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Ge X, Zhou H, Shen F, Yang G, Zhang Y, Zhang X, Li H. SARS-CoV-2 subgenomic RNA: formation process and rapid molecular diagnostic methods. Clin Chem Lab Med 2024; 62:1019-1028. [PMID: 38000044 DOI: 10.1515/cclm-2023-0846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which caused coronavirus disease-2019 (COVID-19) is spreading worldwide and posing enormous losses to human health and socio-economic. Due to the limitations of medical and health conditions, it is still a huge challenge to develop appropriate discharge standards for patients with COVID-19 and to use medical resources in a timely and effective manner. Similar to other coronaviruses, SARS-CoV-2 has a very complex discontinuous transcription process to generate subgenomic RNA (sgRNA). Some studies support that sgRNA of SARS-CoV-2 can only exist when the virus is active and is an indicator of virus replication. The results of sgRNA detection in patients can be used to evaluate the condition of hospitalized patients, which is expected to save medical resources, especially personal protective equipment. There have been numerous investigations using different methods, especially molecular methods to detect sgRNA. Here, we introduce the process of SARS-CoV-2 sgRNA formation and the commonly used molecular diagnostic methods to bring a new idea for clinical detection in the future.
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Affiliation(s)
- Xiao Ge
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Huizi Zhou
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Fangyuan Shen
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Guimao Yang
- Department of Medical Laboratory, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P.R. China
| | - Yubo Zhang
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Xiaoyu Zhang
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Heng Li
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
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Hillung J, Olmo-Uceda MJ, Muñoz-Sánchez JC, Elena SF. Accumulation Dynamics of Defective Genomes during Experimental Evolution of Two Betacoronaviruses. Viruses 2024; 16:644. [PMID: 38675984 PMCID: PMC11053736 DOI: 10.3390/v16040644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Virus-encoded replicases often generate aberrant RNA genomes, known as defective viral genomes (DVGs). When co-infected with a helper virus providing necessary proteins, DVGs can multiply and spread. While DVGs depend on the helper virus for propagation, they can in some cases disrupt infectious virus replication, impact immune responses, and affect viral persistence or evolution. Understanding the dynamics of DVGs alongside standard viral genomes during infection remains unclear. To address this, we conducted a long-term experimental evolution of two betacoronaviruses, the human coronavirus OC43 (HCoV-OC43) and the murine hepatitis virus (MHV), in cell culture at both high and low multiplicities of infection (MOI). We then performed RNA-seq at regular time intervals, reconstructed DVGs, and analyzed their accumulation dynamics. Our findings indicate that DVGs evolved to exhibit greater diversity and abundance, with deletions and insertions being the most common types. Notably, some high MOI deletions showed very limited temporary existence, while others became prevalent over time. We observed differences in DVG abundance between high and low MOI conditions in HCoV-OC43 samples. The size distribution of HCoV-OC43 genomes with deletions differed between high and low MOI passages. In low MOI lineages, short and long DVGs were the most common, with an additional cluster in high MOI lineages which became more prevalent along evolutionary time. MHV also showed variations in DVG size distribution at different MOI conditions, though they were less pronounced compared to HCoV-OC43, suggesting a more random distribution of DVG sizes. We identified hotspot regions for deletions that evolved at a high MOI, primarily within cistrons encoding structural and accessory proteins. In conclusion, our study illustrates the widespread formation of DVGs during betacoronavirus evolution, influenced by MOI and cell- and virus-specific factors.
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Affiliation(s)
- Julia Hillung
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-UV, Catedrático Agustín Escardino Benlloch 9, 46980 Paterna, Valencia, Spain; (J.H.); (M.J.O.-U.); (J.C.M.-S.)
| | - María J. Olmo-Uceda
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-UV, Catedrático Agustín Escardino Benlloch 9, 46980 Paterna, Valencia, Spain; (J.H.); (M.J.O.-U.); (J.C.M.-S.)
| | - Juan C. Muñoz-Sánchez
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-UV, Catedrático Agustín Escardino Benlloch 9, 46980 Paterna, Valencia, Spain; (J.H.); (M.J.O.-U.); (J.C.M.-S.)
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-UV, Catedrático Agustín Escardino Benlloch 9, 46980 Paterna, Valencia, Spain; (J.H.); (M.J.O.-U.); (J.C.M.-S.)
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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Lavezzari D, Mori A, Pomari E, Deiana M, Fadda A, Bertoli L, Sinigaglia A, Riccetti S, Barzon L, Piubelli C, Delledonne M, Capobianchi MR, Castilletti C. Comparative analysis of bioinformatics tools to characterize SARS-CoV-2 subgenomic RNAs. Life Sci Alliance 2023; 6:e202302017. [PMID: 37748810 PMCID: PMC10520259 DOI: 10.26508/lsa.202302017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/27/2023] Open
Abstract
During the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), positive-sense genomic RNA and subgenomic RNAs (sgRNAs) are synthesized by a discontinuous process of transcription characterized by a template switch, regulated by transcription-regulating sequences (TRS). Although poorly known about makeup and dynamics of sgRNAs population and function of its constituents, next-generation sequencing approaches with the help of bioinformatics tools have made a significant contribution to expand the knowledge of sgRNAs in SARS-CoV-2. For this scope to date, Periscope, LeTRS, sgDI-tector, and CORONATATOR have been developed. However, limited number of studies are available to compare the performance of such tools. To this purpose, we compared Periscope, LeTRS, and sgDI-tector in the identification of canonical (c-) and noncanonical (nc-) sgRNA species in the data obtained with the Illumina ARTIC sequencing protocol applied to SARS-CoV-2-infected Caco-2 cells, sampled at different time points. The three software showed a high concordance rate in the identification and in the quantification of c-sgRNA, whereas more differences were observed in nc-sgRNA. Overall, LeTRS and sgDI-tector result to be adequate alternatives to Periscope to analyze Fastq data from sequencing platforms other than Nanopore.
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Affiliation(s)
- Denise Lavezzari
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Antonio Mori
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Elena Pomari
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Michela Deiana
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Antonio Fadda
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Luca Bertoli
- Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Silvia Riccetti
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Chiara Piubelli
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | | | - Maria Rosaria Capobianchi
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Concetta Castilletti
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
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Olmo-Uceda MJ, Muñoz-Sánchez JC, Lasso-Giraldo W, Arnau V, Díaz-Villanueva W, Elena SF. DVGfinder: A Metasearch Tool for Identifying Defective Viral Genomes in RNA-Seq Data. Viruses 2022; 14:v14051114. [PMID: 35632855 PMCID: PMC9144107 DOI: 10.3390/v14051114] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 02/05/2023] Open
Abstract
The generation of different types of defective viral genomes (DVG) is an unavoidable consequence of the error-prone replication of RNA viruses. In recent years, a particular class of DVGs, those containing long deletions or genome rearrangements, has gain interest due to their potential therapeutic and biotechnological applications. Identifying such DVGs in high-throughput sequencing (HTS) data has become an interesting computational problem. Several algorithms have been proposed to accomplish this goal, though all incur false positives, a problem of practical interest if such DVGs have to be synthetized and tested in the laboratory. We present a metasearch tool, DVGfinder, that wraps the two most commonly used DVG search algorithms in a single workflow for the identification of the DVGs in HTS data. DVGfinder processes the results of ViReMa-a and DI-tector and uses a gradient boosting classifier machine learning algorithm to reduce the number of false-positive events. The program also generates output files in user-friendly HTML format, which can help users to explore the DVGs identified in the sample. We evaluated the performance of DVGfinder compared to the two search algorithms used separately and found that it slightly improves sensitivities for low-coverage synthetic HTS data and DI-tector precision for high-coverage samples. The metasearch program also showed higher sensitivity on a real sample for which a set of copy-backs were previously validated.
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Affiliation(s)
- Maria J. Olmo-Uceda
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, 46980 Valencia, Spain; (M.J.O.-U.); (J.C.M.-S.); (W.L.-G.); (V.A.); (W.D.-V.)
| | - Juan C. Muñoz-Sánchez
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, 46980 Valencia, Spain; (M.J.O.-U.); (J.C.M.-S.); (W.L.-G.); (V.A.); (W.D.-V.)
| | - Wilberth Lasso-Giraldo
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, 46980 Valencia, Spain; (M.J.O.-U.); (J.C.M.-S.); (W.L.-G.); (V.A.); (W.D.-V.)
| | - Vicente Arnau
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, 46980 Valencia, Spain; (M.J.O.-U.); (J.C.M.-S.); (W.L.-G.); (V.A.); (W.D.-V.)
| | - Wladimiro Díaz-Villanueva
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, 46980 Valencia, Spain; (M.J.O.-U.); (J.C.M.-S.); (W.L.-G.); (V.A.); (W.D.-V.)
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, 46980 Valencia, Spain; (M.J.O.-U.); (J.C.M.-S.); (W.L.-G.); (V.A.); (W.D.-V.)
- Santa Fe Institute, Santa Fe, NM 87501, USA
- Correspondence: ; Tel.: +34-963-544-779
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