Dataset Information

National Scale Real-Time Surveillance of SARS-CoV-2 Variants Dynamics by Wastewater Monitoring in Israel.

ABSTRACT: In this report, we describe a national-scale monitoring of the SARS-CoV-2 (SC-2) variant dynamics in Israel, using multiple-time sampling of 13 wastewater treatment plants. We used a combination of inclusive and selective quantitative PCR assays that specifically identify variants A19/A20 or B.1.1.7 and tested each sample for the presence and relative viral RNA load of each variant. We show that between December 2020 and March 2021, a complete shift in the SC-2 variant circulation was observed, where the B.1.1.7 replaced the A19 in all examined test points. We further show that the normalized viral load (NVL) values and the average new cases per week reached a peak in January 2021 and then decreased gradually in almost all test points, in parallel with the progression of the national vaccination campaign, during February-March 2021. This study demonstrates the importance of monitoring SC-2 variant by using a combination of inclusive and selective PCR tests on a national scale through wastewater sampling, which is far more amendable for high-throughput monitoring compared with sequencing. This approach may be useful for real-time dynamics surveillance of current and future variants, such as the Omicron (BA.1, BA.2) and other variants.

SUBMITTER: Bar-Or I

PROVIDER: S-EPMC9227326 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature

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National Scale Real-Time Surveillance of SARS-CoV-2 Variants Dynamics by Wastewater Monitoring in Israel.

Bar-Or Itay I Indenbaum Victoria V Weil Merav M Elul Michal M Levi Nofar N Aguvaev Irina I Cohen Zvi Z Levy Virginia V Azar Roberto R Mannasse Batya B Shirazi Rachel R Bucris Efrat E Mor Orna O Sela Brown Alin A Sofer Danit D Zuckerman Neta S NS Mendelson Ella E Erster Oran O

Viruses 20220606 6

In this report, we describe a national-scale monitoring of the SARS-CoV-2 (SC-2) variant dynamics in Israel, using multiple-time sampling of 13 wastewater treatment plants. We used a combination of inclusive and selective quantitative PCR assays that specifically identify variants A19/A20 or B.1.1.7 and tested each sample for the presence and relative viral RNA load of each variant. We show that between December 2020 and March 2021, a complete shift in the SC-2 variant circulation was observed, ...[more]

PMID: 35746700

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Project description:Wastewater-based epidemiology (WBE) complements the clinical surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants' distribution in populations. Many developed nations have established national and regional WBE systems; however, governance and budget constraints could be obstacles for low- and middle-income countries. An urgent need thus exists to identify hotspots to serve as sentinel sites for WBE. We hypothesized that representative wastewater treatment plants (WWTPs) in two international gateway cities, Bangkok and Phuket, Thailand, could be sentineled for SARS-CoV-2 and its variants to reflect the clinical distribution patterns at city level and serve as early indicators of new variants entering the country. Municipal wastewater samples (n = 132) were collected from eight representative municipal WWTPs in Bangkok and Phuket during 19 sampling events from October 2021 to March 2022, which were tested by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) using the US CDC N1 and N2 multiplex and variant (Alpha, Delta, and Omicron BA.1 and BA.2) singleplex assays. The variant detection ratios from Bangkok and Phuket followed similar trends to the national clinical testing data, and each variant's viral loads agreed with the daily new cases (3-d moving average). Omicron BA.1 was detected in Phuket wastewater prior to Bangkok, possibly due to Phuket's WWTPs serving tourist communities. We found that the Omicron BA.1 and BA.2 viral loads predominantly drove the SARS-CoV-2 resurgence. We also noted a shifting pattern in the Bangkok WBE from a 22-d early warning in early 2021 to a near real-time pattern in late 2021. The potential application of tourist hotspots for WBE to indicate the arrival of new variants and re-emerging or unprecedented infectious agents could support tourism-dependent economies by complementing the reduced clinical regulations while maintaining public health protection via wastewater surveillance.

Project description:ObjectiveTo assess the contribution of a digital health real-time monitoring platform towards the achievement of coverage targets during a national immunisation campaign in Indonesia.InterventionsA digital health platform was introduced to facilitate real-time reporting and data visualisation. Health workers submitted reports of children immunised each day by geolocation using mobile phones. Automated reports were generated for programme managers at all levels to enable early responses to coverage gaps.MethodsRisk profiles were generated for each district to assess precampaign immunisation programme performance. Digital health platform use and progress towards targets were monitored continuously throughout the campaign. Study outcomes were total coverage and time to achieve full (100%) coverage. Kaplan-Meier, Cox and linear regression analyses were used to estimate the associations and outcomes after adjusting for district risk profiles. A complementary qualitative assessment explored user experiences and acceptance through interviews with vaccinators and programme managers in provinces and districts selected through multistage random sampling.ResultsBetween August and December 2018, 6462 health facilities registered to use the digital health platform across 28 provinces and 395 districts. After adjusting for precampaign district risk profile and intracampaign delays due to vaccine hesitancy, districts with greater platform utilisation demonstrated higher coverage overall (R2=0.28, p<0.0001) and a shorter interval to achieving full coverage (>75% reporting compliance; Risk Ratio 15.4, 95% CI 5.8 to 40.6). Stronger effects were observed among districts experiencing implementation delays due to vaccine hesitancy. Results from 106 key informant interviews conducted in 6 provinces and 18 districts suggest high degrees of acceptability, ease of use and satisfaction.ConclusionA digital health platform introduced for real-time monitoring of a national immunisation campaign in Indonesia was feasible, well liked and associated with improved problem solving and programme performance, particularly among districts affected by vaccine hesitancy.Trial registration numberISRCTN10850448.

Dataset Information

National Scale Real-Time Surveillance of SARS-CoV-2 Variants Dynamics by Wastewater Monitoring in Israel.

Publications

National Scale Real-Time Surveillance of SARS-CoV-2 Variants Dynamics by Wastewater Monitoring in Israel.

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