Environmental Surveillance of Polioviruses in Rio de Janeiro, Brazil, in Support to the Activities of Global Polio Eradication Initiative

Building-level wastewater surveillance of SARS-CoV-2 is associated with transmission and variant trends in a university setting

The University of South Carolina (UofSC) was among the first universities to include building-level wastewater surveillance of SARS-CoV-2 to complement clinical testing during its reopening in the Fall 2020 semester. In the Spring 2021 semester, 24h composite wastewater samples were collected twice per week from 10 residence halls and the on-campus student isolation and quarantine building. The isolation and quarantine building served as a positive control site. The wastewater was analyzed using RT-ddPCR for the quantification of nucleocapsid genes (N1 and N2) to identify viral transmission trends within residence halls. Log10 SARS-CoV-2 RNA concentrations were compared to both new clinical cases identified in the days following wastewater collection and recovered cases returning to sites during the days preceding sample collection to test temporal and spatial associations. There was a statistically significant positive relationship between the number of cases reported from the sites during the seven-day period following wastewater sampling and the log10 viral RNA copies/L (overall IRR 1.08 (1.02, 1.16) p-value 0.0126). Additionally, a statistically significant positive relationship was identified between the number of cases returning to the residence halls after completing isolation during the seven-day period preceding wastewater sampling and the log10 viral RNA copies/L (overall 1.09 (1.01, 1.17) p-value 0.0222). The statistical significance of both identified cases and recovered return cases on log10 viral RNA copies/L in wastewater indicates the importance of including both types of clinical data in wastewater-based epidemiology (WBE) research. Genetic mutations associated with variants of concern (VOCs) were also monitored. The emergence of the Alpha variant on campus was identified, which contributed to the second wave of COVID-19 cases at UofSC. The study was able to identify sub-community transmission hotspots for targeted intervention in real-time, making WBE cost-effective and creating less of a burden on the general public compared to repeated individual testing methods.

Wastewater Surveillance for Infectious Disease: A Systematic Review

Wastewater surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been shown to be a valuable source of information regarding SARS-CoV-2 transmission and coronavirus disease 2019 (COVID-19) cases. Although the method has been used for several decades to track other infectious diseases, there has not been a comprehensive review outlining all of the pathogens that have been surveilled through wastewater. Herein we identify the infectious diseases that have been previously studied via wastewater surveillance prior to the COVID-19 pandemic. Infectious diseases and pathogens were identified in 100 studies of wastewater surveillance across 38 countries, as were themes of how wastewater surveillance and other measures of disease transmission were linked. Twenty-five separate pathogen families were identified in the included studies, with the majority of studies examining pathogens from the family Picornaviridae, including polio and nonpolio enteroviruses. Most studies of wastewater surveillance did not link what was found in the wastewater to other measures of disease transmission. Among those studies that did, the value reported varied by study. Wastewater surveillance should be considered as a potential public health tool for many infectious diseases. Wastewater surveillance studies can be improved by incorporating other measures of disease transmission at the population-level including disease incidence and hospitalizations.

Environmental Monitoring for Enteroviruses in Maputo, Mozambique—2018

Due to the possibility of wild poliovirus importation from endemic regions and the high circulation of vaccine-derived poliovirus type 2 in the African region, Mozambique implemented a surveillance program to monitor the circulation of enteroviruses in the environment. From January to November 2018, a period that immediately preceded the cVDPV outbreak in Africa, 63 wastewater samples were collected from different areas in Maputo city. A total of 25 samples (39.7%) were positive based on cell culture isolation. Non-polio enteroviruses were found in 24 samples (24/25; 96%), whereas 1 Sabin-related poliovirus was isolated. Neither wild nor vaccine-derived poliovirus was detected. High circulation of EVB species was detected. Environmental surveillance in the One Health approach, if effectively applied as support to acute flaccid paralysis, can be a powerful aid to the public health system to monitor poliovirus besides non-polio enteroviruses in polio-free areas.

Wastewater-Based Epidemiology of Enteric Viruses and Surveillance of Acute Gastrointestinal Illness Outbreaks in a Resource-Limited Region

Acute gastrointestinal illness (AGI) continues to be an important cause of morbidity and mortality among all ages. This study applied the principles of wastewater-based epidemiology for the preventive identification of potential outbreaks of acute viral gastroenteritis and hepatitis A by analyzing the presence of human enteric viruses in influents of small municipal wastewater treatment plants (WWTPs) handling domestic sewage, together with public health reports of acute diarrheal and hepatitis A disease in Costa Rica during 2013. Raw wastewater samples were collected during four seasonal periods with different rainfall levels. The presence of five human enteric viruses (rotavirus A, norovirus GI, norovirus GII, enterovirus, and hepatitis A virus) was studied by endpoint and real-time polymerase chain reaction in influents of five WWTPs. Cases of AGI were analyzed using historical public health reports of endemic levels and quartile ranges for each administrative and territorial area where the WWTPs are located and for its surrounding counties. A tendency for a higher rate of positive viral tests was present 1 week before an increase of AGI cases. Epidemiological weeks categorized as Outbreak (above the 75th percentile) and Success (below the 25th percentile) showed statistically significant differences in terms of positive viral test rates (Wilcoxon test, P = 0.05). Virological monitoring of wastewater in small WWTPs is an appropriate model for epidemiological surveillance of diarrheal and hepatitis A diseases in low- and middle-resource countries.

Environmental Surveillance for Risk Assessment in the Context of a Phase 2 Clinical Trial of Type 2 Novel Oral Polio Vaccine in Panama

Environmental surveillance was recommended for risk mitigation in a novel oral polio vaccine-2 (nOPV2) clinical trial (M5-ABMG) to monitor excretion, potential circulation, and loss of attenuation of the two nOPV2 candidates. The nOPV2 candidates were developed to address the risk of poliovirus (PV) type 2 circulating vaccine-derived poliovirus (cVDPV) as part of the global eradication strategy. Between November 2018 and January 2020, an environmental surveillance study for the clinical trial was conducted in parallel to the M5-ABMG clinical trial at five locations in Panama. The collection sites were located upstream from local treatment plant inlets, to capture the excreta from trial participants and their community. Laboratory analyses of 49 environmental samples were conducted using the two-phase separation method. Novel OPV2 strains were not detected in sewage samples collected during the study period. However, six samples were positive for Sabin-like type 3 PV, two samples were positive for Sabin-like type 1 PV, and non-polio enteroviruses NPEVs were detected in 27 samples. One of the nOPV2 candidates has been granted Emergency Use Listing by the World Health Organization and initial use started in March 2021. This environmental surveillance study provided valuable risk mitigation information to support the Emergency Use Listing application.

Detection of New Delhi metallo-beta-lactamase enzyme gene bla NDM-1 associated with the Int-1 gene in Gram-negative bacteria collected from the effluent treatment plant of a tuberculosis care hospital in Delhi, India

Background

Organisms possessing the bla_NDM-1 gene (responsible for carbapenem resistance) with a class-1 integron can acquire many other antibiotic resistance genes from the community sewage pool and become multidrug-resistant superbugs. In this regard, hospital sewage, which contains a large quantity of residual antibiotics, metals and disinfectants, is being recognized as a significant cause of antimicrobial resistance (AMR) origination and spread across the major centres of the world and is thus routinely investigated as a marker for tracing the origin of drug resistance. Therefore, in this study, an attempt has been made to identify and characterize the carbapenem-resistant microbes associated with integron genes amongst the organisms isolated from the effluent treatment plant (ETP) installed in a tertiary respiratory care hospital in Delhi, India.

Methods

One hundred and thirty-eight organisms belonging to Escherichia, Klebsiella, Pseudomonas and Acinetobacter spp. were collected from the incoming and outgoing sewage lines of the ETP. Carbapenem sensitivity and characterization was performed by the imipenem and imipenem-EDTA disc diffusion method. Later DNA extraction and PCR steps were performed for the Int-1 and bla_NDM-1 genes.

Results

Of the 138 organisms, 86 (62.3 %) were imipenem-resistant (P<0.05). One hundred and twenty-four (89.9 %) organisms had one or both of the genes. Overall, the bla_NDM-1 gene (genotypic resistance) was present in 71 % (98/138) of organisms. 53.6 % (74/138) organisms were double gene-positive (bla_NDM-1 + Int-1), of which 40 were producing the metallo-beta-lactamase enzyme, making up almost 28.9 % (40/138) of the collected organisms.

Conclusion

The current study strengthens the hypothesis that Carbapenem resistant organisms are in a high-circulation burden through the human gut and hospital ETPs are providing an environment for resistance origination and amplification.

Environmental Surveillance of Polioviruses in Armenia, Colombia before Trivalent Oral Polio Vaccine Cessation

Although acute flaccid paralysis (AFP) surveillance is the "gold standard" for detecting cases of polio, environmental surveillance can provide supplementary information in the absence of paralytic poliomyelitis cases. This study aimed to detect the introduction and/or circulation of wild poliovirus or vaccine-derived polioviruses (VDPV) in wastewater, covering a significant population of Armenia, Colombia, before trivalent oral polio vaccine (OPV) cessation. Between March and September 2015, 24 wastewater samples were collected from eight study sites in eight communes of Armenia, Colombia. Virus detection and characterization were performed using both cell culture (i.e., RD or L20B cells) and RT-PCR. Polioviruses were isolated in 11 (45.8%) of 24 wastewater samples. All isolates were identified as Sabin strains (type 1 = 9, type 3 = 2) by intratypic differentiation. Type 2 poliovirus was not detected in any of the samples. No wild poliovirus or VDPV was detected among the isolates. Non-polio enterovirus was identified in 8.3% (2/24) of the samples. This study revealed the excretion of Sabin poliovirus from OPV-immunized individuals, as well as the absence of VDPV and wild poliovirus in wastewaters of Armenia, Colombia. This confirms that environmental surveillance is an effective method, as an additional support to AFP surveillance, to monitor poliovirus during the OPV-to-IPV (inactivated polio vaccine) transition period.

Genetic landscape and macro-evolution of co-circulating Coxsackieviruses A and Vaccine-derived Polioviruses in the Democratic Republic of Congo, 2008-2013

Enteroviruses (EVs) are among the most common viruses infecting humans worldwide but only a few Non-Polio Enterovirus (NPEV) isolates have been characterized in the Democratic Republic of Congo (DR Congo). Moreover, circulating vaccine-derived polioviruses (PVs) [cVDPVs] isolated during multiple outbreaks in DR Congo from 2004 to 2018 have been characterized so far only by the sequences of their VP1 capsid coding gene. This study was carried to i) investigate the circulation and genetic diversity of NPEV and polio vaccine isolates recovered from healthy children and Acute Flaccid Paralysis (AFP) patients, ii) evaluate the occurrence of genetic recombination among EVs belonging to the Enterovirus C species (including PVs) and iii) identify the virological factors favoring multiple emergences of cVDPVs in DR Congo. The biological material considered in this study included i) a collection of 91 Sabin-like PVs, 54 cVDPVs and 150 NPEVs isolated from AFP patients between 2008 and 2012 in DR Congo and iii) a collection of 330 stool specimens collected from healthy children in 2013 in the Kasai Oriental and Maniema provinces of DR Congo. Studied virus isolates were sequenced in four distinct sub-genomic regions 5’-UTR, VP1, 2C^ATPase and 3D^pol. Resulting sequences were compared through comparative phylogenetic analyses. Virus isolation showed that 19.1% (63/330) healthy children were infected by EVs including 17.9% (59/330) of NPEVs and 1.2% (4/330) of type 3 Sabin-like PVs. Only one EV-C type, EV-C99 was identified among the NPEV collection from AFP patients whereas 27.5% of the 69 NPEV isolates typed in healthy children belonged to the EV-C species: CV-A13 (13/69), A20 (5/69) and A17 (1/69). Interestingly, 50 of the 54 cVDPVs featured recombinant genomes containing exogenous sequences in at least one of the targeted non-structural regions of their genomes: 5’UTR, 2C^ATPase and 3D^pol. Some of these non-vaccine sequences of the recombinant cVDPVs were strikingly related to homologous sequences from co-circulating CV-A17 and A20 in the 2C^ATPase region as well as to those from co-circulating CV-A13, A17 and A20 in the 3D^pol region. This study provided the first evidence uncovering CV-A20 strains as major recombination partners of PVs. High quality AFP surveillance, sensitive environmental surveillance and efficient vaccination activities remain essential to ensure timely detection and efficient response to recombinant cVDPVs outbreaks in DR Congo. Such needs are valid for any epidemiological setting where high frequency and genetic diversity of Coxsackieviruses A13, A17 and A20 provide a conducive viral ecosystem for the emergence of virulent recombinant cVDPVs.

The strategy of the Global Polio Eradication Initiative is based on the surveillance of patients suffering from Acute Flaccid Paralysis (AFP) and mass vaccination with live-attenuated vaccine strains of polioviruses (PVs) in endemic areas. However, vaccine strains of PVs can circulate and replicate for a long time when the vaccine coverage of the population is low. Such prolonged circulation and replication of vaccine strains of PVs can result to the emergence of circulating vaccine-derived polioviruses [cVDPVs] that are as virulent as wild PVs. In this study, we performed the molecular characterization of a large collection of 377 virus isolates recovered from paralyzed patients between 2008 and 2012 in DR Congo and healthy children in 2013 in the Kasai Oriental and Maniema provinces of DR Congo. We found that the genetic diversity of enteroviruses of the species Enterovirus C is more important than previously reported. Interestingly, 50 of the 54 cVDPVs featured recombinant genomes containing exogenous sequences of the 2C ATPase and/or 3D polymerase coding genes acquired from co-circulating Coxsackieviruses A13, A17 and A20. Coxsackieviruses A20 strains were identified for the first time as major partners of genetic recombination with co-circulating live-attenuated polio vaccine strains.

Our findings highlight the need to reinforce and maintain high quality surveillance of PVs and efficient immunization activities in order to ensure early detection and control of emerging cVDPVs in all settings where high frequency and diversity of Coxsackieviruses A13, A17 and A20 have been documented.

Dissemination of enteroviruses in the production chain of organic lettuce in Rio de Janeiro, Brazil

This study aimed to survey the environmental dissemination of enterovirus (EV) in a site of organic lettuce situated in the mountainous region of the state of Rio de Janeiro, Brazil. For this purpose, a total of 96 environmental samples, including water and lettuce samples obtained in different stages of the production chain (e.g., irrigation water, seedlings, lettuces grown, and washed lettuces ready-to-eat), were analyzed. EV genomes were detected in 12.5% (12/96) of the tested samples (eight from irrigation water and 4 from lettuce samples). Levels of viral concentration ranged from 3.37 × 103 to 4.72 × 106 genomic copies per liter (gc L-1 ) and from 2.14 × 104 to 5.56 × 104 genome copies per 25 grams (gc 25 g-1 ) for the water and lettuce samples, respectively. Such findings suggest that the use of viruses as human fecal contamination markers must be considered in order to improve food safety in organic supply chains.

An Environmental Surveillance in Uruguay Reveals the Presence of Highly Divergent Types of Human Enterovirus Species C and a High Frequency of Species A and B Types

Information about Human Enterovirus circulation in Uruguay is scarce. The aim of this study was to generate the first description about their circulation in the country through the study of sewage samples collected before and after the switch from Oral Poliovirus Vaccine to Inactivated Poliovirus Vaccine. Viruses were concentrated by an adsorption-elution to a negatively charged membrane, and real-time quantitative PCR and qualitative PCR methods were used to detect, quantify, and characterize enteroviruses. Positive samples were inoculated in RD cells and two passages were performed. Additionally, RD+ samples were subsequently passed onto L20B cells. Human Enteroviruses were detected in 67.6% of the samples, with concentrations between 4.9 and 6.6 Log₁₀ genomic copies per liter. 10% of positive samples replicated in RD cells, of which none in L20B cells. Molecular characterization of Human Enterovirus strains directly detected from sewage sample concentrates allowed the identification of highly divergent members of species C such as Enterovirus C99 and Coxsackievirus A13, as well as the frequent detection of species A and B members (particularly Coxsackievirus A16 and Echovirus 6, respectively). Other detected types were Coxsackievirus A2, A22, B1, B5, Echovirus 5, and 9. The characterization of viruses isolated in cell culture revealed the presence of Echovirus 6 and Coxsackievirus B3. Despite the absence of poliovirus, a wide circulation of different enterovirus types was evidenced in Uruguayan sewage samples, highlighting that the local populations are exposed to different kinds of diseases originated by several human enterovirus.

Insights from a Systematic Search for Information on Designs, Costs, and Effectiveness of Poliovirus Environmental Surveillance Systems

Poliovirus surveillance plays a critical role in achieving and certifying eradication and will play a key role in the polio endgame. Environmental surveillance can provide an opportunity to detect circulating polioviruses prior to the observation of any acute flaccid paralysis cases. We completed a systematic review of peer-reviewed publications on environmental surveillance for polio including the search terms "environmental surveillance" or "sewage," and "polio," "poliovirus," or "poliomyelitis," and compared characteristics of the resulting studies. The review included 146 studies representing 101 environmental surveillance activities from 48 countries published between 1975 and 2016. Studies reported taking samples from sewage treatment facilities, surface waters, and various other environmental sources, although they generally did not present sufficient details to thoroughly evaluate the sewage systems and catchment areas. When reported, catchment areas varied from 50 to over 7.3 million people (median of 500,000 for the 25% of activities that reported catchment areas, notably with 60% of the studies not reporting this information and 16% reporting insufficient information to estimate the catchment area population size). While numerous studies reported the ability of environmental surveillance to detect polioviruses in the absence of clinical cases, the review revealed very limited information about the costs and limited information to support quantitative population effectiveness of conducting environmental surveillance. This review motivates future studies to better characterize poliovirus environmental surveillance systems and the potential value of information that they may provide in the polio endgame.

Comparison of ELISA and dual stage real time RT-PCR to differentiate Sabin like and non-Sabin like poliovirus isolates

Environmental surveillance of polioviruses has been used as an important tool in monitoring circulation of wild polioviruses and/or Vaccine derived polioviruses in sewage samples. It is important to distinguish Sabin like isolates from non-Sabin like; ELISA & dual stage real time RT-PCR have been used for the same. Current study was carried out on sewage isolates to compare ELISA & RT-PCR with sequencing to distinguish Sabin like from non-Sabin like. Out of 468 sewage specimens, 91 (19.44%) were non-polio enteroviruses positive and 377 (80.56%) were polio positive by virus isolation method. A total of 488 polio virus isolates were detected by L20B and RD route which were further subjected to ELISA and RT-PCR. The results were compared with sequencing. On comparison, the specificity of ELISA was only 66.67% in spite of very low sensitivity (3.43%). The sensitivity of RT-PCR was 97.71% which makes it a good primary screening test for detection of non-Sabin like viruses. However, the specificity was only 33.33%. RT-PCR appears to be a sensitive tool for detecting non-Sabin like viruses however; the isolates which are non-Sabin like by RT-PCR may not necessarily be mutated viruses. ELISA cannot be used for differentiation of Sabin likes from non-Sabin likes due to low sensitivity.