Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater

Lee, Wei Lin; Armas, Federica; Guarneri, Flavia; Gu, Xiaoqiong; Formenti, Nicoletta; Wu, Fuqing; Chandra, Franciscus; Parisio, Giovanni; Chen, Hongjie; Xiao, Amy; Romeo, Claudia; Scali, Federico; Tonni, Matteo; Leifels, Mats; Chua, Feng Jun Desmond; Kwok, Wee Chiew; Tay, Joey YR; Pasquali, Paolo; Thompson, Janelle R.; Alborali, Giovanni Loris; Alm, Eric J.

doi:10.1016/j.watres.2022.118809

Cited by 31 publications

(19 citation statements)

References 46 publications

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“…Furthermore, Beta and Omicron variants have been successfully detected in wastewater in Hong Kong using this method (Xu et al 2022a ). Lee et al targeted a segment of mutation Q493R-Q498R in the SARS-CoV-2 spike gene and used AS RT-qPCR reaction to detect this Omicron variants in wastewater (Lee et al 2022 ). La Rosa et al designed 3 nested PCR assays to detect detectable variants in wastewater samples and showed that the long-nested RT-PCR detected 3 positive samples and the 2 short-nested RT-PCRs detected 15 and 16 positive samples, respectively, indicating that the short-nested RT-PCR method was slightly more sensitive (La Rosa et al 2021 ).…”

Section: Resultsmentioning

confidence: 99%

SARS-CoV-2 surveillance in medical and industrial wastewater—a global perspective: a narrative review

Yang

Guo

Møhlenberg

et al. 2023

Environ Sci Pollut Res

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The novel coronavirus SARS-CoV-2 has spread at an unprecedented rate since late 2019, leading to the global COVID-19 pandemic. During the pandemic, being able to detect SARS-CoV-2 in human populations with high coverage quickly is a huge challenge. As SARS-CoV-2 is excreted in human excreta and thus exposed to the aqueous environment through sewers, the goal is to develop an ideal, non-invasive, cost-effective epidemiological method for detecting SARS-CoV-2. Wastewater surveillance has gained widespread interest and is increasingly being investigated as an effective early warning tool for monitoring the spread and evolution of the virus. This review emphasizes important findings on SARS-CoV-2 wastewater-based epidemiology (WBE) in different continents and techniques used to detect SARS-CoV-2 in wastewater during the period 2020–2022. The results show that WBE is a valuable population-level method for monitoring SARS-CoV-2 and is a valuable early warning alert. It can assist policymakers in formulating relevant policies to avoid the negative impacts of early or delayed action. Such strategy can also help avoid unnecessary wastage of medical resources, rationalize vaccine distribution, assist early detection, and contain large-scale outbreaks.

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Section: Resultsmentioning

confidence: 99%

SARS-CoV-2 surveillance in medical and industrial wastewater—a global perspective: a narrative review

Yang

Guo

Møhlenberg

et al. 2023

Environ Sci Pollut Res

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“…Researchers recently developed an end-to-end analysis pipeline to reconstruct the infection dynamics of different VOCs from wastewater sequencing data, and validated on multiple datasets (Schumann et al, 2022). Additionally, allele-specific PCR assays are also widely used to quantify the distribution of VOCs in the sewersheds (Heijnen et al, 2021;Lee et al, 2021;Lee et al, 2022). Thus, wastewater surveillance integrated with genomic sequencing and mutation-specific technologies are critical for tracking specific viral strains and emerging variants in the population.…”

Section: Sars-cov-2mentioning

confidence: 99%

Not a waste: Wastewater surveillance to enhance public health

et al. 2023

Self Cite

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Domestic wastewater, when collected and evaluated appropriately, can provide valuable health-related information for a community. As a relatively unbiased and non-invasive approach, wastewater surveillance may complement current practices towards mitigating risks and protecting population health. Spurred by the COVID-19 pandemic, wastewater programs are now widely implemented to monitor viral infection trends in sewersheds and inform public health decision-making. This review summarizes recent developments in wastewater-based epidemiology for detecting and monitoring communicable infectious diseases, dissemination of antimicrobial resistance, and illicit drug consumption. Wastewater surveillance, a quickly advancing Frontier in environmental science, is becoming a new tool to enhance public health, improve disease prevention, and respond to future epidemics and pandemics.

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“…The expertise and infrastructure developed through the “lessons-learned” from the environmental surveillance of SARS-CoV-2 can help pave the development of similar efforts for zoonotic diseases that are already widespread or that harbour a pandemic risk. In countries and regions where, clinical diagnostic capabilities are underdeveloped, environmental surveillance (e.g., of communal wastewater), the monitoring of sentinel animal and particularly susceptible human populations can serve to a complement cost-and labour-intensive clinical approaches [ 102 ]. Arthropod-borne viruses like dengue virus and yellow fever virus are causing a significant burden of disease and annual economic losses in tropical regions worldwide are a prime target for such surveillance efforts, as traditional, monitoring focussing on clinical diagnostics is long known to be insufficient.…”

Section: Environmental Surveillance Via the One Health Approachmentioning

confidence: 99%

“…Arthropod-borne viruses like dengue virus and yellow fever virus are causing a significant burden of disease and annual economic losses in tropical regions worldwide are a prime target for such surveillance efforts, as traditional, monitoring focussing on clinical diagnostics is long known to be insufficient. Laborious (sylvatic) surveillance of mammalian hosts or insect vectors in a defined geographical context could act as a bridging technology until more systematic and tailored surveillance strategies of communal sewage are introduced [ 102 , 103 ]. Moreover, comparable to SARS-CoV-2 monitoring efforts, the timely detection of arbovirus genomes in communal sewage could allow for the implementation of non-pharmaceutical interventions such as the removal of stagnant water from streets and parks as potential mosquito breeding grounds, or the distribution of mosquito nets or more drastically the release of genetically modified male mosquitoes [ 104 ].…”

Section: Environmental Surveillance Via the One Health Approachmentioning

confidence: 99%

The one health perspective to improve environmental surveillance of zoonotic viruses: lessons from COVID-19 and outlook beyond

Leifels

Rahman

Sam

et al. 2022

ISME Communications

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The human population has doubled in the last 50 years from about 3.7 billion to approximately 7.8 billion. With this rapid expansion, more people live in close contact with wildlife, livestock, and pets, which in turn creates increasing opportunities for zoonotic diseases to pass between animals and people. At present an estimated 75% of all emerging virus-associated infectious diseases possess a zoonotic origin, and outbreaks of Zika, Ebola and COVID-19 in the past decade showed their huge disruptive potential on the global economy. Here, we describe how One Health inspired environmental surveillance campaigns have emerged as the preferred tools to monitor human-adjacent environments for known and yet to be discovered infectious diseases, and how they can complement classical clinical diagnostics. We highlight the importance of environmental factors concerning interactions between animals, pathogens and/or humans that drive the emergence of zoonoses, and the methodologies currently proposed to monitor them—the surveillance of wastewater, for example, was identified as one of the main tools to assess the spread of SARS-CoV-2 by public health professionals and policy makers during the COVID-19 pandemic. One-Health driven approaches that facilitate surveillance, thus harbour the potential of preparing humanity for future pandemics caused by aetiological agents with environmental reservoirs. Via the example of COVID-19 and other viral diseases, we propose that wastewater surveillance is a useful complement to clinical diagnosis as it is centralized, robust, cost-effective, and relatively easy to implement.

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Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater

Cited by 31 publications

References 46 publications

SARS-CoV-2 surveillance in medical and industrial wastewater—a global perspective: a narrative review

SARS-CoV-2 surveillance in medical and industrial wastewater—a global perspective: a narrative review

Not a waste: Wastewater surveillance to enhance public health

The one health perspective to improve environmental surveillance of zoonotic viruses: lessons from COVID-19 and outlook beyond

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