RT-qPCR and ATOPlex sequencing for the sensitive detection of SARS-CoV-2 RNA for wastewater surveillance

Ahmed, Warish; Bivins, Aaron; Metcalfe, Suzanne; Smith, Wendy; Ziels, Ryan M.; Korajkic, Asja; McMinn, Brian R.; Graber, Tyson E.; Simpson, Stuart L.

doi:10.1016/j.watres.2022.118621

Cited by 20 publications

(11 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Second, to effectively detect SARS-CoV-2 RNA at low concentrations, multiple PCR targets based on different regions of the SARS-CoV-2 genome should be used. Ahmed et al showed that combining multiple assays can increase SARS-CoV-2 RNA detection sensitivity ( Ahmed et al, 2022 ). As recommended by Ahmed et al (2022) , we took the presence of at least one of the targets to indicate presence of SARS-CoV-2 RNA.…”

Section: Discussionmentioning

confidence: 99%

“…Ahmed et al showed that combining multiple assays can increase SARS-CoV-2 RNA detection sensitivity ( Ahmed et al, 2022 ). As recommended by Ahmed et al (2022) , we took the presence of at least one of the targets to indicate presence of SARS-CoV-2 RNA. While the detection rate, as a percentage, did not differ greatly when only one gene was considered, almost 2/3 of the samples that tested positive for SARS-CoV-2 RNA showed detection of one gene and not the other.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Wastewater monitoring of SARS-CoV-2 RNA at K-12 schools: comparison to pooled clinical testing data

Kim

Boehm

2023

PeerJ

View full text Add to dashboard Cite

Background Wastewater measurements of SARS-CoV-2 RNA have been extensively used to supplement clinical data on COVID-19. Most examples in the literature that describe wastewater monitoring for SARS-CoV-2 RNA use samples from wastewater treatment plants and individual buildings that serve as the primary residence of community members. However, wastewater surveillance can be an attractive supplement to clinical testing in K-12 schools where individuals only spend a portion of their time but interact with others in close proximity, increasing risk of potential transmission of disease. Methods Wastewater samples were collected from two K-12 schools in California and divided into solid and liquid fractions to be processed for detection of SARS-CoV-2. The resulting detection rate in each wastewater fraction was compared to each other and the detection rate in pooled clinical specimens. Results Most wastewater samples were positive for SARS-CoV-2 RNA when clinical testing was positive (75% for solid samples and 100% for liquid samples). Wastewater samples continued to test positive for SARS-CoV-2 RNA when clinical testing was negative or in absence of clinical testing (83% for both solid and liquid samples), indicating presence of infected individuals in the schools. Wastewater solids had a higher concentration of SARS-CoV-2 than wastewater liquids on an equivalent mass basis by three orders of magnitude.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Wastewater monitoring of SARS-CoV-2 RNA at K-12 schools: comparison to pooled clinical testing data

Kim

Boehm

2023

PeerJ

View full text Add to dashboard Cite

show abstract

“…Second, to effectively detect SARS-CoV-2 RNA at low concentrations, multiple PCR targets based on different regions of the SARS-CoV-2 genome should be used. Ahmed et al showed that combining multiple assays can increase SARS-CoV-2 RNA detection sensitivity (Ahmed et al, 2022). As recommended by Ahmed et al (Ahmed et al, 2022), we took the presence of at least one of the targets to indicate presence of SARS-CoV-2 RNA.…”

Section: Discussionmentioning

confidence: 99%

“…Ahmed et al showed that combining multiple assays can increase SARS-CoV-2 RNA detection sensitivity (Ahmed et al, 2022). As recommended by Ahmed et al (Ahmed et al, 2022), we took the presence of at least one of the targets to indicate presence of SARS-CoV-2 RNA. While the detection rate, as a percentage, did not differ greatly when only one gene was considered, almost ⅔ of the samples that tested positive for SARS-CoV-2 RNA showed detection of one gene and not the other.…”

Section: Discussionmentioning

confidence: 99%

Wastewater monitoring of SARS-CoV-2 RNA at K-12 schools: Comparison to pooled clinical testing data

Kim

Boehm

2022

Preprint

View full text Add to dashboard Cite

Background. Wastewater measurements of SARS-CoV-2 RNA have been extensively used to supplement clinical data on COVID-19. Most examples in the literature that describe wastewater monitoring for SARS-CoV-2 RNA use samples from wastewater treatment plants and individual buildings that serve as the primary residence of community members. However, wastewater surveillance can be an attractive supplement to clinical testing in K-12 schools where individuals only spend a portion of their time but interact with others in close proximity, increasing risk of potential transmission of disease. Methods. Wastewater samples were collected from two K-12 schools in California and divided into solid and liquid fractions to be processed for detection of SARS-CoV-2. The resulting detection rate in each wastewater fraction was compared to each other and the detection rate in pooled clinical specimens. Results. Most wastewater samples were positive for SARS-CoV-2 RNA when clinical testing was positive (75% for solid samples and 100% for liquid samples). Wastewater samples continued to test positive for SARS-CoV-2 RNA when clinical testing was negative or in absence of clinical testing (83% for both solid and liquid samples), indicating presence of infected individuals in the schools. Wastewater solids had a higher concentration of SARS-CoV-2 than wastewater liquids on an equivalent mass basis by three orders of magnitude.

show abstract

“…New PCR methods are required to analyze wastewater samples, as trace signal is lost in the complex sample matrix for conventional RT-PCR to analyze and is often never found due to amplification inhibitors [ 51 , 52 ]. The dPCR amplification mechanism has enabled the use of wastewater for SARS-CoV-2 detection, giving near real-time population data from several countries spanning the globe [ 53 , 54 , 55 ]. Because urine and feces contain fragments of the SARS-CoV-2 genome, this allows for high spatial and temporal resolutions of VOCs spreading through a community-level population by way of one, individual sample.…”

Section: Multiplex Viral Rna Detection and Amplification Methodsmentioning

confidence: 99%

Emerging Multiplex Nucleic Acid Diagnostic Tests for Combating COVID-19

et al. 2022

View full text Add to dashboard Cite

The COVID-19 pandemic caused by SARS-CoV-2 has drawn attention to the need for fast and accurate diagnostic testing. Concerns from emerging SARS-CoV-2 variants and other circulating respiratory viral pathogens further underscore the importance of expanding diagnostic testing to multiplex detection, as single-plex diagnostic testing may fail to detect emerging variants and other viruses, while sequencing can be too slow and too expensive as a diagnostic tool. As a result, there have been significant advances in multiplex nucleic-acid-based virus diagnostic testing, creating a need for a timely review. This review first introduces frequent nucleic acid targets for multiplex virus diagnostic tests, then proceeds to a comprehensive and up-to-date overview of multiplex assays that incorporate various detection reactions and readout modalities. The performances, advantages, and disadvantages of these assays are discussed, followed by highlights of platforms that are amenable for point-of-care use. Finally, this review points out the remaining technical challenges and shares perspectives on future research and development. By examining the state of the art and synthesizing existing development in multiplex nucleic acid diagnostic tests, this review can provide a useful resource for facilitating future research and ultimately combating COVID-19.

show abstract

RT-qPCR and ATOPlex sequencing for the sensitive detection of SARS-CoV-2 RNA for wastewater surveillance

Cited by 20 publications

References 45 publications

Wastewater monitoring of SARS-CoV-2 RNA at K-12 schools: comparison to pooled clinical testing data

Wastewater monitoring of SARS-CoV-2 RNA at K-12 schools: comparison to pooled clinical testing data

Wastewater monitoring of SARS-CoV-2 RNA at K-12 schools: Comparison to pooled clinical testing data

Emerging Multiplex Nucleic Acid Diagnostic Tests for Combating COVID-19

Contact Info

Product

Resources

About