TY - JOUR
T1 - Monitoring SARS-CoV-2 variant transitions using differences in diagnostic cycle threshold values of target genes
AU - Bordoy, Antoni E.
AU - Saludes, Verónica
AU - Panisello Yagüe, David
AU - Clarà, Gemma
AU - Soler, Laia
AU - Paris de León, Alexia
AU - Casañ, Cristina
AU - Blanco-Suárez, Ana
AU - Guerrero-Murillo, Mercedes
AU - Rodríguez-Ponga, Beatriz
AU - Noguera-Julian, Marc
AU - Català-Moll, Francesc
AU - Pey, Irina
AU - Armengol, Maria Pilar
AU - Casadellà, Maria
AU - Parera, Mariona
AU - Pluvinet, Raquel
AU - Sumoy, Lauro
AU - Clotet, Bonaventura
AU - Giménez, Montserrat
AU - Martró, Elisa
AU - Cardona, Pere Joan
AU - Blanco, Ignacio
N1 - Funding Information:
We thank the COVID Unit of Laboratori Clínic Metropolitana Nord at Hospital Universitari Germans Trias i Pujol for their contribution in generating SARS-CoV-2 RT-PCR diagnostics data, as well as all members of the Can Ruti Sequencing Hub for their efforts in generating SARS-CoV-2 WGS data. Finally, the authors thank the CERCA Programme/Generalitat de Catalunya for their support of the Germans Trias i Pujol Research Institute (IGTP).
Publisher Copyright:
© 2022, The Author(s).
PY - 2022/12
Y1 - 2022/12
N2 - Monitoring the emergence of new SARS-CoV-2 variants is important to detect potential risks of increased transmission or disease severity. We investigated the identification of SARS-CoV-2 variants from real-time reverse transcriptase polymerase chain reaction (RT-PCR) routine diagnostics data. Cycle threshold (Ct) values of positive samples were collected from April 2021 to January 2022 in the Northern Metropolitan Area of Barcelona (n = 15,254). Viral lineage identification from whole genome sequencing (WGS) was available for 4618 (30.3%) of these samples. Pairwise differences in the Ct values between gene targets (ΔCt) were analyzed for variants of concern or interest circulating in our area. A specific delay in the Ct of the N-gene compared to the RdRp-gene (ΔCtNR) was observed for Alpha, Delta, Eta and Omicron. Temporal differences in ΔCtNR correlated with the dynamics of viral replacement of Alpha by Delta and of Delta by Omicron according to WGS results. Using ΔCtNR, prediction of new variants of concern at early stages of circulation was achieved with high sensitivity and specificity (91.1% and 97.8% for Delta; 98.5% and 90.8% for Omicron). Thus, tracking population-wide trends in ΔCt values obtained from routine diagnostics testing in combination with WGS could be useful for real-time management and response to local epidemics.
AB - Monitoring the emergence of new SARS-CoV-2 variants is important to detect potential risks of increased transmission or disease severity. We investigated the identification of SARS-CoV-2 variants from real-time reverse transcriptase polymerase chain reaction (RT-PCR) routine diagnostics data. Cycle threshold (Ct) values of positive samples were collected from April 2021 to January 2022 in the Northern Metropolitan Area of Barcelona (n = 15,254). Viral lineage identification from whole genome sequencing (WGS) was available for 4618 (30.3%) of these samples. Pairwise differences in the Ct values between gene targets (ΔCt) were analyzed for variants of concern or interest circulating in our area. A specific delay in the Ct of the N-gene compared to the RdRp-gene (ΔCtNR) was observed for Alpha, Delta, Eta and Omicron. Temporal differences in ΔCtNR correlated with the dynamics of viral replacement of Alpha by Delta and of Delta by Omicron according to WGS results. Using ΔCtNR, prediction of new variants of concern at early stages of circulation was achieved with high sensitivity and specificity (91.1% and 97.8% for Delta; 98.5% and 90.8% for Omicron). Thus, tracking population-wide trends in ΔCt values obtained from routine diagnostics testing in combination with WGS could be useful for real-time management and response to local epidemics.
UR - http://www.scopus.com/inward/record.url?scp=85144184626&partnerID=8YFLogxK
U2 - 10.1038/s41598-022-25719-9
DO - 10.1038/s41598-022-25719-9
M3 - Article
C2 - 36528712
AN - SCOPUS:85144184626
SN - 2045-2322
VL - 12
JO - SCIENTIFIC REPORTS
JF - SCIENTIFIC REPORTS
IS - 1
M1 - 21818
ER -