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SARS-CoV-2 Continuous Genetic Divergence and Changes in Multiplex RT-PCR Detection Pattern on Positive Retesting Median 150 Days after Initial Infection

Being in the epicenter of the COVID-19 pandemic, our lab tested 193,054 specimens for SARS-CoV-2 RNA by diagnostic multiplex reverse transcription polymerase chain reaction (mRT-PCR) starting in March 2020, of which 17,196 specimens resulted positive. To investigate the dynamics of virus molecular e...

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Autores principales: Liu, Dakai, Rodriguez, George D., Zhou, Hang-Yu, Cheng, Ye-Xiao, Li, Xiaofeng, Tang, Wenwen, Prasad, Nishant, Chen, Chun-Cheng, Singh, Vishnu, Konadu, Eric, James, Keither K., Bahamon, Maria F., Chen, Yvonne, Segal-Maurer, Sorana, Wu, Aiping, Rodgers, William Harry
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9181733/
https://www.ncbi.nlm.nih.gov/pubmed/35682933
http://dx.doi.org/10.3390/ijms23116254
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author Liu, Dakai
Rodriguez, George D.
Zhou, Hang-Yu
Cheng, Ye-Xiao
Li, Xiaofeng
Tang, Wenwen
Prasad, Nishant
Chen, Chun-Cheng
Singh, Vishnu
Konadu, Eric
James, Keither K.
Bahamon, Maria F.
Chen, Yvonne
Segal-Maurer, Sorana
Wu, Aiping
Rodgers, William Harry
author_facet Liu, Dakai
Rodriguez, George D.
Zhou, Hang-Yu
Cheng, Ye-Xiao
Li, Xiaofeng
Tang, Wenwen
Prasad, Nishant
Chen, Chun-Cheng
Singh, Vishnu
Konadu, Eric
James, Keither K.
Bahamon, Maria F.
Chen, Yvonne
Segal-Maurer, Sorana
Wu, Aiping
Rodgers, William Harry
author_sort Liu, Dakai
collection PubMed
description Being in the epicenter of the COVID-19 pandemic, our lab tested 193,054 specimens for SARS-CoV-2 RNA by diagnostic multiplex reverse transcription polymerase chain reaction (mRT-PCR) starting in March 2020, of which 17,196 specimens resulted positive. To investigate the dynamics of virus molecular evolution and epidemiology, whole genome amplification (WGA) and Next Generation Sequencing (NGS) were performed on 9516 isolates. 7586 isolates with a high quality were further analyzed for the mutation frequency and spectrum. Lastly, we evaluated the utility of the mRT-PCR detection pattern among 26 reinfected patients with repeat positive testing three months after testing negative from the initial infection. Our results show a continuation of the genetic divergence in viral genomes. Furthermore, our results indicate that independent mutations in the primer and probe regions of the nucleocapsid gene amplicon and envelope gene amplicon accumulate over time. Some of these mutations correlate with the changes of detection pattern of viral targets of mRT-PCR. Our data highlight the significance of a continuous genetic divergence on a gene amplification-based assay, the value of the mRT-PCR detection pattern for complementing the clinical diagnosis of reinfection, and the potential for WGA and NGS to identify mutation hotspots throughout the entire viral genome to optimize the design of the PCR-based gene amplification assay.
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spelling pubmed-91817332022-06-10 SARS-CoV-2 Continuous Genetic Divergence and Changes in Multiplex RT-PCR Detection Pattern on Positive Retesting Median 150 Days after Initial Infection Liu, Dakai Rodriguez, George D. Zhou, Hang-Yu Cheng, Ye-Xiao Li, Xiaofeng Tang, Wenwen Prasad, Nishant Chen, Chun-Cheng Singh, Vishnu Konadu, Eric James, Keither K. Bahamon, Maria F. Chen, Yvonne Segal-Maurer, Sorana Wu, Aiping Rodgers, William Harry Int J Mol Sci Article Being in the epicenter of the COVID-19 pandemic, our lab tested 193,054 specimens for SARS-CoV-2 RNA by diagnostic multiplex reverse transcription polymerase chain reaction (mRT-PCR) starting in March 2020, of which 17,196 specimens resulted positive. To investigate the dynamics of virus molecular evolution and epidemiology, whole genome amplification (WGA) and Next Generation Sequencing (NGS) were performed on 9516 isolates. 7586 isolates with a high quality were further analyzed for the mutation frequency and spectrum. Lastly, we evaluated the utility of the mRT-PCR detection pattern among 26 reinfected patients with repeat positive testing three months after testing negative from the initial infection. Our results show a continuation of the genetic divergence in viral genomes. Furthermore, our results indicate that independent mutations in the primer and probe regions of the nucleocapsid gene amplicon and envelope gene amplicon accumulate over time. Some of these mutations correlate with the changes of detection pattern of viral targets of mRT-PCR. Our data highlight the significance of a continuous genetic divergence on a gene amplification-based assay, the value of the mRT-PCR detection pattern for complementing the clinical diagnosis of reinfection, and the potential for WGA and NGS to identify mutation hotspots throughout the entire viral genome to optimize the design of the PCR-based gene amplification assay. MDPI 2022-06-02 /pmc/articles/PMC9181733/ /pubmed/35682933 http://dx.doi.org/10.3390/ijms23116254 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Liu, Dakai
Rodriguez, George D.
Zhou, Hang-Yu
Cheng, Ye-Xiao
Li, Xiaofeng
Tang, Wenwen
Prasad, Nishant
Chen, Chun-Cheng
Singh, Vishnu
Konadu, Eric
James, Keither K.
Bahamon, Maria F.
Chen, Yvonne
Segal-Maurer, Sorana
Wu, Aiping
Rodgers, William Harry
SARS-CoV-2 Continuous Genetic Divergence and Changes in Multiplex RT-PCR Detection Pattern on Positive Retesting Median 150 Days after Initial Infection
title SARS-CoV-2 Continuous Genetic Divergence and Changes in Multiplex RT-PCR Detection Pattern on Positive Retesting Median 150 Days after Initial Infection
title_full SARS-CoV-2 Continuous Genetic Divergence and Changes in Multiplex RT-PCR Detection Pattern on Positive Retesting Median 150 Days after Initial Infection
title_fullStr SARS-CoV-2 Continuous Genetic Divergence and Changes in Multiplex RT-PCR Detection Pattern on Positive Retesting Median 150 Days after Initial Infection
title_full_unstemmed SARS-CoV-2 Continuous Genetic Divergence and Changes in Multiplex RT-PCR Detection Pattern on Positive Retesting Median 150 Days after Initial Infection
title_short SARS-CoV-2 Continuous Genetic Divergence and Changes in Multiplex RT-PCR Detection Pattern on Positive Retesting Median 150 Days after Initial Infection
title_sort sars-cov-2 continuous genetic divergence and changes in multiplex rt-pcr detection pattern on positive retesting median 150 days after initial infection
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9181733/
https://www.ncbi.nlm.nih.gov/pubmed/35682933
http://dx.doi.org/10.3390/ijms23116254
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