis

The recovery of polymeric substances from excess sludge is gaining significant research interest in future wastewater treatment technologies. We present a surfactant-enhanced ultrasonic method to extract mixed polymeric substances with typical functional groups from excess sludge. Four potential reasons were revealed for the higher efficiency upon ultrasonication with surfactant: low surface tension, damage of non-covalent bonds between extracellular polymeric substances and cells, enhanced dissolution of polymeric substances, and release of intracellular polymeric substances caused by cell lysis. The increase in extraction efficiency after the addition of cetyltrimethylammonium bromide and sodium dodecyl sulfate reached the maximum of 76.5% and 53.1%, respectively. The contents of polysaccharides, proteins, and DNA were approximately 50% of the total polymeric substances, and the content of protein was higher than that of polysaccharide; the concentration change of the surfactant had a minimal effect on these contents. For the polymeric substances extracted via ultrasonication with surfactant, the size was smaller than that for the non-surfactant extraction; moreover, the contents of metals decreased significantly (Al: 0.18% → 0%; Na: 0.15% → 0%; Ca: 0.24% → 0.11%), which was probably caused by the interaction between the surfactant and metal ions in the excess sludge. The surfactant had a negligible effect on the properties of polymeric substances, adsorption capacity of polymeric substances for heavy metal ions, and dewatering performance of sludge. The recycled polymeric substances may be used as a substitute for commercial adsorbents of heavy metal ions. Thus, the obtained results provide further insight into the recovery of polymeric substances from excess sludge via the surfactant-enhanced ultrasonic method.

Prevalence of emerging torque teno virus (TTV) in drinking water, natural waters and wastewater networks (DWNWWS): A systematic review and meta-analysis of the viral pollution marker of faecal and anthropocentric contaminations

The emerging torque teno virus (TTV) has been identified as a biohazard marker of anthropocentric pollution and contamination in drinking water, natural water and wastewater systems (DWNWWS). Therefore, this study aimed at assessing prevalence of TTV in DWNWWS. The study systematically identified and meta-analyzed published studies on TTV prevalence in DWNWWS hosted in Dimensions, Google Scholar, PubMed, Web of Science, and Scopus databases using a random-effects model and mixed-effects meta-regression model for sensitivity analysis. Furthermore, the meta-analysis was stratified to estimate water type-specific TTV prevalence. The study found a total of 58 articles, of which 13 articles subdivided into 31 studies with 374 TTV positive cases and 862 total sample sizes were systematically reviewed and meta-analyzed. The pooled prevalence of TTV in DWNWWS was 37.18% (95%CI: 23.76-55.55%). Prevalence of TTV was significantly different across water types and it was 56.67% (95%CI: 36.94-75.46%) in wastewater, 26.72% (95%CI: 6.87-52.56%) in river water, and 17.17% (95%CI: 0.54-45.39%) in drinking water. TTV incidence in seawater and groundwater was 0% and 25.0% respectively. Funnel plots constructed and associated statistics of rank correlation test and Egger's regression test in this study, show lack of publication bias in the pooled prevalence of TTV in DWNWWS. Although, sample type (QM(df = 1) = 6.9656, p = 0.0083) and concentration methods (QM(df = 1) = 3.8055, p = 0.0511) significantly moderated and accounted for 15.39% and 6.00% of heterogeneity in the prevalence of TTV in DWNWWS respectively. In conclusion, research focus/monitoring activities on TTV is generally inadequate and potential risk of TTV in DWNWWS is underappreciated in most nations; the analyzed studies were from 7 countries (USA, Japan, Italy, Iran, Germany, Egypt, and Brazil). Finally, inefficient concentration method severely influences the prevalence of TTV in DWNWWS and could give rise to underestimation of TTV and mar TTV-based source-tracking of anthropogenic pollutions.

The novel SARS-CoV-2 pandemic: Possible environmental transmission, detection, persistence and fate during wastewater and water treatment

The contagious SARS-CoV-2 virus, responsible for COVID-19 disease, has infected over 27 million people across the globe within a few months. While literature on SARS-CoV-2 indicates that its transmission may occur predominantly via aerosolization of virus-laden droplets, the possibility of alternate routes of transmission and/or reinfection via the environment requires considerable scientific attention. This review aims to collate information on possible transmission routes of this virus, to ascertain its fate in the environment. Concomitant with the presence of SARS-CoV-2 viral RNA in faeces and saliva of infected patients, studies also indicated its occurrence in raw wastewater, primary sludge and river water. Therefore sewerage system could be a possible route of virus outbreak, a possible tool to assess viral community spread and future surveillance technique. Hence, this review looked into detection, occurrence and fate of SARS-CoV-2 during primary, secondary, and tertiary wastewater and water treatment processes based on published literature on SARS-CoV and other enveloped viruses. The review also highlights the need for focused research on occurrence and fate of SARS-CoV-2 in various environmental matrices. Utilization of this information in environmental transmission models developed for other enveloped and enteric viruses can facilitate risk assessment studies. Preliminary research efforts with SARS-CoV-2 and established scientific reports on other coronaviruses indicate that the threat of virus transmission from the aquatic environment may be currently non-existent. However, the presence of viral RNA in wastewater provides an early warning that highlights the need for effective sewage treatment to prevent a future outbreak of SARS-CoV-2.

Residuals, sludge, and biosolids: Advancements in the field

Advancements in the field of residuals, sludge, and biosolids have been made in 2019. This review outlines the major contributions of researchers that have been published in peer-reviewed journals and conference proceedings throughout 2019 and includes brief summaries from over 125 articles. The review is organized in sections including life cycle and risk assessments; characteristics, quality, and measurement including micropollutants, nanoparticles, pathogens, and metals; sludge treatment technologies including dewatering, digestion, composting, and wetlands; disposal and reuse including adsorbents, land application and agricultural uses, nutrient recovery, and innovative uses; odor and air emissions; and energy issues.

Genetic diversity of norovirus genogroup I, II, IV and sapovirus in environmental water in Thailand

BACKGROUND

Enteric caliciviruses, including noroviruses (NoVs) and sapoviruses (SaVs) are the most significant pathogens associated with waterborne and foodborne outbreaks of nonbacterial acute gastroenteritis in humans worldwide.

METHODS

In this study, 126 environmental water samples collected from 6 different sources in Chiang Mai, Thailand from November 2016 to July 2018 were examined for the presence of genogroups I, II, IV (GI, GII, GIV) NoVs and SaVs by using RT-nested PCR assays, genome sequencing, and phylogenetic analysis, RESULTS: Forty out of 126 (31.7%) water samples were positive for one or more caliciviruses throughout the years of study with high prevalence in winter. Among 126 tested specimens, 34 (27.0%), 30 (23.8%), 3 (2.4%), and 2 (1.6%) were positive for NoV GI, GII, GIV, and SaV, respectively. For NoV GI, 6 different genotypes were identified with the most predominant of GI.1 genotype (17 strains). In addition, 6 different genotypes of GII were detected with high prevalence of GII.17 (12 strains) and GII.2 (11 strains). It was interesting to note that our study reported the detection of NoV GIV for the first time in water samples in Thailand, and all were GIV.1 genotype. For SaV detection, only 2 water samples were positive for SaV GI.

CONCLUSIONS

The data revealed heterogeneity and highly dynamic distribution of NoV GI, GII, GIV, and SaV in environmental water in Chiang Mai, Thailand, during the study period of 2016-2018.

Norovirus Monitoring in Oysters Using Two Different Extraction Methods

Detection of noroviruses in bivalve shellfish is difficult because of the low concentration of norovirus and the presence of reverse transcription (RT)-PCR inhibitors. This study aimed to assess the presence of noroviruses in oysters extracted using a proteinase K extraction (ISO 15216 method) and an adsorption-elution method. Seventy oyster samples were extracted using the two extraction methods and evaluated using RT-nested PCR. The results showed norovirus detection rates at an equal frequency of 28.6%, of which a total of 48 (68.6%) samples had corresponding positive or negative results, while there were 22 (31.4%) samples with discrepant results. Norovirus genogroup (G)I, GII, and mixed GI and GII were detected in 20%, 4.3%, and 4.3% of samples, respectively, by the proteinase K extraction method, which comprised of GI.2, GI.5b, GI.6b, GII.4, and GII.17 genotypes. With the adsorption-elution method noroviruses were detected in 17.1%, 8.6%, and 2.9% of samples, respectively, which comprised of GI.2, GII.2, GII.4, and GII.17 genotypes. All norovirus-positive oyster samples were further estimated for genome copy number using RT-quantitative PCR. The oyster samples processed using the adsorption-elution method contained norovirus GI of 3.36 × 10¹-1.06 × 10⁵ RNA copies/g of digestive tissues and GII of 1.29 × 10³-1.62 × 10⁴ RNA copies/g. Only GII (2.20 × 10¹ and 7.83 × 10¹ RNA copies/g) could be quantified in samples prepared using the proteinase K extraction method. The results demonstrate the different performance of the two sample-processing methods, and suggest the use of either extraction method in combination with RT-nested PCR for molecular surveillance of norovirus genotypes in oysters.