RT-ddPCR Wastewater Monitoring of COVID-19 Across the Eastern Upper Peninsula of Michigan

Jarvie, Michelle M.; Reed, Moriah; Southwell, Benjamin; Wright, Derek D.; Nguyen, Thu  Ngoc Thi

doi:10.2139/ssrn.4090302

Cited by 3 publications

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Chronic Shedding of a SARS-CoV-2 Alpha Variant Lineage Q.3/Q.4 in Wastewater

Conway,

Yang,

Revord

et al. 2023

Preprint

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Central Michigan University (CMU) participated in a state-wide SARS-CoV-2 wastewater monitoring program since 2021. Wastewater samples were collected from on-campus sites and nine off-campus wastewater treatment plants servicing small metropolitan and rural communities. SARS-CoV-2 genome copies were quantified using droplet digital PCR and results were reported to the health department. One rural, off-campus site consistently produced higher concentrations of SARS-CoV-2 genome copies. Samples from this site were sequenced and initially contained predominately Alpha variant lineage Q.3, which transitioned to lineage Q.4. Alpha variant lineage Q.3/Q.4 was detected at this site beginning in fall 2021 and continued until summer 2023. Mutational analysis of reconstructed genes revealed divergence from the Alpha variant lineage Q.3 clinical sequence over time, including numerous mutations in the surface glycoprotein RBD and NTD. We discuss the possibility that a chronic SARS-CoV-2 infection accumulated adaptive mutations that promoted long-term infection. This study reveals that small wastewater treatment plants can enhance resolution of rare events and facilitate reconstruction of viral genomes due to the relative lack of contaminating sequences.

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Chronic Shedding of a SARS-CoV-2 Alpha Variant Lineage Q.3/Q.4 in Wastewater

Conway,

Yang,

Revord

et al. 2023

Preprint

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Wastewater sequencing from a rural community enables identification of widespread adaptive mutations in a SARS-CoV-2 Alpha variant

Conway,

Novay,

Pusch

et al. 2024

Preprint

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Background: Central Michigan University (CMU) participated in a state-wide wastewater monitoring program starting in 2021. One rural site consistently produced higher concentrations of SARS-CoV-2 genome copies. Samples from this site were sequenced retrospectively and exclusively contained a derivative of Alpha variant lineage B.1.1.7 that shed from the same site for 20-28 months. Results: Complete reconstruction of each SARS-CoV-2 open reading frame (ORF) and alignment to an early B.1.1.7 clinical isolate identified novel mutations that were selected in non-structural (nsp1, nsp2, nsp3, nsp4, nsp5/3CLpro, nsp6, RdRp, nsp15, nsp16, ORF3a, ORF6, ORF7a, and ORF7b) and structural genes (Spike, M, and N). These were rare mutations that have not accumulated in clinical samples worldwide. Mutational analysis revealed divergence from the reference Alpha variant lineage sequence over time. We present each of the mutations on available structural models and discuss the potential role of these mutations during a chronic infection. Conclusions: This study further supports that small wastewater treatment plants can enhance resolution of rare events and facilitate reconstruction of viral genomes due to the relative lack of contaminating sequences and identifies mutations that may be associated with chronic infections.

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Chronic shedding of a SARS-CoV-2 Alpha variant in wastewater

Conway,

Yang,

Revord

et al. 2024

BMC Genomics

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Background Central Michigan University (CMU) participated in a state-wide SARS-CoV-2 wastewater monitoring program since 2021. Wastewater samples were collected from on-campus sites and nine off-campus wastewater treatment plants servicing small metropolitan and rural communities. SARS-CoV-2 genome copies were quantified using droplet digital PCR and results were reported to the health department. Results One rural, off-campus site consistently produced higher concentrations of SARS-CoV-2 genome copies. Samples from this site were sequenced and contained predominately a derivative of Alpha variant lineage B.1.1.7, detected from fall 2021 through summer 2023. Mutational analysis of reconstructed genes revealed divergence from the Alpha variant lineage sequence over time, including numerous mutations in the Spike RBD and NTD. Conclusions We discuss the possibility that a chronic SARS-CoV-2 infection accumulated adaptive mutations that promoted long-term infection. This study reveals that small wastewater treatment plants can enhance resolution of rare events and facilitate reconstruction of viral genomes due to the relative lack of contaminating sequences.

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RT-ddPCR Wastewater Monitoring of COVID-19 Across the Eastern Upper Peninsula of Michigan

Cited by 3 publications

References 0 publications

Chronic Shedding of a SARS-CoV-2 Alpha Variant Lineage Q.3/Q.4 in Wastewater

Chronic Shedding of a SARS-CoV-2 Alpha Variant Lineage Q.3/Q.4 in Wastewater

Wastewater sequencing from a rural community enables identification of widespread adaptive mutations in a SARS-CoV-2 Alpha variant

Chronic shedding of a SARS-CoV-2 Alpha variant in wastewater

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