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Ceballos-Garzon A, Comtet-Marre S, Peyret P. Applying targeted gene hybridization capture to viruses with a focus to SARS-CoV-2. Virus Res 2024; 340:199293. [PMID: 38101578 PMCID: PMC10767490 DOI: 10.1016/j.virusres.2023.199293] [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: 04/03/2023] [Revised: 11/08/2023] [Accepted: 12/03/2023] [Indexed: 12/17/2023]
Abstract
Although next-generation sequencing technologies are advancing rapidly, many research topics often require selective sequencing of genomic regions of interest. In addition, sequencing low-titre viruses is challenging, especially for coronaviruses, which are the largest RNA viruses. Prior to sequencing, enrichment of viral particles can help to significantly increase target sequence information as well as avoid large sequencing efforts and, consequently, can increase sensitivity and reduce sequencing costs. Targeting nucleic acids using capture by hybridization is another efficient method that can be performed by applying complementary probes (DNA or RNA baits) to directly enrich genetic information of interest while removing background non-target material. In studies where sequence capture by hybridization has been applied to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, most authors agree that this technique is useful to easily access sequence targets in complex samples. Furthermore, this approach allows for complete or near-complete sequencing of the viral genome, even in samples with low viral load or poor nucleic acid integrity. In addition, this strategy is highly efficient at discovering new variants by facilitating downstream investigations, such as phylogenetics, epidemiology, and evolution. Commercial kits, as well as in-house protocols, have been developed for enrichment of viral sequences. However, these kits have multiple variations in procedure, with differences in performance. This review compiles and describes studies in which hybridization capture has been applied to SARS-CoV-2 variant genomes.
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Affiliation(s)
| | | | - Pierre Peyret
- Université Clermont Auvergne, INRAE, MEDiS, 63000, Clermont-Ferrand, France.
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2
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Gonzalez-Alba JM, Rojo-Alba S, Perez-Martinez Z, Boga JA, Alvarez-Arguelles ME, Gomez J, Herrero P, Costales I, Alba LM, Martin-Rodriguez G, Campo R, Castelló-Abietar C, Sandoval M, Abreu-Salinas F, Coto E, Rodriguez M, Rubianes P, Sanchez ML, Vazquez F, Antuña L, Álvarez V, Melón García S. Monitoring and tracking the spread of SARS-CoV-2 in Asturias, Spain. Access Microbiol 2023; 5:000573.v4. [PMID: 37841093 PMCID: PMC10569657 DOI: 10.1099/acmi.0.000573.v4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023] Open
Abstract
Mutational analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can quantify the relative importance of variants over time, enable dominant mutations to be identified, and facilitate near real-time detection, comparison and tracking of evolving variants. SARS-CoV-2 in Asturias, an autonomous community of Spain with a large ageing population, and high levels of migration and tourism, was monitored and tracked from the beginning of the pandemic in February 2020 until its decline and stabilization in August 2021, and samples were characterized using whole genomic sequencing and single nucleotide polymorphisms. Data held in the GISAID database were analysed to establish patterns in the appearance and persistence of SARS-CoV-2 strains. Only 138 non-synonymous mutations occurring in more than 1 % of the population with SARS-CoV-2 were found, identifying ten major variants worldwide (seven arose before January 2021), 19 regional and one local. In Asturias only 17 different variants were found. After vaccination, no further regional major variants were found. Only half of the defined variants circulated and no new variants were generated, indicating that infection control measures such as rapid diagnosis, isolation and vaccination were efficient.
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Affiliation(s)
- Jose Maria Gonzalez-Alba
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Susana Rojo-Alba
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Zulema Perez-Martinez
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Jose A. Boga
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Marta Elena Alvarez-Arguelles
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Juan Gomez
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Genética Molecular, Oviedo, Spain
| | - Pablo Herrero
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Urgencias, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Isabel Costales
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Luz Maria Alba
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Gabriel Martin-Rodriguez
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Rainer Campo
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Cristian Castelló-Abietar
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Marta Sandoval
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Fátima Abreu-Salinas
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Eliecer Coto
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Genética Molecular, Oviedo, Spain
| | - Mercedes Rodriguez
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Pablo Rubianes
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Urgencias, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Maria Luisa Sanchez
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Fernando Vazquez
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Luis Antuña
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Urgencias, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Victoria Álvarez
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Genética Molecular, Oviedo, Spain
| | - Santiago Melón García
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
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3
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Khan M, Li L, Haak L, Payen SH, Carine M, Adhikari K, Uppal T, Hartley PD, Vasquez-Gross H, Petereit J, Verma SC, Pagilla K. Significance of wastewater surveillance in detecting the prevalence of SARS-CoV-2 variants and other respiratory viruses in the community - A multi-site evaluation. One Health 2023; 16:100536. [PMID: 37041760 PMCID: PMC10074727 DOI: 10.1016/j.onehlt.2023.100536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/13/2023] Open
Abstract
Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral genome in wastewater has proven to be useful for tracking the trends of virus prevalence within the community. The surveillance also provides precise and early detection of any new and circulating variants, which aids in response to viral outbreaks. Site-specific monitoring of SARS-CoV-2 variants provides valuable information on the prevalence of new or emerging variants in the community. We sequenced the genomic RNA of viruses present in the wastewater samples and analyzed for the prevalence of SARS-CoV-2 variants as well as other respiratory viruses for a period of one year to account for seasonal variations. The samples were collected from the Reno-Sparks metropolitan area on a weekly basis between November 2021 to November 2022. Samples were analyzed to detect the levels of SARS-CoV-2 genomic copies and variants identification. This study confirmed that wastewater monitoring of SARS-CoV-2 variants can be used for community surveillance and early detection of circulating variants and supports wastewater-based epidemiology (WBE) as a complement to clinical respiratory virus testing as a healthcare response effort. Our study showed the persistence of the SARS-CoV-2 virus throughout the year compared to a seasonal presence of other respiratory viruses, implicating SARS-CoV-2's broad genetic diversity and strength to persist and infect susceptible hosts. Through secondary analysis, we further identified antimicrobial resistance (AMR) genes in the same wastewater samples and found WBE to be a feasible tool for community AMR detection and monitoring.
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Affiliation(s)
- Majid Khan
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV 89557, USA
| | - Lin Li
- Department of Civil and Environmental Engineering, University of Nevada, MS258, Reno, NV 89557, USA
| | - Laura Haak
- Department of Civil and Environmental Engineering, University of Nevada, MS258, Reno, NV 89557, USA
| | - Shannon Harger Payen
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV 89557, USA
| | - Madeline Carine
- Department of Civil and Environmental Engineering, University of Nevada, MS258, Reno, NV 89557, USA
| | - Kabita Adhikari
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV 89557, USA
| | - Timsy Uppal
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV 89557, USA
| | - Paul D. Hartley
- Nevada Genomics Center, University of Nevada, Reno, NV 89557, USA
| | - Hans Vasquez-Gross
- Nevada Bioinformatics Center (RRID:SCR_017802), University of Nevada, Reno, NV 89557, USA
| | - Juli Petereit
- Nevada Bioinformatics Center (RRID:SCR_017802), University of Nevada, Reno, NV 89557, USA
| | - Subhash C. Verma
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV 89557, USA
| | - Krishna Pagilla
- Department of Civil and Environmental Engineering, University of Nevada, MS258, Reno, NV 89557, USA
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Payen SH, Gorzalski A, Siao DD, Pandori M, Verma SC, Rossetto CC. Analysis of SARS-CoV-2 variants from patient specimens in Nevada from October 2020 to August 2021. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 111:105434. [PMID: 37059256 PMCID: PMC10098042 DOI: 10.1016/j.meegid.2023.105434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 04/16/2023]
Abstract
In early 2020, the emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the human population quickly developed into a global pandemic. SARS-CoV-2 is the etiological agent of coronavirus disease 2019 (COVID-19) which has a broad range of respiratory illnesses. As the virus circulates, it acquires nucleotide changes. These mutations are potentially due to the inherent differences in the selection pressures within the human population compared to the original zoonotic reservoir of SARS-CoV-2 and formerly naïve humans. The acquired mutations will most likely be neutral, but some may have implications for viral transmission, disease severity and resistance to therapies or vaccines. This is a follow-up study from our early report (Hartley et al. J Genet Genomics. 01202021;48(1):40-51) which detected a rare variant (nsp12, RdRp P323F) circulating within Nevada in mid 2020 at high frequency. The primary goals of the current study were to determine the phylogenetic relationship of the SARS-CoV-2 genomes within Nevada and to determine if there are any unusual variants within Nevada compared to the current database of SARS-CoV-2 sequences. Whole genome sequencing and analysis of SARS-CoV-2 from 425 positively identified nasopharyngeal/nasal swab specimens were performed from October 2020 to August 2021 to determine any variants that could result in potential escape from current therapeutics. Our analysis focused on nucleotide mutations that generated amino acid variations in the viral Spike (S) protein, Receptor binding domain (RBD) and the RNA-dependent RNA-polymerase (RdRp) complex. The data indicate that SARS-CoV-2 sequences from Nevada did not contain any unusual variants that had not been previously reported. Additionally, we did not detect the previously identified the RdRp P323F variant in any of the samples. This suggests that the rare variant we detected before was only able to circulate because of the stay-at-home orders and semi-isolation experience during the early months of the pandemic. IMPORTANCE: SARS-COV-2 continues to circulate in the human population. In this study, SARS-CoV-2 positive nasopharyngeal/nasal swab samples were used for whole genome sequencing to determine the phylogenetic relationship of SARS-CoV-2 sequences within Nevada from October 2020 to August 2021. The resulting data is being added to a continually growing database of SARS-CoV-2 sequences that will be important for understanding the transmission and evolution of the virus as it spreads around the globe.
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Affiliation(s)
- Shannon Harger Payen
- Department of Microbiology & Immunology; School of Medicine, University of Nevada, Reno
| | | | | | - Mark Pandori
- School of Medicine, University of Nevada, Reno; Nevada State Public Health Lab
| | - Subhash C Verma
- Department of Microbiology & Immunology; School of Medicine, University of Nevada, Reno
| | - Cyprian C Rossetto
- Department of Microbiology & Immunology; School of Medicine, University of Nevada, Reno.
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5
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Hill HJ, Uppal T, Hau D, Pandit SG, Arias-Umana J, Foster AJ, Gorzalski A, Pflughoeft KJ, Burnham-Marusich AR, Reed DE, Gates-Hollingsworth MA, Gumbleton L, Verma SC, AuCoin DP. Comparison of a Prototype SARS-CoV-2 Lateral Flow IMMUNOASSAY with the BinaxNOW TM COVID-19 Antigen CARD. Viruses 2022; 14:v14122609. [PMID: 36560613 PMCID: PMC9786212 DOI: 10.3390/v14122609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus responsible for the COVID-19 pandemic. From the onset of the pandemic, rapid antigen tests have quickly proved themselves to be an accurate and accessible diagnostic platform. The initial (and still most commonly used antigen tests) for COVID-19 diagnosis were constructed using monoclonal antibodies (mAbs) specific to severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid protein (NP). These mAbs are able to bind SARS-CoV-2 NP due to high homology between the two viruses. However, since first being identified in 2019, SARS-CoV-2 has continuously mutated, and a multitude of variants have appeared. These mutations have an elevated risk of leading to possible diagnostic escape when using tests produced with SARS-CoV-derived mAbs. Here, we established a library of 18 mAbs specific to SARS-CoV-2 NP and used two of these mAbs (1CV7 and 1CV14) to generate a prototype antigen-detection lateral flow immunoassay (LFI). A side-by-side analysis of the 1CV7/1CV14 LFI and the commercially available BinaxNOWTM COVID-19 Antigen CARD was performed. Results indicated the 1CV7/1CV14 LFI outperformed the BinaxNOWTM test in the detection of BA.2, BA.2.12.1, and BA.5 Omicron sub-variants when testing remnant RT-PCR positive patient nasopharyngeal swabs diluted in viral transport media.
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Affiliation(s)
- Haydon J. Hill
- Department of Microbiology and Immunology, Reno School of Medicine, University of Nevada, Reno, NV 89557, USA
| | - Timsy Uppal
- Department of Microbiology and Immunology, Reno School of Medicine, University of Nevada, Reno, NV 89557, USA
| | - Derrick Hau
- Department of Microbiology and Immunology, Reno School of Medicine, University of Nevada, Reno, NV 89557, USA
| | - Sujata G. Pandit
- Department of Microbiology and Immunology, Reno School of Medicine, University of Nevada, Reno, NV 89557, USA
| | - Jose Arias-Umana
- Department of Microbiology and Immunology, Reno School of Medicine, University of Nevada, Reno, NV 89557, USA
| | - Abigail J. Foster
- Department of Microbiology and Immunology, Reno School of Medicine, University of Nevada, Reno, NV 89557, USA
| | | | | | | | - Dana E. Reed
- Department of Microbiology and Immunology, Reno School of Medicine, University of Nevada, Reno, NV 89557, USA
| | | | | | - Subhash C. Verma
- Department of Microbiology and Immunology, Reno School of Medicine, University of Nevada, Reno, NV 89557, USA
| | - David P. AuCoin
- Department of Microbiology and Immunology, Reno School of Medicine, University of Nevada, Reno, NV 89557, USA
- DxDiscovery Incorporated, Reno, NV 89557, USA
- Correspondence:
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6
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Li L, Uppal T, Hartley PD, Gorzalski A, Pandori M, Picker MA, Verma SC, Pagilla K. Detecting SARS-CoV-2 variants in wastewater and their correlation with circulating variants in the communities. Sci Rep 2022; 12:16141. [PMID: 36167869 PMCID: PMC9514676 DOI: 10.1038/s41598-022-20219-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 09/09/2022] [Indexed: 11/09/2022] Open
Abstract
Detection of SARS-CoV-2 viral load in wastewater has been highly informative in estimating the approximate number of infected individuals in the surrounding communities. Recent developments in wastewater monitoring to determine community prevalence of COVID-19 further extends into identifying SARS-CoV-2 variants, including those being monitored for having enhanced transmissibility. We sequenced genomic RNA derived from wastewater to determine the variants of coronaviruses circulating in the communities. Wastewater samples were collected from Truckee Meadows Water Reclamation Facility (TMWRF) from November 2020 to June 2021. SARS-CoV-2 variants resulting from wastewater were compared with the variants detected in infected individuals' clinical specimens (nasal/nasopharyngeal swabs) during the same period and found conclusively in agreement. Therefore, wastewater monitoring for SARS-CoV-2 variants in the community is a feasible strategy as a complementary tool to clinical specimen testing in the latter's absence.
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Affiliation(s)
- Lin Li
- Department of Civil and Environmental Engineering, University of Nevada, MS258, Reno, NV, 89557, USA
| | - Timsy Uppal
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV, 89557, USA
| | - Paul D Hartley
- Nevada Genomics Center, University of Nevada, Reno, NV, 89557, USA
| | | | - Mark Pandori
- Nevada State Public Health Laboratory, Reno, NV, USA
- Department of Pathology and Laboratory Medicine, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Michael A Picker
- Southern Nevada Public Health Laboratory of the Southern Nevada Health District, Las Vegas, NV, USA
| | - Subhash C Verma
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV, 89557, USA.
| | - Krishna Pagilla
- Department of Civil and Environmental Engineering, University of Nevada, MS258, Reno, NV, 89557, USA.
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7
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Sun C, Xie C, Bu GL, Zhong LY, Zeng MS. Molecular characteristics, immune evasion, and impact of SARS-CoV-2 variants. Signal Transduct Target Ther 2022; 7:202. [PMID: 35764603 PMCID: PMC9240077 DOI: 10.1038/s41392-022-01039-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/16/2022] [Accepted: 05/22/2022] [Indexed: 01/18/2023] Open
Abstract
The persistent COVID-19 pandemic since 2020 has brought an enormous public health burden to the global society and is accompanied by various evolution of the virus genome. The consistently emerging SARS-CoV-2 variants harboring critical mutations impact the molecular characteristics of viral proteins and display heterogeneous behaviors in immune evasion, transmissibility, and the clinical manifestation during infection, which differ each strain and endow them with distinguished features during populational spread. Several SARS-CoV-2 variants, identified as Variants of Concern (VOC) by the World Health Organization, challenged global efforts on COVID-19 control due to the rapid worldwide spread and enhanced immune evasion from current antibodies and vaccines. Moreover, the recent Omicron variant even exacerbated the global anxiety in the continuous pandemic. Its significant evasion from current medical treatment and disease control even highlights the necessity of combinatory investigation of the mutational pattern and influence of the mutations on viral dynamics against populational immunity, which would greatly facilitate drug and vaccine development and benefit the global public health policymaking. Hence in this review, we summarized the molecular characteristics, immune evasion, and impacts of the SARS-CoV-2 variants and focused on the parallel comparison of different variants in mutational profile, transmissibility and tropism alteration, treatment effectiveness, and clinical manifestations, in order to provide a comprehensive landscape for SARS-CoV-2 variant research.
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Affiliation(s)
- Cong Sun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Chu Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Guo-Long Bu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Lan-Yi Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Mu-Sheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China. .,Guangdong-Hong Kong Joint Laboratory for RNA Medicine, 510060, Guangzhou, China.
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8
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Li L, Uppal T, Hartley PD, Gorzalski A, Pandori M, Picker MA, Verma SC, Pagilla K. Detecting SARS-CoV-2 Variants in Wastewater and Their Correlation With Circulating Variants in the Communities. RESEARCH SQUARE 2022:rs.3.rs-1435729. [PMID: 35313589 PMCID: PMC8936115 DOI: 10.21203/rs.3.rs-1435729/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Detection of SARS-CoV-2 viral load in wastewater has been highly informative in estimating the approximate number of infected individuals in the surrounding communities. Recent developments in wastewater monitoring to determine community prevalence of COVID-19 further extends into identifying SARS-CoV-2 variants, including those being monitored for having enhanced transmissibility. We sequenced genomic RNA derived from wastewater to determine the variants of coronaviruses circulating in the communities. Wastewater samples were collected from Truckee Meadows Water Reclamation Facility (TMWRF) from November 2021 to June 2021 were analyzed for SARS-CoV-2 variants and were compared with the variants detected in the clinical specimens (nasal/nasopharyngeal swabs) of infected individuals during the same period. The comparison was found to be conclusively in agreement. Therefore, wastewater monitoring for SARS-CoV-2 variants in the community is a feasible strategy both as a complementary tool to clinical specimen testing and in the latter's absence.
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Affiliation(s)
| | - Timsy Uppal
- University of Nevada, Reno School of Medicine
| | | | | | | | - Michael A Picker
- Southern Nevada Public Health Laboratory of the Southern Nevada Health District
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9
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A Global Mutational Profile of SARS-CoV-2: A Systematic Review and Meta-Analysis of 368,316 COVID-19 Patients. Life (Basel) 2021; 11:life11111224. [PMID: 34833100 PMCID: PMC8620851 DOI: 10.3390/life11111224] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 12/20/2022] Open
Abstract
Since its first detection in December 2019, more than 232 million cases of COVID-19, including 4.7 million deaths, have been reported by the WHO. The SARS-CoV-2 viral genomes have evolved rapidly worldwide, causing the emergence of new variants. This systematic review and meta-analysis was conducted to provide a global mutational profile of SARS-CoV-2 from December 2019 to October 2020. The review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA), and a study protocol was lodged with PROSPERO. Data from 62 eligible studies involving 368,316 SARS-CoV-2 genomes were analyzed. The mutational data analyzed showed most studies detected mutations in the Spike protein (n = 50), Nucleocapsid phosphoprotein (n = 34), ORF1ab gene (n = 29), 5′-UTR (n = 28) and ORF3a (n = 25). Under the random-effects model, pooled prevalence of SARS-CoV-2 variants was estimated at 95.1% (95% CI; 93.3–96.4%; I2 = 98.952%; p = 0.000) while subgroup meta-analysis by country showed majority of the studies were conducted ‘Worldwide’ (n = 10), followed by ‘Multiple countries’ (n = 6) and the USA (n = 5). The estimated prevalence indicated a need to continuously monitor the prevalence of new mutations due to their potential influence on disease severity, transmissibility and vaccine effectiveness.
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10
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Van Poelvoorde LAE, Delcourt T, Coucke W, Herman P, De Keersmaecker SCJ, Saelens X, Roosens NHC, Vanneste K. Strategy and Performance Evaluation of Low-Frequency Variant Calling for SARS-CoV-2 Using Targeted Deep Illumina Sequencing. Front Microbiol 2021; 12:747458. [PMID: 34721349 PMCID: PMC8548777 DOI: 10.3389/fmicb.2021.747458] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/21/2021] [Indexed: 12/24/2022] Open
Abstract
The ongoing COVID-19 pandemic, caused by SARS-CoV-2, constitutes a tremendous global health issue. Continuous monitoring of the virus has become a cornerstone to make rational decisions on implementing societal and sanitary measures to curtail the virus spread. Additionally, emerging SARS-CoV-2 variants have increased the need for genomic surveillance to detect particular strains because of their potentially increased transmissibility, pathogenicity and immune escape. Targeted SARS-CoV-2 sequencing of diagnostic and wastewater samples has been explored as an epidemiological surveillance method for the competent authorities. Currently, only the consensus genome sequence of the most abundant strain is taken into consideration for analysis, but multiple variant strains are now circulating in the population. Consequently, in diagnostic samples, potential co-infection(s) by several different variants can occur or quasispecies can develop during an infection in an individual. In wastewater samples, multiple variant strains will often be simultaneously present. Currently, quality criteria are mainly available for constructing the consensus genome sequence, and some guidelines exist for the detection of co-infections and quasispecies in diagnostic samples. The performance of detection and quantification of low-frequency variants using whole genome sequencing (WGS) of SARS-CoV-2 remains largely unknown. Here, we evaluated the detection and quantification of mutations present at low abundances using the mutations defining the SARS-CoV-2 lineage B.1.1.7 (alpha variant) as a case study. Real sequencing data were in silico modified by introducing mutations of interest into raw wild-type sequencing data, or by mixing wild-type and mutant raw sequencing data, to construct mixed samples subjected to WGS using a tiling amplicon-based targeted metagenomics approach and Illumina sequencing. As anticipated, higher variation and lower sensitivity were observed at lower coverages and allelic frequencies. We found that detection of all low-frequency variants at an abundance of 10, 5, 3, and 1%, requires at least a sequencing coverage of 250, 500, 1500, and 10,000×, respectively. Although increasing variability of estimated allelic frequencies at decreasing coverages and lower allelic frequencies was observed, its impact on reliable quantification was limited. This study provides a highly sensitive low-frequency variant detection approach, which is publicly available at https://galaxy.sciensano.be, and specific recommendations for minimum sequencing coverages to detect clade-defining mutations at certain allelic frequencies. This approach will be useful to detect and quantify low-frequency variants in both diagnostic (e.g., co-infections and quasispecies) and wastewater [e.g., multiple variants of concern (VOCs)] samples.
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Affiliation(s)
- Laura A. E. Van Poelvoorde
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Thomas Delcourt
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Wim Coucke
- Quality of Laboratories, Sciensano, Brussels, Belgium
| | - Philippe Herman
- Expertise and Service Provision, Sciensano, Brussels, Belgium
| | | | - Xavier Saelens
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | | | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
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11
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Extractionless nucleic acid detection: a high capacity solution to COVID-19 testing. Diagn Microbiol Infect Dis 2021; 101:115458. [PMID: 34274751 PMCID: PMC8222080 DOI: 10.1016/j.diagmicrobio.2021.115458] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/12/2021] [Accepted: 06/13/2021] [Indexed: 11/29/2022]
Abstract
We describe an extractionless real-time reverse transcriptase-PCR (rRT-PCR) protocol for SARS-CoV-2 nucleic acid detection using heat as an accurate cost-effective high-capacity solution to COVID-19 testing. We present the effect of temperature, transport media, rRT-PCR mastermixes and gene assays on SARS-CoV-2 gene amplification and limits of detection. Utilizing our heated methodology, our limits of detection were 12.5 and 1 genome copy/reaction for singleplex E- and N1-gene assays, respectively, and 1 genome copy/reaction by utilizing an E/N1 or Orf1ab/N1 multiplex assay combination. Using this approach, we detected up to 98% of COVID-19 positive patient samples analyzed in our various cohorts including a significant percentage of weak positives. Importantly, this extractionless approach will allow for >2-fold increase in testing capacity with existing instruments, circumvent the additional need for expensive extraction devices, provide the sensitivity needed for COVID-19 detection and significantly reduce the turn-around time of reporting COVID-19 test results.
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