COVID-19 Crisis Creates Opportunity towards Global Monitoring & Surveillance

Changes to Public Health Surveillance Methods Due to the COVID-19 Pandemic: Scoping Review

BACKGROUND

Public health surveillance plays a vital role in informing public health decision-making. The onset of the COVID-19 pandemic in early 2020 caused a widespread shift in public health priorities. Global efforts focused on COVID-19 monitoring and contact tracing. Existing public health programs were interrupted due to physical distancing measures and reallocation of resources. The onset of the COVID-19 pandemic intersected with advancements in technologies that have the potential to support public health surveillance efforts.

OBJECTIVE

This scoping review aims to explore emergent public health surveillance methods during the early COVID-19 pandemic to characterize the impact of the pandemic on surveillance methods.

METHODS

A scoping search was conducted in multiple databases and by scanning key government and public health organization websites from March 2020 to January 2022. Published papers and gray literature that described the application of new or revised approaches to public health surveillance were included. Papers that discussed the implications of novel public health surveillance approaches from ethical, legal, security, and equity perspectives were also included. The surveillance subject, method, location, and setting were extracted from each paper to identify trends in surveillance practices. Two public health epidemiologists were invited to provide their perspectives as peer reviewers.

RESULTS

Of the 14,238 unique papers, a total of 241 papers describing novel surveillance methods and changes to surveillance methods are included. Eighty papers were review papers and 161 were single studies. Overall, the literature heavily featured papers detailing surveillance of COVID-19 transmission (n=187). Surveillance of other infectious diseases was also described, including other pathogens (n=12). Other public health topics included vaccines (n=9), mental health (n=11), substance use (n=4), healthy nutrition (n=1), maternal and child health (n=3), antimicrobial resistance (n=2), and misinformation (n=6). The literature was dominated by applications of digital surveillance, for example, by using big data through mobility tracking and infodemiology (n=163). Wastewater surveillance was also heavily represented (n=48). Other papers described adaptations to programs or methods that existed prior to the COVID-19 pandemic (n=9). The scoping search also found 109 papers that discuss the ethical, legal, security, and equity implications of emerging surveillance methods. The peer reviewer public health epidemiologists noted that additional changes likely exist, beyond what has been reported and available for evidence syntheses.

CONCLUSIONS

The COVID-19 pandemic accelerated advancements in surveillance and the adoption of new technologies, especially for digital and wastewater surveillance methods. Given the investments in these systems, further applications for public health surveillance are likely. The literature for surveillance methods was dominated by surveillance of infectious diseases, particularly COVID-19. A substantial amount of literature on the ethical, legal, security, and equity implications of these emerging surveillance methods also points to a need for cautious consideration of potential harm.

Real-time sewage surveillance for SARS-CoV-2 in Dhaka, Bangladesh versus clinical COVID-19 surveillance: a longitudinal environmental surveillance study (December, 2019-December, 2021)

BACKGROUND

Clinical surveillance for COVID-19 has typically been challenging in low-income and middle-income settings. From December, 2019, to December, 2021, we implemented environmental surveillance in a converging informal sewage network in Dhaka, Bangladesh, to investigate SARS-CoV-2 transmission across different income levels of the city compared with clinical surveillance.

METHODS

All sewage lines were mapped, and sites were selected with estimated catchment populations of more than 1000 individuals. We analysed 2073 sewage samples, collected weekly from 37 sites, and 648 days of case data from eight wards with varying socioeconomic statuses. We assessed the correlations between the viral load in sewage samples and clinical cases.

FINDINGS

SARS-CoV-2 was consistently detected across all wards (low, middle, and high income) despite large differences in reported clinical cases and periods of no cases. The majority of COVID-19 cases (26 256 [55·1%] of 47 683) were reported from Ward 19, a high-income area with high levels of clinical testing (123 times the number of tests per 100 000 individuals compared with Ward 9 [middle-income] in November, 2020, and 70 times the number of tests per 100 000 individuals compared with Ward 5 [low-income] in November, 2021), despite containing only 19·4% of the study population (142 413 of 734 755 individuals). Conversely, a similar quantity of SARS-CoV-2 was detected in sewage across different income levels (median difference in high-income vs low-income areas: 0·23 log10 viral copies + 1). The correlation between the mean sewage viral load (log10 viral copies + 1) and the log10 clinical cases increased with time (r = 0·90 in July-December, 2021 and r=0·59 in July-December, 2020). Before major waves of infection, viral load quantity in sewage samples increased 1-2 weeks before the clinical cases.

INTERPRETATION

This study demonstrates the utility and importance of environmental surveillance for SARS-CoV-2 in a lower-middle-income country. We show that environmental surveillance provides an early warning of increases in transmission and reveals evidence of persistent circulation in poorer areas where access to clinical testing is limited.

FUNDING

Bill & Melinda Gates Foundation.

Gut-on-a-chip for disease models

The intestinal tract is a vital organ responsible for digestion and absorption in the human body and plays an essential role in pathogen invasion. Compared with other traditional models, gut-on-a-chip has many unique advantages, and thereby, it can be considered as a novel model for studying intestinal functions and diseases. Based on the chip design, we can replicate the in vivo microenvironment of the intestine and study the effects of individual variables on the experiment. In recent years, it has been used to study several diseases. To better mimic the intestinal microenvironment, the structure and function of gut-on-a-chip are constantly optimised and improved. Owing to the complexity of the disease mechanism, gut-on-a-chip can be used in conjunction with other organ chips. In this review, we summarise the human intestinal structure and function as well as the development and improvement of gut-on-a-chip. Finally, we present and discuss gut-on-a-chip applications in inflammatory bowel disease (IBD), viral infections and phenylketonuria. Further improvement of the simulation and high throughput of gut-on-a-chip and realisation of personalised treatments are the problems that should be solved for gut-on-a-chip as a disease model.

Evaluation of viral concentration and extraction methods for SARS-CoV-2 recovery from wastewater using droplet digital and quantitative RT-PCR

The ongoing pandemic caused by the emergence of SARS-CoV-2 has resulted in millions of deaths worldwide despite the various measures announced by the authorities. Wastewater-based epidemiology has the ability to provide a day-to-day estimation of the number of infected people in a fast and cost-effective manner. However, owing to the complex nature of wastewater, wastewater monitoring for viral genome copies is affected by the extensive viral fragmentation that takes place all the way to the sewage and the analytical lab. The aim of this study was to evaluate different methodologies for the concentration and extraction of viruses in wastewaters and to select and improve an option that maximizes the recovery of SARS-CoV-2. We compare 5 different concentration methods and 4 commercially available kits for the RNA extraction. To evaluate the performance and the recovery of these, SARS-CoV-2 isolated from patients was used as a spike control. Additionally, the presence of SARS-CoV-2 in all wastewater samples was determined using reverse transcription quantitative PCR (RT-qPCR) and reverse transcription droplet digital PCR (RT-ddPCR), targeting three genetic markers (N1, N2 and N3). Using spiked samples, recoveries were estimated 2.1–37.6% using different extraction kits and 0.1–2.1% using different concentration kits. It was found that a direct capture-based method, evaluated against a variety of concentration methods, is the best in terms of recovery, time and cost. Interestingly, we noticed a good agreement between the results provided by RT-qPCR and RT-ddPCR in terms of recovery. This evaluation can serve as a guide for laboratories establishing a protocol to perform wastewater monitoring of SARS-CoV-2. Overall, data presented here reinforces the validity of WBE for SARS-CoV-2 surveillance, uncovers potential caveats in the selection of concentration and extraction protocols and points towards optimal solutions to maximize its potential.

Integration of RT-LAMP and Microfluidic Technology for Detection of SARS-CoV-2 in Wastewater as an Advanced Point-of-Care Platform

Development of lab-on-a-chip (LOC) system based on integration of reverse transcription loop-mediated isothermal amplification (RT-LAMP) and microfluidic technology is expected to speed up SARS-CoV-2 diagnostics allowing early intervention. In the current work, reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) and RT-LAMP assays were performed on extracted RNA of seven wastewater samples from COVID-19 hotspots. RT‑LAMP assay was also performed on wastewater samples without RNA extraction. Current detection of SARS-CoV-2 is mainly by RT-qPCR of ORF (ORF1ab) and N genes so we targeted both to find the best target gene for SARS-CoV-2 detection. We also performed RT-LAMP with/without RNA extraction inside microfluidic device to target both genes. Positivity rates of RT-qPCR and RT-LAMP performed on extracted RNA were 100.0% (7/7) and 85.7% (6/7), respectively. RT-qPCR results revealed that all 7 wastewater samples were positive for N gene (Ct range 37-39), and negative for ORF1ab, suggesting that N gene could be the best target gene for SARS-CoV-2 detection. RT-LAMP of N and ORF (ORF1a) genes performed on wastewater samples without RNA extraction indicated that all 7 samples remains pink (negative). The color remains pink in all microchannels except microchannels which subjected to RT-LAMP for targeting N region after RNA extraction (yellow color) in 6 out of 7 samples. This study shows that SARS-CoV-2 was successfully detected from wastewater samples using RT-LAMP in microfluidic chips. This study brings the novelty involving the use of wastewater samples for detection of SARS-CoV-2 without previous virus concentration and with/without RNA extraction.

Passive Samplers, an Important Tool for Continuous Monitoring of the COVID-19 Pandemic

The global pandemic caused by COVID-19 has resulted in major costs around the world, costs with dimensions in every aspect, from peoples' daily living to the global economy. As the pandemic progresses, the virus evolves, and more vaccines become available, and the 'battle against the virus' continues. As part of the battle, Wastewater-Based Epidemiology (WBE) technologies are being widely deployed in essential roles for SARS-CoV-2 detection and monitoring. While focusing on demonstrating the advantages of passive samplers as a tool in WBE, this review provides a holistic view of the current WBE applications in monitoring SARS-CoV-2 with the integration of the most up-to-date data. A novel scenario example based on a recent Nanjing (China) outbreak in July 2021 is used to illustrate the potential benefits of using passive samplers to monitor COVID-19 and to facilitate effective control of future major outbreaks. The presented contents and how the application of passive samplers indicates that this technology can be beneficial at different levels, varying from building to community to regional. Countries and regions that have the pandemic well under control or have low positive case occurrences have the potential to significantly benefit from deploying passive samplers as a measure to identify and suppress outbreaks.

The challenges of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing in low-middle income countries and possible cost-effective measures in resource-limited settings

Diagnostic testing for the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection remains a challenge around the world, especially in low-middle-income countries (LMICs) with poor socio-economic backgrounds. From the beginning of the pandemic in December 2019 to August 2021, a total of approximately 3.4 billion tests were performed globally. The majority of these tests were restricted to high income countries. Reagents for diagnostic testing became a premium, LMICs either cannot afford or find manufacturers unwilling to supply them with expensive analytical reagents and equipment. From March to December 2020 obtaining testing kits for SARS-CoV-2 testing was a challenge. As the number of SARS-CoV-2 infection cases increases globally, large-scale testing still remains a challenge in LMICs. The aim of this review paper is to compare the total number and frequencies of SARS-CoV-2 testing in LMICs and high-income countries (HICs) using publicly available data from Worldometer COVID-19, as well as discussing possible interventions and cost-effective measures to increase testing capability in LMICs. In summary, HICs conducted more SARS-CoV-2 testing (USA: 192%, Australia: 146%, Switzerland: 124% and Canada: 113%) compared to middle-income countries (MICs) (Vietnam: 43%, South Africa: 29%, Brazil: 27% and Venezuela: 12%) and low-income countries (LICs) (Bangladesh: 6%, Uganda: 4% and Nigeria: 1%). Some of the cost-effective solutions to counteract the aforementioned problems includes using saliva instead of oropharyngeal or nasopharyngeal swabs, sample pooling, and testing high-priority groups to increase the number of mass testing in LMICs.

Ayurvedic Response to COVID-19 Pandemic in Kerala, India and Its Impact on Quarantined Individuals - A Community Case Study

The SARS-CoV-2 infection has resulted in massive loss of valuable human lives, extensive destruction of livelihoods and financial crisis of unprecedented levels across the globe. Kerala, a province in India, like the rest of the country, launched preventive and control measures to mitigate the impact of COVID-19 early in 2020. The Government of Kerala started 1206 Ayur Raksha Clinics and associated Task Forces across the state in April 2020 to improve the reach and penetration of Ayurvedic preventive, therapeutic and convalescent care strategies for the COVID-19 pandemic. The implementation framework of the strategy was properly designed, and had a decentralized, people-centered, and participatory approach. Kerala has robust public health machinery with adequate human resource and infrastructure in the conventional medicine sector. This community case study examines how the decentralized organizational framework was effectively utilized for facilitating the delivery of Ayurvedic services in the COVID-19 situation. Key observations from the study are: Ayurvedic programs implemented systematically, under an organized framework with social participation enables wider utilization of the services. Such a framework is easily replicable even in resource-poor settings. Rather than a pluralistic approach, an integrative health system approach may be more viable in the Kerala scenario in public health emergencies.

Sewage Systems Surveillance for SARS-CoV-2: Identification of Knowledge Gaps, Emerging Threats, and Future Research Needs

The etiological agent for novel coronavirus (COVID-19, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), not only affects the human respiratory system, but also the gastrointestinal tract resulting in gastrointestinal manifestations. The high rate of asymptomatic infected individuals has challenged the estimation of infection spread based on patients' surveillance, and thus alternative approaches such as wastewater-based epidemiology (WBE) have been proposed. Accordingly, the number of publications on this topic has increased substantially. The present systematic review thus aimed at providing state-of-the-knowledge on the occurrence and existing methods for sampling procedures, detection/quantification of SARS-CoV-2 in sewage samples, as well as anticipating challenges and providing future research direction to improve the current scientific knowledge. Articles were collected from three scientific databases. Only studies reporting measurements of virus in stool, urine, and wastewater samples were included. Results showed that improving the scientific community's understanding in these avenues is essential if we are to develop appropriate policy and management tools to address this pandemic pointing particularly towards WBE as a new paradigm in public health. It was also evident that standardized protocols are needed to ensure reproducibility and comparability of outcomes. Areas that require the most improvements are sampling procedures, concentration/enrichment, detection, and quantification of virus in wastewater, as well as positive controls. Results also showed that selecting the most accurate population estimation method for WBE studies is still a challenge. While the number of people infected in an area could be approximately estimated based on quantities of virus found in wastewater, these estimates should be cross-checked by other sources of information to draw a more comprehensive conclusion. Finally, wastewater surveillance can be useful as an early warning tool, a management tool, and/or a way for investigating vaccination efficacy and spread of new variants.

Sewage Systems Surveillance for SARS-CoV-2: Identification of Knowledge Gaps, Emerging Threats, and Future Research Needs

The etiological agent for novel coronavirus (COVID-19, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), not only affects the human respiratory system, but also the gastrointestinal tract resulting in gastrointestinal manifestations. The high rate of asymptomatic infected individuals has challenged the estimation of infection spread based on patients' surveillance, and thus alternative approaches such as wastewater-based epidemiology (WBE) have been proposed. Accordingly, the number of publications on this topic has increased substantially. The present systematic review thus aimed at providing state-of-the-knowledge on the occurrence and existing methods for sampling procedures, detection/quantification of SARS-CoV-2 in sewage samples, as well as anticipating challenges and providing future research direction to improve the current scientific knowledge. Articles were collected from three scientific databases. Only studies reporting measurements of virus in stool, urine, and wastewater samples were included. Results showed that improving the scientific community's understanding in these avenues is essential if we are to develop appropriate policy and management tools to address this pandemic pointing particularly towards WBE as a new paradigm in public health. It was also evident that standardized protocols are needed to ensure reproducibility and comparability of outcomes. Areas that require the most improvements are sampling procedures, concentration/enrichment, detection, and quantification of virus in wastewater, as well as positive controls. Results also showed that selecting the most accurate population estimation method for WBE studies is still a challenge. While the number of people infected in an area could be approximately estimated based on quantities of virus found in wastewater, these estimates should be cross-checked by other sources of information to draw a more comprehensive conclusion. Finally, wastewater surveillance can be useful as an early warning tool, a management tool, and/or a way for investigating vaccination efficacy and spread of new variants.

One-Year Update on Salivary Diagnostic of COVID-19

Background: Coronavirus disease 2019 (COVID-19) is a global health problem, which is challenging healthcare worldwide. In this critical review, we discussed the advantages and limitations in the implementation of salivary diagnostic platforms of COVID-19. The diagnostic test of COVID-19 by invasive nasopharyngeal collection is uncomfortable for patients and requires specialized training of healthcare professionals in order to obtain an appropriate collection of samples. Additionally, these professionals are in close contact with infected patients or suspected cases of COVID-19, leading to an increased contamination risk for frontline healthcare workers. Although there is a colossal demand for novel diagnostic platforms with non-invasive and self-collection samples of COVID-19, the implementation of the salivary platforms has not been implemented for extensive scale testing. Up to date, several cross-section and clinical trial studies published in the last 12 months support the potential of detecting SARS-CoV-2 RNA in saliva as a biomarker for COVID-19, providing a self-collection, non-invasive, safe, and comfortable procedure. Therefore, the salivary diagnosis is suitable to protect healthcare professionals and other frontline workers and may encourage patients to get tested due to its advantages over the current invasive methods. The detection of SARS-CoV-2 in saliva was substantial also in patients with a negative nasopharyngeal swab, indicating the presence of false negative results. Furthermore, we expect that salivary diagnostic devices for COVID-19 will continue to be used with austerity without excluding traditional gold standard specimens to detect SARS-CoV-2.