Wastewater-based monitoring of SARS-CoV-2 at UK airports and its potential role in international public health surveillance

Co-infections of SARS-CoV-2 with respiratory syncytial virus and human influenza A in patients with symptoms of COVID-19 in Ghana: A retrospective study

Background

During the COVID-19 pandemic the aetiology of respiratory illnesses were narrowed to SARS-CoV-2. This prevented diagnosis of other pathogens and patients were not notified of the accurate diagnosis of their illnesses when SARS-CoV-2 was absent. It is therefore important to look back and determine what else was present but was missed.

Objective

This retrospective study sought to gain insights into prevalence of respiratory syncytial virus (RSV) and influenza A alongside SARS-CoV-2 in patients who reported with clinical symptoms of respiratory illnesses.

Methods

Samples from patients who had reported of respiratory symptoms were selected at random from a pool. RNA was extracted and RT-PCR was performed for SARS-CoV-2, RSV and Influenza A in parallel. Data on the clinical symptoms was extracted from case-base forms and analysed.

Results

Of the 400 symptomatic samples tested, prevalence of SARS-CoV-2, influenza A and RSV was 20.3 %, 2.0 % and 0.5 % respectively. Only one sample tested positive for SARS-CoV-2 and influenza A. About 77 % of the symptomatic cases did not test positive for any of the three agents. Cough (79 %) was the most common symptom followed by fever and chills, headache, sore throat and runny nose.

Conclusion

The large proportion of symptomatic cases that tested negative for all three respiratory viruses raises a flag and a need for more investigations into the actual burden of respiratory aetiologic agents during the pandemic. With the low levels of co-infections, parallel testing may not be needed however, a strong case for multiplex tests for respiratory agents exists.

Use of wastewater from passenger ships to assess the movement of COVID-19 and other pathogenic viruses across maritime international boundaries

Objective

The worldwide spread of SARS-CoV-2 and the resulting COVID-19 pandemic has been driven by international travel. This has led to the desire to develop surveillance approaches which can estimate the rate of import of pathogenic organisms across international borders. The aim of this study was to investigate the use of wastewater-based approaches for the surveillance of viral pathogens on commercial short-haul (3.5 h transit time) roll-on/roll-off passenger/freight ferries operating between the UK and the Republic of Ireland.

Methods

Samples of toilet-derived wastewater (blackwater) were collected from two commercial ships over a 4-week period and analysed for SARS-CoV-2, influenza, enterovirus, norovirus, the faecal-marker virus crAssphage and a range of physical and chemical indicators of wastewater quality.

Results

A small proportion of the wastewater samples were positive for SARS-CoV-2 (8% of the total), consistent with theoretical predictions of detection frequency (4%-15% of the total) based on the national COVID-19 Infection Survey and defecation behaviour. In addition, norovirus was detected in wastewater at low frequency. No influenza A/B viruses, enterovirus or enterovirus D68 were detected throughout the study period.

Conclusion

We conclude that testing of wastewater from ships that cross international maritime boundaries may provide a cost-effective and relatively unbiased method to estimate the flow of infected individuals between countries. The approach is also readily applicable for the surveillance of other disease-causing agents.

Usefulness of aircraft and airport wastewater for monitoring multiple pathogens including SARS-CoV-2 variants

BACKGROUND

As global travel resumed in coronavirus disease 2019 (COVID-19) endemicity, the potential of aircraft wastewater monitoring to provide early warning of disease trends for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and other infectious diseases, particularly at international air travel hubs, was recognized. We therefore assessed and compared the feasibility of testing wastewater from inbound aircraft and airport terminals for 18 pathogens including SARS-CoV-2 in Singapore, a popular travel hub in Asia.

METHODS

Wastewater samples collected from inbound medium- and long-haul flights and airport terminals were tested for SARS-CoV-2. Next Generation Sequencing was carried out on positive samples to identify SARS-CoV-2 variants. Airport and aircraft samples were further tested for 17 other pathogens through quantitative reverse transcription polymerase chain reaction.

RESULTS

The proportion of SARS-CoV-2-positive samples and the average virus load was higher for wastewater samples from aircraft as compared with airport terminals. Cross-correlation analyses indicated that viral load trends from airport wastewater led local COVID-19 case trends by 2-5 days. A total of 10 variants (44 sub-lineages) were successfully identified from aircraft wastewater and airport terminals, and four variants of interest and one variant under monitoring were detected in aircraft and airport wastewater 18-31 days prior to detection in local clinical cases. The detection of five respiratory and four enteric viruses in aircraft wastewater samples further underscores the potential to expand aircraft wastewater to monitoring pathogens beyond SARS-CoV-2.

CONCLUSION

Our findings demonstrate the feasibility of aircraft wastewater testing for monitoring infectious diseases threats, potentially detecting signals before clinical cases are reported. The triangulation of similar datapoints from aircraft wastewater of international travel nodes could therefore serve as a useful early warning system for global health threats.

Combining wastewater surveillance and case data in estimating the time-varying effective reproduction number

Wastewater surveillance has been increasingly acknowledged as a useful tool for monitoring transmission dynamics of infections of public health concern, including the coronavirus disease (COVID-19). While a range of models have been proposed to estimate the time-varying effective reproduction number (Rt) utilizing clinical data, few have harnessed the viral concentration in wastewater samples to do so, leaving uncertainties about the potential precision gains with its use. In this study, we developed a Bayesian hierarchical model which simultaneously reconstructed the latent infection trajectory and estimated Rt. Focusing on the 2022 and early 2023 COVID-19 transmission trends in Singapore, where mass community wastewater surveillance has become routine, we performed estimations using a spectrum of data sources, including reported case counts, hospital admissions, deaths, and wastewater viral loads. We further explored the performance of our wastewater model across various scenarios with different sampling strategies. The results showed consistent estimates derived from models employing diverse data streams, while models incorporating more wastewater samples exhibited greater uncertainty and variation in the inferred Rts. Additionally, our analysis revealed prominent day-of-the-week effect in reported case counts and substantial temporal variations in ascertainment rates. In response to these findings, we advocate for a hybrid approach leveraging both clinical and wastewater surveillance data to account for changes in case-ascertainment rates. Furthermore, our study demonstrates the possibility of reducing sampling frequency or sample size without compromising estimation accuracy for Rt, highlighting the potential for optimizing resource allocation in surveillance efforts while maintaining robust insights into the transmission dynamics of infectious diseases.

Long-term wastewater monitoring of SARS-CoV-2 viral loads and variants at the major international passenger hub Amsterdam Schiphol Airport: A valuable addition to COVID-19 surveillance

Wastewater-based epidemiological surveillance at municipal wastewater treatment plants has proven to play an important role in COVID-19 surveillance. Considering international passenger hubs contribute extensively to global transmission of viruses, wastewater surveillance at this type of location may be of added value as well. The aim of this study is to explore the potential of long-term wastewater surveillance at a large passenger hub as an additional tool for public health surveillance during different stages of a pandemic. Here, we present an analysis of SARS-CoV-2 viral loads in airport wastewater by reverse-transcription quantitative polymerase chain reaction (RT-qPCR) from the beginning of the COVID-19 pandemic in Feb 2020, and an analysis of SARS-CoV-2 variants by whole-genome next-generation sequencing from Sep 2020, both until Sep 2022, in the Netherlands. Results are contextualized using (inter)national measures and data sources such as passenger numbers, clinical surveillance data and national wastewater surveillance data. Our findings show that wastewater surveillance was possible throughout the study period, irrespective of measures, as viral loads were detected and quantified in 98.6 % (273/277) of samples. Emergence of SARS-CoV-2 variants, identified in 91.0 % (161/177) of sequenced samples, coincided with increases in viral loads. Furthermore, trends in viral load and variant detection in airport wastewater closely followed, and in some cases preceded, trends in national daily average viral load in wastewater and variants detected in clinical surveillance. Wastewater-based epidemiology at a large international airport is a valuable addition to classical COVID-19 surveillance and the developed expertise can be applied in pandemic preparedness plans for other (emerging) pathogens in the future.

Wastewater sequencing as a powerful tool to reveal SARS-CoV-2 variant introduction and spread in French Guiana, South America

The origin of introduction of a new pathogen in a country, the evolutionary dynamics of an epidemic within a country, and the role of cross-border areas on pathogen dynamics remain complex to disentangle and are often poorly understood. For instance, cross-border areas represent the ideal location for the sharing of viral variants between countries, with international air travel, land travel and waterways playing an important role in the cross-border spread of infectious diseases. Unfortunately, monitoring the point of entry and the evolutionary dynamics of viruses in space and time within local populations remain challenging. Here we tested the efficiency of wastewater-based epidemiology and genotyping in monitoring Covid-19 epidemiology and SARS-CoV-2 variant dynamics in French Guiana, a tropical country located in South America. Our results suggest that wastewater-based epidemiology and genotyping are powerful tools to monitor variant introduction and disease evolution within a tropical country but the inclusion of both clinical and wastewater samples could still improve our understanding of genetic diversity co-circulating. Wastewater sequencing also revealed the cryptic transmission of SARS-CoV-2 variants within the country. Interestingly, we found some amino acid changes specific to the variants co-circulating in French Guiana, suggesting a local evolution of the SARS-CoV-2 variants after their introduction. More importantly, our results showed that the proximity to bordering countries was not the origin of the emergence of the French Guianese B.1.160.25 variant, but rather that this variant emerged from an ancestor B.1.160 variant introduced by European air plane travelers, suggesting thus that air travel remains a significant risk for cross-border spread of infectious diseases. Overall, we suggest that wastewater-based epidemiology and genotyping provides a cost effective and non-invasive approach for pathogen monitoring and an early-warning tool for disease emergence and spread within a tropical country.

Cross-continental comparative experiences of wastewater surveillance and a vision for the 21st century

The COVID-19 pandemic has brought the epidemiological value of monitoring wastewater into sharp focus. The challenges of implementing and optimising wastewater monitoring vary significantly from one region to another, often due to the array of different wastewater systems around the globe, as well as the availability of resources to undertake the required analyses (e.g. laboratory infrastructure and expertise). Here we reflect on the local and shared challenges of implementing a SARS-CoV-2 monitoring programme in two geographically and socio-economically distinct regions, São Paulo state (Brazil) and Wales (UK), focusing on design, laboratory methods and data analysis, and identifying potential guiding principles for wastewater surveillance fit for the 21st century. Our results highlight the historical nature of region-specific challenges to the implementation of wastewater surveillance, including previous experience of using wastewater surveillance, stakeholders involved, and nature of wastewater infrastructure. Building on those challenges, we then highlight what an ideal programme would look like if restrictions such as resource were not a constraint. Finally, we demonstrate the value of bringing multidisciplinary skills and international networks together for effective wastewater surveillance.

Comparison of gene targets and sampling regimes for SARS-CoV-2 quantification for wastewater epidemiology in UK prisons

Prisons are high-risk settings for infectious disease transmission, due to their enclosed and semi-enclosed environments. The proximity between prisoners and staff, and the diversity of prisons reduces the effectiveness of non-pharmaceutical interventions, such as social distancing. Therefore, alternative health monitoring methods, such as wastewater-based epidemiology (WBE), are needed to track pathogens, including SARS-CoV-2. This pilot study assessed WBE to quantify SARS-CoV-2 prevalence in prison wastewater to determine its utility within a health protection system for residents. The study analysed 266 samples from six prisons in England over a 12-week period for nucleoprotein 1 (N1 gene) and envelope protein (E gene) using quantitative reverse transcriptase-polymerase chain reaction. Both gene assays successfully detected SARS-CoV-2 fragments in wastewater samples, with both genes significantly correlating with COVID-19 case numbers across the prisons (p < 0.01). However, in 25% of the SARS-positive samples, only one gene target was detected, suggesting that both genes be used to reduce false-negative results. No significant differences were observed between 14- and 2-h composite samples, although 2-h samples showed greater signal variance. Population normalisation did not improve correlations between the N1 and E genes and COVID-19 case data. Overall, WBE shows considerable promise for health protection in prison settings.

Unveiling indicator, enteric, and respiratory viruses in aircraft lavatory wastewater using adsorption-extraction and Nanotrap® Microbiome A Particles workflows

The effective detection of viruses in aircraft wastewater is crucial to establish surveillance programs for monitoring virus spread via aircraft passengers. This study aimed to compare the performance of two virus concentration workflows, adsorption-extraction (AE) and Nanotrap® Microbiome A Particles (NMAP), in detecting the prevalence and concentrations of 15 endogenous viruses including ssDNA, dsDNA, ssRNA in 24 aircraft lavatory wastewater samples. The viruses tested included two indicator viruses, four enteric viruses, and nine respiratory viruses. The results showed that cross-assembly phage (crAssphage), human polyomavirus (HPyV), rhinovirus A (RhV A), and rhinovirus B (RhV B) were detected in all wastewater samples using both workflows. However, enterovirus (EV), human norovirus GII (HNoV GII), human adenovirus (HAdV), bocavirus (BoV), parechovirus (PeV), epstein-barr virus (EBV). Influenza A virus (IAV), and respiratory syncytial virus B (RsV B) were infrequently detected by both workflows, and hepatitis A virus (HAV), influenza B virus (IBV), and respiratory syncytial virus B (RsV A) were not detected in any samples. The NMAP workflow had greater detection rates of RNA viruses (EV, PeV, and RsV B) than the AE workflow, while the AE workflow had greater detection rates of DNA viruses (HAdV, BoV, and EBV) than the NMAP workflow. The concentration of each virus was also analyzed, and the results showed that crAssphage had the highest mean concentration (6.76 log10 GC/12.5 mL) followed by HPyV (5.46 log10 GC/12.5 mL using the AE workflow, while the mean concentrations of enteric and respiratory viruses ranged from 2.48 to 3.63 log10 GC/12.5 mL. Using the NMAP workflow, the mean concentration of crAssphage was 5.18 log10 GC/12.5 mL and the mean concentration of HPyV was 4.20 log10 GC/12.5 mL, while mean concentrations of enteric and respiratory viruses ranged from 2.55 to 3.74 log10 GC/12.5 mL. Significantly higher (p < 0.05) mean concentrations of crAssphage and HPyV were observed when employing the AE workflow in comparison to the NMAP workflow. Conversely, the NMAP workflow yielded significantly greater (p < 0.05) concentrations of RhV A, and RhV B compared to the AE workflow. The findings of this study can aid in the selection of an appropriate concentration workflow for virus surveillance studies and contribute to the development of efficient virus detection methods.

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.

Evaluating the theoretical performance of aircraft wastewater monitoring as a tool for SARS-CoV-2 surveillance

Air travel plays an important role in the cross-border spread of infectious diseases. During the SARS-CoV-2 pandemic many countries introduced strict border testing protocols to monitor the incursion of the virus. However, high implementation costs and significant inconvenience to passengers have led public health authorities to consider alternative methods of disease surveillance at borders. Aircraft wastewater monitoring has been proposed as one such alternative. In this paper we assess the theoretical limits of aircraft wastewater monitoring and compare its performance to post-arrival border screening approaches. Using an infectious disease model, we simulate an unmitigated SARS-CoV-2 epidemic originating in a seed country and spreading to the United Kingdom (UK) through daily flights. We use a probabilistic approach to estimate the time of first detection in the UK in aircraft wastewater and respiratory swab screening. Across a broad range of model parameters, our analysis indicates that the median time between the first incursion and detection in wastewater would be approximately 17 days (IQR: 7-28 days), resulting in a median of 25 cumulative cases (IQR: 6-84 cases) in the UK at the point of detection. Comparisons to respiratory swab screening suggest that aircraft wastewater monitoring is as effective as random screening of 20% of passengers at the border, using a test with 95% sensitivity. For testing regimes with sensitivity of 85% or less, the required coverage to outperform wastewater monitoring increases to 30%. Analysis of other model parameters suggests that wastewater monitoring is most effective when used on long-haul flights where probability of defecation is above 30%, and when the target pathogen has high faecal shedding rates and reasonable detectability in wastewater. These results demonstrate the potential use cases of aircraft wastewater monitoring and its utility in a wider system of public health surveillance.