Accessible and Validated Processing of SARS-CoV-2 from Wastewater

Rondeau, Nicole C.; Rose, Oliver J; Ariyan, Lina A; Mailloux, Brian J.; Miranda, JJ L.

doi:10.1128/mra.00174-21

Cited by 4 publications

(7 citation statements)

References 6 publications

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“…Previous studies detected almost all influenza in solid fractions that could be trapped by filters or high-speed centrifugation ( 9 , 10 ). Our ultrafiltration protocol consisting of filtration and low-speed centrifugation ( 5 ) did not yield similar results. We were instead able to obtain influenza from the liquid phase as well as from different solid fractions.…”

Section: Discussionmentioning

confidence: 89%

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Building-level wastewater surveillance localizes interseasonal influenza variation

Germano,

Flores,

Freed

et al. 2024

mSphere

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Influenza virus poses a recurring threat to public health and infects many populations in annual waves of generally unpredictable magnitude and timing. We aimed to detect the arrival and estimate the case magnitude of seasonal influenza A in urban New York City college dormitory buildings. Our wastewater-based surveillance (WBS) program measured viral RNA in the sewage outflow of three dormitories at Barnard College in 2021 and 2022. Wastewater test positivity strongly correlated with New York County clinical cases (Kendall’s τ = 0.58). Positive wastewater samples are also associated with campus clinical cases. The 2022 data stand in stark contrast to the 2021 results by revealing the more frequent and earlier presence of influenza A. The increase in positive tests is significant ( P < 0.01). It is further noteworthy that positive samples were not evenly distributed among buildings. Surveillance additionally identified the influenza A H3 subtype but did not detect any influenza B. We also systematically analyzed our viral purification protocol to identify in which fraction influenza can be found. While virus can be found in solid fractions, a substantial quantity remains in the final liquid fraction. Our work focuses on individual buildings rather than larger sewersheds because buildings may localize interseasonal influenza variation to specific subpopulations. Our results highlight the potential value of building-level WBS in measuring influenza incidence to help guide public health intervention. IMPORTANCE Seasonal influenza remains a major public health burden. We monitored influenza A in dormitory wastewater of a New York City college in 2021 and 2022. Longitudinal samples acquired over consecutive years allowed measurement of individual buildings between seasons. We uncovered building-level changes in the magnitude and timing of test positivity concordant with clinical cases. Surveillance also localized the heterogeneity of influenza variation during the large 2022 seasonal surge. The ability to detect such changes could be leveraged as part of a public health response.

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Section: Discussionmentioning

confidence: 89%

“…We also systematically analyzed our viral purification protocol to identify in which fraction influenza can be found. Our accessible approach ( 5 ) includes sequential steps using a 20 µm filter, low-speed centrifugation, a 0.22 µm filter, and ultrafiltration to enrich for viruses ( Fig. 4A ).…”

Section: Resultsmentioning

confidence: 99%

Building-level wastewater surveillance localizes interseasonal influenza variation

Germano,

Flores,

Freed

et al. 2024

mSphere

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“…Wastewater was prepared, RNA was purified, and PCR was performed according to our published protocol for accessible processing of SARS-CoV-2 from wastewater ( 25 ). An undiluted solution and a 1:10-diluted RNA solution, both in technical duplicate, were tested for each sample.…”

Section: Methodsmentioning

confidence: 99%

“…For PCR testing, we used primers specific for either the wild-type sequence of SARS-CoV-2 or the Δ69/Δ70 spike protein deletion as packaged in the S.delH69V70 TaqMan SARS-CoV-2 mutation panel assay (Thermo Fisher Scientific, Waltham, MA) ( 26 ). We used 0.5 μL of the 40× stock solution per 20-μL reaction mixture in our adaptation of the CDC PCR assay ( 25 ). This deletion within the S protein found in the B.1.1.7 α variant is also found in the B.1.525 η variant, but this variant did not spread significantly in New York City.…”

Section: Methodsmentioning

confidence: 99%

Building-Level Detection Threshold of SARS-CoV-2 in Wastewater

et al. 2023

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“…Other work has found the building-level detection threshold of SARS-CoV-2 in wastewater down to 1 true positive case is possible. 20 But previous wastewater models have focused on estimating the numbers of infected individuals from a wastewater RNA concentration 6,13,21 ; where our model differs rather is in estimating at least one individual from a wastewater RNA concentrations to guide a facility population health response regardless of the number of cases. Because we know conditions of confinement were a concern during the COVID-19 pandemic 22,23 in terms of physical distancing and access to water, sanitation and hygiene facilities, it was additionally important but also unique for our model to consider the occupancy rate directly tied to both the clinical and wastewater concentrations.…”

Section: Sensitivitymentioning

confidence: 99%

Projections of wastewater as an indicator of COVID-19 cases in corrections facilities: a modelling study

Han,

Linares,

Holm

et al. 2023

Preprint

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BackgroundAlthough prison facilities are not fully isolated from the communities they are located within, the majority of the population is confined and requires high levels of health vigilance and protection. This study sought to examine the dynamic relationship between facility level wastewater viral RNA concentration and probability of at least one positive COVID-19 case within the facility.MethodsThe study period was January 11, 2021 through May 12, 2023. Wastewater samples were collected and analyzed for SARS-CoV-2 (N1) and pepper mild mottle virus (PMMoV) three times per week across 14 prison facilities in Kentucky (USA). Confirmed positive clinical case reports were also provided. A hierarchical Bayesian spatial-temporal model with a latent lagged process was developed.FindingsWe modeled a facility-specific SARS-CoV-2 (N1) normalized by PMMoV wastewater ratio associated with at least one COVID-19 facility case with an 80% probability. The ratio differs among facilities. Across the 14 facilities, our model demonstrates an average capture rate of 94·95% via the N1/PMMoV threshold withpts≥ 0·5. However, it is noteworthy as theptsthreshold is set higher, such as at 0·9 or above, the model’s average capture rate reduces to 60%. This robust performance underscores the model’s effectiveness in accurately detecting the presence of positive COVID-19 cases of incarcerated people.InterpretationThe findings of this study provide a correction facility-specific threshold model for public health response based on frequent wastewater surveillance.

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Accessible and Validated Processing of SARS-CoV-2 from Wastewater

Cited by 4 publications

References 6 publications

Building-level wastewater surveillance localizes interseasonal influenza variation

Building-level wastewater surveillance localizes interseasonal influenza variation

Building-Level Detection Threshold of SARS-CoV-2 in Wastewater

Projections of wastewater as an indicator of COVID-19 cases in corrections facilities: a modelling study

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