TY - JOUR
T1 - Variations in the persistence of 5′-end genomic and subgenomic SARS-CoV-2 RNAs in wastewater from aircraft, airports and wastewater treatment plants
AU - Tang, Man Hung Eric
AU - Bennedbaek, Marc
AU - Gunalan, Vithiagaran
AU - Qvesel, Amanda Gammelby
AU - Thorsen, Theis Hass
AU - Larsen, Nicolai Balle
AU - Rasmussen, Lasse Dam
AU - Krogsgaard, Lene Wulff
AU - Rasmussen, Morten
AU - Stegger, Marc
AU - Alexandersen, Soren
N1 - Publisher Copyright:
© 2024
PY - 2024/5
Y1 - 2024/5
N2 - Wastewater sequencing has become a powerful supplement to clinical testing in monitoring SARS-CoV-2 infections in the post-COVID-19 pandemic era. While its applications in measuring the viral burden and main circulating lineages in the community have proved their efficacy, the variations in sequencing quality and coverage across the different regions of the SARS-CoV-2 genome are not well understood. Furthermore, it is unclear how different sample origins, viral extraction and concentration methods and environmental factors impact the reads sequenced from wastewater. Using high-coverage, amplicon-based, paired-end read sequencing of viral RNA extracted from wastewater collected directly from aircraft, pooled from different aircraft and airport buildings or from regular wastewater plants, we assessed the genome coverage across the sample groups with a focus on the 5′-end region covering the leader sequence and investigated whether it was possible to detect subgenomic RNA from viral material recovered from wastewater. We identified distinct patterns in the persistence of the different genomic regions across the different types of wastewaters and the existence of chimeric reads mapping to non-amplified regions. Our findings suggest that preservation of the 5′-end of the genome and the ability to detect subgenomic RNA reads, though highly susceptible to environment and sample processing conditions, may be indicative of the quality and amount of the viral RNA present in wastewater.
AB - Wastewater sequencing has become a powerful supplement to clinical testing in monitoring SARS-CoV-2 infections in the post-COVID-19 pandemic era. While its applications in measuring the viral burden and main circulating lineages in the community have proved their efficacy, the variations in sequencing quality and coverage across the different regions of the SARS-CoV-2 genome are not well understood. Furthermore, it is unclear how different sample origins, viral extraction and concentration methods and environmental factors impact the reads sequenced from wastewater. Using high-coverage, amplicon-based, paired-end read sequencing of viral RNA extracted from wastewater collected directly from aircraft, pooled from different aircraft and airport buildings or from regular wastewater plants, we assessed the genome coverage across the sample groups with a focus on the 5′-end region covering the leader sequence and investigated whether it was possible to detect subgenomic RNA from viral material recovered from wastewater. We identified distinct patterns in the persistence of the different genomic regions across the different types of wastewaters and the existence of chimeric reads mapping to non-amplified regions. Our findings suggest that preservation of the 5′-end of the genome and the ability to detect subgenomic RNA reads, though highly susceptible to environment and sample processing conditions, may be indicative of the quality and amount of the viral RNA present in wastewater.
KW - SARS-CoV-2
KW - Subgenomic RNA
KW - Transcription/replication
KW - Wastewater
UR - http://www.scopus.com/inward/record.url?scp=85191317061&partnerID=8YFLogxK
U2 - 10.1016/j.heliyon.2024.e29703
DO - 10.1016/j.heliyon.2024.e29703
M3 - Journal article
C2 - 38694057
AN - SCOPUS:85191317061
SN - 2405-8440
VL - 10
JO - Heliyon
JF - Heliyon
IS - 9
M1 - e29703
ER -