Monitoring SARS-CoV-2 variants in wastewater during periods of low clinical case surveillance in Ethiopia

TY - JOUR

T1 - Monitoring SARS-CoV-2 variants in wastewater during periods of low clinical case surveillance in Ethiopia

AU - Gebremicael, Gebremedhin

AU - Dinssa, Daniel Abera

AU - Gebreegziabxier, Atsbeha

AU - Mengistu, Yohannes

AU - Getu, Melak

AU - Chalchisa, Dinknesh

AU - Berhanu, Girma

AU - Mulugeta, Firehiwot

AU - Melese, Daniel

AU - Norberg, Ashley

AU - Snyder, Sarah

AU - Abubeker, Rajiha

AU - Abdela, Saro

AU - Kebede, Abebaw

AU - Ali, Abraham

AU - Tessema, Sofonias K.

AU - de Wit, Tobias F. Rinke

AU - Tadesse, Gemechu

AU - Kebede, Yenew

AU - Hailu, Mesay

AU - Tessema, Masresha

AU - Hull, Noah C.

AU - Tollera, Getachew

AU - Wolday, Dawit

N1 - Publisher Copyright: © 2025 Gebremicael et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

PY - 2025/8/26

Y1 - 2025/8/26

N2 - Wastewater-based genomic surveillance is a cost-effective approach for tracking outbreaks like severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A 2023 study in Addis Ababa, Ethiopia, revealed two infection waves in March and August, with the latter undetected by clinical surveillance. This study analyzed the viral spread and evolution in the population during periods of low reported cases. Viral concentration was performed following the Ceres Technology protocol, and RNA was extracted using the QIAamp Viral RNA Mini Kit. Quantitative PCR was performed using the TaqPath COVID-19 Kit. Samples with cycle threshold values ≤32 were used for sequencing. Library preparation and sequencing were performed using the Illumina COVIDSeq protocol, and data analysis was conducted using the Freyja pipeline on Terra.bio. SARS-CoV-2 viral load in wastewater began rising on 6 March 2023, peaking on 16 March 2023, before declining until early May 2023. A resurgence occurred from 3 to 21 August 2023. In March 2023, XBB.1.5 (34%), XBB* (20%), and CH.1.1 (15%) were dominant. By April–May 2023, XBB.1.5 rose to 51% but declined to 14% in June 2023, while XBB* increased to 41%. In August 2023, XBB* (52%) and XBB.1.5 (31%) co-dominated. Key spike protein mutations (G142D, V213G, T478K, S494P, S477N) correlated with higher viral loads. Wastewater surveillance of SARS-CoV-2 reveals seasonal and behavioral transmission patterns. A March peak linked to XBB.1.5 and XBB* saw XBB.1.5 dominance through May 2023, later declining. An August 2023 resurgence with XBB* co-dominance suggests viral evolution and waning immunity. Key spike mutations correlate with higher viral loads, emphasizing wastewater surveillance’s predictive value.

AB - Wastewater-based genomic surveillance is a cost-effective approach for tracking outbreaks like severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A 2023 study in Addis Ababa, Ethiopia, revealed two infection waves in March and August, with the latter undetected by clinical surveillance. This study analyzed the viral spread and evolution in the population during periods of low reported cases. Viral concentration was performed following the Ceres Technology protocol, and RNA was extracted using the QIAamp Viral RNA Mini Kit. Quantitative PCR was performed using the TaqPath COVID-19 Kit. Samples with cycle threshold values ≤32 were used for sequencing. Library preparation and sequencing were performed using the Illumina COVIDSeq protocol, and data analysis was conducted using the Freyja pipeline on Terra.bio. SARS-CoV-2 viral load in wastewater began rising on 6 March 2023, peaking on 16 March 2023, before declining until early May 2023. A resurgence occurred from 3 to 21 August 2023. In March 2023, XBB.1.5 (34%), XBB* (20%), and CH.1.1 (15%) were dominant. By April–May 2023, XBB.1.5 rose to 51% but declined to 14% in June 2023, while XBB* increased to 41%. In August 2023, XBB* (52%) and XBB.1.5 (31%) co-dominated. Key spike protein mutations (G142D, V213G, T478K, S494P, S477N) correlated with higher viral loads. Wastewater surveillance of SARS-CoV-2 reveals seasonal and behavioral transmission patterns. A March peak linked to XBB.1.5 and XBB* saw XBB.1.5 dominance through May 2023, later declining. An August 2023 resurgence with XBB* co-dominance suggests viral evolution and waning immunity. Key spike mutations correlate with higher viral loads, emphasizing wastewater surveillance’s predictive value.

KW - COVID-19

KW - Freyja analysis

KW - genomic surveillance

KW - SARS-CoV-2

KW - wastewater based epidemiology

UR - https://www.scopus.com/pages/publications/105014129990

U2 - 10.1128/msphere.00229-25

DO - 10.1128/msphere.00229-25

M3 - Article

C2 - 40728295

AN - SCOPUS:105014129990

SN - 2379-5042

VL - 10

JO - mSphere

JF - mSphere

IS - 8

M1 - e00229-25

ER -