tetano
Editor, Senior Moderator
Sci Total Environ
. 2022 Jul 29;157546.
doi: 10.1016/j.scitotenv.2022.157546. Online ahead of print.
Temporal dynamics of SARS-CoV-2 genome and detection of variants of concern in wastewater influent from two metropolitan areas in Arkansas
Camila S Silva[SUP] 1 [/SUP], Volodymyr Tryndyak[SUP] 2 [/SUP], Luísa Camacho[SUP] 2 [/SUP], Mohammed S Orloff[SUP] 3 [/SUP], Austin Porter[SUP] 4 [/SUP], Kelley Garner[SUP] 5 [/SUP], Lisa Mullis[SUP] 6 [/SUP], Marli Azevedo[SUP] 6 [/SUP]
Affiliations
Abstract
Although SARS-CoV-2 can cause severe illness and death, a percentage of the infected population is asymptomatic. This, along with other factors, such as insufficient diagnostic testing and underreporting due to self-testing, contributes to the silent transmission of SARS-CoV-2 and highlights the importance of implementing additional surveillance tools. The fecal shedding of the virus from infected individuals enables its detection in community wastewater, and this has become a valuable public health tool worldwide as it allows the monitoring of the disease on a populational scale. Here, we monitored the presence of SARS-CoV-2 and its dynamic genomic changes in wastewater sampled from two metropolitan areas in Arkansas during major surges of COVID-19 cases and assessed how the viral titers in these samples related to the clinical case counts between late April 2020 and January 2022. The levels of SARS-CoV-2 RNA were quantified by reverse-transcription quantitative polymerase chain reaction (RT-qPCR) using a set of TaqMan assays targeting three different viral genes (encoding ORF1ab polyprotein, surface glycoprotein, and nucleocapsid phosphoprotein). An allele-specific RT-qPCR approach was used to screen the samples for SARS-CoV-2 mutations. The identity and genetic diversity of the virus were further investigated through amplicon-based RNA sequencing, and SARS-CoV-2 variants of concern were detected in wastewater samples throughout the duration of this study. Our data show how changes in the virus genome can affect the sensitivity of specific RT-qPCR assays used in COVID-19 testing with the surge of new variants. A significant association was observed between viral titers in wastewater and recorded number of COVID-19 cases in the areas studied, except when assays failed to detect targets due to the presence of particular variants. These findings support the use of wastewater surveillance as a reliable complementary tool for monitoring SARS-CoV-2 and its genetic variants at the community level.
Keywords: Arkansas; COVID-19; Coronavirus; SARS-CoV-2; Variants of concern; Wastewater.
. 2022 Jul 29;157546.
doi: 10.1016/j.scitotenv.2022.157546. Online ahead of print.
Temporal dynamics of SARS-CoV-2 genome and detection of variants of concern in wastewater influent from two metropolitan areas in Arkansas
Camila S Silva[SUP] 1 [/SUP], Volodymyr Tryndyak[SUP] 2 [/SUP], Luísa Camacho[SUP] 2 [/SUP], Mohammed S Orloff[SUP] 3 [/SUP], Austin Porter[SUP] 4 [/SUP], Kelley Garner[SUP] 5 [/SUP], Lisa Mullis[SUP] 6 [/SUP], Marli Azevedo[SUP] 6 [/SUP]
Affiliations
- PMID: 35914602
- DOI: 10.1016/j.scitotenv.2022.157546
Abstract
Although SARS-CoV-2 can cause severe illness and death, a percentage of the infected population is asymptomatic. This, along with other factors, such as insufficient diagnostic testing and underreporting due to self-testing, contributes to the silent transmission of SARS-CoV-2 and highlights the importance of implementing additional surveillance tools. The fecal shedding of the virus from infected individuals enables its detection in community wastewater, and this has become a valuable public health tool worldwide as it allows the monitoring of the disease on a populational scale. Here, we monitored the presence of SARS-CoV-2 and its dynamic genomic changes in wastewater sampled from two metropolitan areas in Arkansas during major surges of COVID-19 cases and assessed how the viral titers in these samples related to the clinical case counts between late April 2020 and January 2022. The levels of SARS-CoV-2 RNA were quantified by reverse-transcription quantitative polymerase chain reaction (RT-qPCR) using a set of TaqMan assays targeting three different viral genes (encoding ORF1ab polyprotein, surface glycoprotein, and nucleocapsid phosphoprotein). An allele-specific RT-qPCR approach was used to screen the samples for SARS-CoV-2 mutations. The identity and genetic diversity of the virus were further investigated through amplicon-based RNA sequencing, and SARS-CoV-2 variants of concern were detected in wastewater samples throughout the duration of this study. Our data show how changes in the virus genome can affect the sensitivity of specific RT-qPCR assays used in COVID-19 testing with the surge of new variants. A significant association was observed between viral titers in wastewater and recorded number of COVID-19 cases in the areas studied, except when assays failed to detect targets due to the presence of particular variants. These findings support the use of wastewater surveillance as a reliable complementary tool for monitoring SARS-CoV-2 and its genetic variants at the community level.
Keywords: Arkansas; COVID-19; Coronavirus; SARS-CoV-2; Variants of concern; Wastewater.