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Brochu HN, Song K, Zhang Q, Zeng Q, Shafi A, Robinson M, Humphrey J, Croy B, Peavy L, Perera M, Parker S, Pruitt J, Munroe J, Ghatti R, Urban TJ, Harris AB, Alfego D, Norvell B, Levandoski M, Krueger B, Williams JD, Boles D, Nye MB, Dale SE, Sapeta M, Petropoulos CJ, Meltzer J, Eisenberg M, Cohen O, Letovsky S, Iyer LK. A program for real-time surveillance of SARS-CoV-2 genetics. Sci Rep 2024; 14:20249. [PMID: 39215120 PMCID: PMC11364650 DOI: 10.1038/s41598-024-70697-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
The COVID-19 pandemic brought forth an urgent need for widespread genomic surveillance for rapid detection and monitoring of emerging SARS-CoV-2 variants. It necessitated design, development, and deployment of a nationwide infrastructure designed for sequestration, consolidation, and characterization of patient samples that disseminates de-identified information to public authorities in tight turnaround times. Here, we describe our development of such an infrastructure, which sequenced 594,832 high coverage SARS-CoV-2 genomes from isolates we collected in the United States (U.S.) from March 13th 2020 to July 3rd 2023. Our sequencing protocol ('Virseq') utilizes wet and dry lab procedures to generate mutation-resistant sequencing of the entire SARS-CoV-2 genome, capturing all major lineages. We also characterize 379 clinically relevant SARS-CoV-2 multi-strain co-infections and ensure robust detection of emerging lineages via simulation. The modular infrastructure, sequencing, and analysis capabilities we describe support the U.S. Centers for Disease Control and Prevention national surveillance program and serve as a model for rapid response to emerging pandemics at a national scale.
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Affiliation(s)
- Hayden N Brochu
- Labcorp Center for Excellence in Data Science, AI and Bioinformatics, Burlington, NC, 27215, USA
| | - Kuncheng Song
- Labcorp Center for Excellence in Data Science, AI and Bioinformatics, Burlington, NC, 27215, USA
| | - Qimin Zhang
- Labcorp Center for Excellence in Data Science, AI and Bioinformatics, Burlington, NC, 27215, USA
| | - Qiandong Zeng
- Labcorp Center for Excellence in Data Science, AI and Bioinformatics, Burlington, NC, 27215, USA
| | - Adib Shafi
- Labcorp Center for Excellence in Data Science, AI and Bioinformatics, Burlington, NC, 27215, USA
| | - Matthew Robinson
- Labcorp Center for Excellence in Data Science, AI and Bioinformatics, Burlington, NC, 27215, USA
| | - Jake Humphrey
- Labcorp Center for Excellence in Data Science, AI and Bioinformatics, Burlington, NC, 27215, USA
| | - Bobbi Croy
- Labcorp Information Technology, Burlington, NC, 27215, USA
| | - Lydia Peavy
- Labcorp Research and Development, Burlington, NC, 27215, USA
| | - Minoli Perera
- Labcorp Research and Development, Burlington, NC, 27215, USA
| | - Scott Parker
- Labcorp Research and Development, Burlington, NC, 27215, USA
| | - John Pruitt
- Labcorp Research and Development, Burlington, NC, 27215, USA
| | - Jason Munroe
- Labcorp Consumer Genetics Department, Burlington, NC, 27215, USA
| | | | - Thomas J Urban
- Labcorp Research and Development, Burlington, NC, 27215, USA
| | - Ayla B Harris
- Labcorp Research and Development, Burlington, NC, 27215, USA
| | - David Alfego
- Labcorp Center for Excellence in Data Science, AI and Bioinformatics, Burlington, NC, 27215, USA
| | - Brian Norvell
- Labcorp Research and Development, Burlington, NC, 27215, USA
| | - Michael Levandoski
- Labcorp Research and Development, Burlington, NC, 27215, USA
- Q2 Solutions, an IQVIA Business, Durham, NC, 27703, USA
| | - Brian Krueger
- Labcorp Research and Development, Burlington, NC, 27215, USA
- BaseX Scientific, LLC, Chapel Hill, NC, 27516, USA
| | | | - Deborah Boles
- Labcorp Research and Development, Burlington, NC, 27215, USA
| | - Melinda B Nye
- Labcorp Center for Esoteric Testing, Burlington, NC, 27215, USA
| | - Suzanne E Dale
- Labcorp Center for Esoteric Testing, Burlington, NC, 27215, USA
| | - Michael Sapeta
- Labcorp Center for Esoteric Testing, Burlington, NC, 27215, USA
| | | | | | | | - Oren Cohen
- Labcorp Drug Development, Burlington, NC, 27215, USA
- Fortrea Inc, Durham, NC, 27703, USA
| | - Stanley Letovsky
- Labcorp Center for Excellence in Data Science, AI and Bioinformatics, Burlington, NC, 27215, USA
| | - Lakshmanan K Iyer
- Labcorp Center for Excellence in Data Science, AI and Bioinformatics, Burlington, NC, 27215, USA.
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2
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Manuelpillai B, Zendt M, Chang-Rabley E, Ricotta EE. Stuck in pandemic uncertainty: a review of the persistent effects of COVID-19 infection in immune-deficient people. Clin Microbiol Infect 2024; 30:1007-1011. [PMID: 38552795 PMCID: PMC11254561 DOI: 10.1016/j.cmi.2024.03.027] [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: 01/17/2024] [Revised: 03/04/2024] [Accepted: 03/23/2024] [Indexed: 04/15/2024]
Abstract
BACKGROUND People who are immune-deficient/disordered (IDP) are underrepresented in COVID-19 studies. Specifically, there is limited research on post-SARS-CoV-2 infection outcomes, including viral persistence and long-term sequelae in these populations. OBJECTIVES This review aimed to examine the published literature on the occurrence of persistent SARS-CoV-2 positivity, relapse, reinfections, variant coinfection, and post-acute sequelae of COVID-19 in IDP. Although the available literature largely centred on those with secondary immunodeficiencies, studies on people with inborn errors of immunity are also included. SOURCES PubMed was searched using medical subject headings terms to identify relevant articles from the last 4 years. Articles on primary and secondary immunodeficiencies were chosen, and a special emphasis was placed on including articles that studied people with inborn errors of immunity. The absence of extensive cohort studies including these individuals has limited most articles in this review to case reports, whereas the articles focusing on secondary immunodeficiencies include larger cohort, case-control, and cross-sectional studies. Articles focusing solely on HIV/AIDS were excluded. CONTENT Scientific literature suggests that IDP of any age are more likely to experience persistent SARS-CoV-2 infections. Although adult IDP exhibits a higher rate of post-acute sequelae of COVID-19, milder COVID-19 infections in children may reduce their risk of experiencing post-acute sequelae of COVID-19. Reinfections and coinfections may occur at a slightly higher rate in IDP than in the general population. IMPLICATIONS Although IDP experience increased viral persistence and inter-host evolution, it is unlikely that enough evidence can be generated at the population-level to support or refute the hypothesis that infections in IDP are significantly more likely to result in variants of concern than infections in the general population. Additional research on the relationship between viral persistence and the rate of long-term sequelae in IDP could inform the understanding of the immune response to SARS-CoV-2 in IDP and the general population.
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Affiliation(s)
- Bevin Manuelpillai
- Rollins School of Public Health, Emory University, Atlanta, GA, USA; Epidemiology and Data Management Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mackenzie Zendt
- Epidemiology and Data Management Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Emma Chang-Rabley
- Epidemiology and Data Management Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Emily E Ricotta
- Epidemiology and Data Management Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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3
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Nankivell BJ, P'ng C, Tran T, Draper J, Ko D, Luu I, Basile K, Kable K, Sciberras F, Wong G, Kok J. The Effects of COVID-19 in Kidney Transplantation: Evidence From Tissue Pathology. Transplantation 2024:00007890-990000000-00817. [PMID: 39020461 DOI: 10.1097/tp.0000000000005121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Abstract
BACKGROUND The biological effects of SARS-CoV-2 infection in transplanted kidneys are uncertain with little pathological information. METHODS This single-center, prospective observational study evaluated kidney transplant biopsies from recipients of deceased donors with COVID-19, current recipients contracting SARS-CoV-2 Omicron variant in 2022, against prior BK virus (BKV) infection and uninfected (without SARS-CoV-2 or BKV) samples, as respective positive and negative comparators (n = 503 samples). RESULTS We demonstrated nonvirus tubular injury in implanted tissue from infected donors and prevalent recipients with mild acute COVID-19 and acute kidney injury, excluding direct viral infection as a cause of kidney damage. COVID particles were absent in 4116 ultrastructural images of 295 renal tubules from 4 patients with acute COVID-19. No viral cytopathic effect, viral allograft nephropathy, or SARS-CoV-2 RNA was detected in acute tissues, nor in 128 sequential samples from infected donors or recipients with COVID-19. Following recipient COVID-19 (mean 16.8 ± 12.0 wk post-infection), the biopsy-prevalence of rejection was 33.0% (n = 100 biopsies) versus 13.4% for contemporaneous uninfected controls (n = 337; P < 0.001). Prior COVID-19 was an independent risk factor for incident rejection using multivariable generalized estimating equation adjusted for competing risks (odds ratio, 2.195; 95% confidence interval, 1.189-4.052; P = 0.012). Landmark and matched-pair analyses confirmed an association of SARS-CoV-2 with subsequent transplant rejection, with a similar pattern following BKV infection. CONCLUSIONS Transplantation from COVID-19+ deceased donors yielded good recipient outcomes without evidence of viral tissue transmission. Acute kidney injury during COVID-19 was mediated by archetypical tubular injury and infection correlated with an increased risk of subsequent rejection.
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Affiliation(s)
- Brian J Nankivell
- Department of Renal Medicine, Westmead Hospital, Westmead, NSW, Australia
| | - Chow P'ng
- Tissue Pathology and Diagnostic Oncology and Electron Microscopy Units, Westmead Hospital, Westmead, NSW, Australia
| | - Thomas Tran
- Tissue Pathology and Diagnostic Oncology and Electron Microscopy Units, Westmead Hospital, Westmead, NSW, Australia
| | - Jenny Draper
- Centre for Infectious Diseases & Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - Danny Ko
- Centre for Infectious Diseases & Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - Ivan Luu
- Centre for Infectious Diseases & Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - Kerri Basile
- Centre for Infectious Diseases & Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - Kathy Kable
- Department of Renal Medicine, Westmead Hospital, Westmead, NSW, Australia
| | | | - Germaine Wong
- Department of Renal Medicine, Westmead Hospital, Westmead, NSW, Australia
| | - Jen Kok
- Centre for Infectious Diseases & Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
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Trende R, Darling TL, Gan T, Wang D, Boon AC. Barcoded SARS-CoV-2 viruses define the impact of time and route of transmission on the transmission bottleneck in a Syrian hamster model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.08.597602. [PMID: 38915710 PMCID: PMC11195048 DOI: 10.1101/2024.06.08.597602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The transmission bottleneck, defined as the number of viruses that transmit from one host to infect another, is an important determinant of the rate of virus evolution and the level of immunity required to protect against virus transmission. Despite its importance, SARS-CoV-2's transmission bottleneck remains poorly characterized, in part due to a lack of quantitative measurement tools. To address this, we adapted a SARS-CoV-2 reverse genetics system to generate a pool of >200 isogenic SARS-CoV-2 viruses harboring specific 6-nucleotide barcodes inserted in ORF10, a non-translated ORF. We directly inoculated donor Syrian hamsters intranasally with this barcoded virus pool and exposed a paired naïve contact hamster to each donor. Following exposure, the nasal turbinates, trachea, and lungs were collected, viral titers were measured, and the number of barcodes in each tissue were enumerated to quantify the transmission bottleneck. The duration and route (airborne, direct contact, and fomite) of exposure were varied to assess their impact on the transmission bottleneck. In airborne-exposed hamsters, the transmission bottleneck increased with longer exposure durations. We found that direct contact exposure produced the largest transmission bottleneck (average 27 BCs), followed by airborne exposure (average 16 BCs) then fomite exposure (average 8 BCs). Interestingly, we detected unique BCs in both the upper and lower respiratory tract of contact animals from all routes of exposure, suggesting that SARS-CoV-2 can directly infect hamster lungs. Altogether, these findings highlight the utility of barcoded viruses as tools to rigorously study virus transmission. In the future, barcoded SARS-CoV-2 will strengthen studies of immune factors that influence virus transmission.
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Affiliation(s)
- Reed Trende
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, MO 63110, USA
| | - Tamarand L. Darling
- Department of Medicine, Washington University School of Medicine in St. Louis, MO 63110, USA
| | - Tianyu Gan
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, MO 63110, USA
| | - David Wang
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, MO 63110, USA
| | - Adrianus C.M. Boon
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, MO 63110, USA
- Department of Medicine, Washington University School of Medicine in St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, MO 63110, USA
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5
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Du H, Du Z, Wang L, Wang H, Jia M, Zhang C, Liu Y, Zhang C, Zhang Y, Zhang R, Zhang S, Zhang N, Ma Z, Chen C, Liu W, Zeng H, Gao GF, Hou X, Bi Y. Fulminant myocarditis induced by SARS-CoV-2 infection without severe lung involvement: insights into COVID-19 pathogenesis. J Genet Genomics 2024; 51:608-616. [PMID: 38447818 DOI: 10.1016/j.jgg.2024.02.007] [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: 11/17/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/08/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection often leads to pulmonary complications. Cardiovascular sequelae, including myocarditis and heart failure, have also been reported. Here, the study presents two fulminant myocarditis cases infected by SARS-CoV-2 exhibiting remarkable elevation of cardiac biomarkers without significant pulmonary injury, as determined by imaging examinations. Immunohistochemical staining reveals the viral antigen within cardiomyocytes, indicating that SARS-CoV-2 could directly infect the myocardium. The full viral genomes from respiratory, anal, and myocardial specimens are obtained via next-generation sequencing. Phylogenetic analyses of the whole genome and spike gene indicate that viruses in the myocardium/pericardial effusion and anal swabs are closely related and cluster together yet diverge from those in the respiratory samples. In addition, unique mutations are found in the anal/myocardial strains compared to the respiratory strains, suggesting tissue-specific virus mutation and adaptation. These findings indicate genetically distinct SARS-CoV-2 variants have infiltrated and disseminated within myocardial tissues, independent of pulmonary injury, and point to different infection routes between the myocardium and respiratory tract, with myocardial infections potentially arising from intestinal infection. These findings highlight the potential for systemic SARS-CoV-2 infection and the importance of a thorough multi-organ assessment in patients for a comprehensive understanding of the pathogenesis of COVID-19.
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Affiliation(s)
- Han Du
- College of Life Science and Technology, Xinjiang University, Urumchi, Xinjiang 830046, China; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China
| | - Zhongtao Du
- Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China
| | - Liang Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China
| | - Hong Wang
- Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China
| | - Mingjun Jia
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China; College of Veterinary Medicine, Shanxi Agricultural University, Taiyuan, Shanxi 030031, China
| | - Chunge Zhang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China; College of Veterinary Medicine, Shanxi Agricultural University, Taiyuan, Shanxi 030031, China
| | - Cheng Zhang
- College of Life Science and Technology, Xinjiang University, Urumchi, Xinjiang 830046, China; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China
| | - Ya Zhang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China
| | - Ruifeng Zhang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China
| | - Shuang Zhang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China
| | - Ning Zhang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenghai Ma
- College of Life Science and Technology, Xinjiang University, Urumchi, Xinjiang 830046, China
| | - Chen Chen
- Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Wenjun Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Zeng
- Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China.
| | - George F Gao
- College of Life Science and Technology, Xinjiang University, Urumchi, Xinjiang 830046, China; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiaotong Hou
- Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China.
| | - Yuhai Bi
- College of Life Science and Technology, Xinjiang University, Urumchi, Xinjiang 830046, China; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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6
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Sayama Y, Sakagami A, Okamoto M, Sakamoto M, Koizumi H, Kimura Y, Dapat C, Saito M, Suzuki Y, Sasaki M, Sugawara N, Oshitani H. Identification of Various Recombinants in a Patient Coinfected With the Different SARS-CoV-2 Variants. Influenza Other Respir Viruses 2024; 18:e13340. [PMID: 38890805 PMCID: PMC11187932 DOI: 10.1111/irv.13340] [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: 10/12/2023] [Revised: 03/18/2024] [Accepted: 05/30/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Viral recombination that occurs by exchanging genetic materials between two viral genomes coinfecting the same host cells is associated with the emergence of new viruses with different virulence. Herein, we detected a patient coinfected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta and Omicron variants and identified various recombinants in the SARS-CoV-2 full-length spike gene using long-read and Sanger sequencing. METHODS Samples from five patients in Japan with household transmission of coronavirus disease 2019 (COVID-19) were analyzed using molecular assays for detection and identification of SARS-CoV-2. Whole-genome sequencing was conducted using multiplex PCR with short-read sequencing. RESULTS Among the five SARS-CoV-2-positive patients, the mutation-specific assay identified the Delta variant in three, the Omicron variant in one, and an undetermined in one. The undermined patient was identified as Delta using whole-genome sequencing, but samples showed a mixed population of Delta and Omicron variants. This patient was analyzed for viral quasispecies by long-read and Sanger sequencing using a full-length spike gene amplicon. In addition to the Delta and Omicron sequences, the viral quasispecies analysis identified nine different genetic recombinant sequences with various breakpoints between Delta and Omicron sequences. The nine detected recombinant sequences in the spike gene showed over 99% identity with viruses that were detected during the Delta and Omicron cocirculation period from the United States and Europe. CONCLUSIONS This study demonstrates that patients coinfected with different SARS-CoV-2 variants can generate various viral recombinants and that various recombinant viruses may be produced during the cocirculation of different variants.
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Affiliation(s)
- Yusuke Sayama
- Department of VirologyTohoku University of Graduate School of MedicineSendaiMiyagiJapan
| | - Akie Sakagami
- Department of MicrobiologyMiyagi Prefectural Institute of Public Health and EnvironmentSendaiMiyagiJapan
| | - Michiko Okamoto
- Department of VirologyTohoku University of Graduate School of MedicineSendaiMiyagiJapan
| | - Masahiro Sakamoto
- Department of VirologyTohoku University of Graduate School of MedicineSendaiMiyagiJapan
| | - Hikari Koizumi
- Department of MicrobiologyMiyagi Prefectural Institute of Public Health and EnvironmentSendaiMiyagiJapan
| | - Yoko Kimura
- Department of MicrobiologyMiyagi Prefectural Institute of Public Health and EnvironmentSendaiMiyagiJapan
| | - Clyde Dapat
- Department of VirologyTohoku University of Graduate School of MedicineSendaiMiyagiJapan
| | - Mayuko Saito
- Department of VirologyTohoku University of Graduate School of MedicineSendaiMiyagiJapan
| | - Yuko Suzuki
- Department of MicrobiologyMiyagi Prefectural Institute of Public Health and EnvironmentSendaiMiyagiJapan
| | - Mie Sasaki
- Department of MicrobiologyMiyagi Prefectural Institute of Public Health and EnvironmentSendaiMiyagiJapan
| | - Naoko Sugawara
- Department of MicrobiologyMiyagi Prefectural Institute of Public Health and EnvironmentSendaiMiyagiJapan
| | - Hitoshi Oshitani
- Department of VirologyTohoku University of Graduate School of MedicineSendaiMiyagiJapan
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7
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Williams RC, Farkas K, Garcia-Delgado A, Adwan L, Kevill JL, Cross G, Weightman AJ, Jones DL. Simultaneous detection and characterization of common respiratory pathogens in wastewater through genomic sequencing. WATER RESEARCH 2024; 256:121612. [PMID: 38642537 DOI: 10.1016/j.watres.2024.121612] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 04/22/2024]
Abstract
Genomic surveillance of SARS-CoV-2 has given insight into the evolution and epidemiology of the virus and its variant lineages during the COVID-19 pandemic. Expanding this approach to include a range of respiratory pathogens can better inform public health preparedness for potential outbreaks and epidemics. Here, we simultaneously sequenced 38 pathogens including influenza viruses, coronaviruses and bocaviruses, to examine the abundance and seasonality of respiratory pathogens in urban wastewater. We deployed a targeted bait capture method and short-read sequencing (Illumina Respiratory Virus Oligos Panel; RVOP) on composite wastewater samples from 8 wastewater treatment plants (WWTPs) and one associated hospital site. By combining seasonal sampling with whole genome sequencing, we were able to concurrently detect and characterise a range of common respiratory pathogens, including SARS-CoV-2, adenovirus and parainfluenza virus. We demonstrated that 38 respiratory pathogens can be detected at low abundances year-round, that hospital pathogen diversity is higher in winter vs. summer sampling events, and that significantly more viruses are detected in raw influent compared to treated effluent samples. Finally, we compared detection sensitivity of RT-qPCR vs. next generation sequencing for SARS-CoV-2, enteroviruses, influenza A/B, and respiratory syncytial viruses. We conclude that both should be used in combination; RT-qPCR allowed accurate quantification, whilst genomic sequencing detected pathogens at lower abundance. We demonstrate the valuable role of wastewater genomic surveillance and its contribution to the field of wastewater-based epidemiology, gaining rapid understanding of the seasonal presence and persistence for common respiratory pathogens. By simultaneously monitoring seasonal trends and early warning signs of many viruses circulating in communities, public health agencies can implement targeted prevention and rapid response plans.
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Affiliation(s)
- Rachel C Williams
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK.
| | - Kata Farkas
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Alvaro Garcia-Delgado
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Latifah Adwan
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Jessica L Kevill
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Gareth Cross
- Science Evidence Advice Division, Health and Social Services Group, Welsh Government, Cathays Park, Cardiff, CF10 3NQ, UK
| | - Andrew J Weightman
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK
| | - Davey L Jones
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; Food Futures Institute, Murdoch University, Murdoch WA 6150, Australia
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8
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Tonon E, Cecchetto R, Diani E, Medaina N, Turri G, Lagni A, Lotti V, Gibellini D. Surfing the Waves of SARS-CoV-2: Analysis of Viral Genome Variants Using an NGS Survey in Verona, Italy. Microorganisms 2024; 12:846. [PMID: 38792676 PMCID: PMC11124265 DOI: 10.3390/microorganisms12050846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/16/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
The availability of new technologies for deep sequencing, including next-generation sequencing (NGS), allows for the detection of viral genome variations. The epidemiological determination of SARS-CoV-2 viral genome changes during the pandemic waves displayed the genome evolution and subsequent onset of variants over time. These variants were often associated with a different impact on viral transmission and disease severity. We investigated, in a retrospective study, the trend of SARS-CoV-2-positive samples collected from the start of the Italian pandemic (January 2020) to June 2023. In addition, viral RNAs extracted from 938 nasopharyngeal swab samples were analyzed using NGS between February 2022 and June 2023. Sequences were analyzed with bioinformatic tools to identify lineages and mutations and for phylogenetic studies. Six pandemic waves were detected. In our samples, we predominantly detected BA.2, BQ.1, BA.5.1, BA.5.2, and, more recently, XBB.1 and its subvariants. The data describe the SARS-CoV-2 genome evolution involved in viral interactions with the host and the dynamics of specific genome mutations and deletions.
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Affiliation(s)
- Emil Tonon
- Department of Diagnostic and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy; (E.T.); (R.C.); (A.L.); (V.L.); (D.G.)
- UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy; (N.M.); (G.T.)
| | - Riccardo Cecchetto
- Department of Diagnostic and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy; (E.T.); (R.C.); (A.L.); (V.L.); (D.G.)
- UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy; (N.M.); (G.T.)
| | - Erica Diani
- Department of Diagnostic and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy; (E.T.); (R.C.); (A.L.); (V.L.); (D.G.)
- UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy; (N.M.); (G.T.)
| | - Nicoletta Medaina
- UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy; (N.M.); (G.T.)
| | - Giona Turri
- UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy; (N.M.); (G.T.)
| | - Anna Lagni
- Department of Diagnostic and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy; (E.T.); (R.C.); (A.L.); (V.L.); (D.G.)
| | - Virginia Lotti
- Department of Diagnostic and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy; (E.T.); (R.C.); (A.L.); (V.L.); (D.G.)
| | - Davide Gibellini
- Department of Diagnostic and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy; (E.T.); (R.C.); (A.L.); (V.L.); (D.G.)
- UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy; (N.M.); (G.T.)
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9
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Alfonsi T, Bernasconi A, Chiara M, Ceri S. Data-driven recombination detection in viral genomes. Nat Commun 2024; 15:3313. [PMID: 38632281 PMCID: PMC11024102 DOI: 10.1038/s41467-024-47464-5] [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: 07/18/2023] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
Recombination is a key molecular mechanism for the evolution and adaptation of viruses. The first recombinant SARS-CoV-2 genomes were recognized in 2021; as of today, more than ninety SARS-CoV-2 lineages are designated as recombinant. In the wake of the COVID-19 pandemic, several methods for detecting recombination in SARS-CoV-2 have been proposed; however, none could faithfully confirm manual analyses by experts in the field. We hereby present RecombinHunt, an original data-driven method for the identification of recombinant genomes, capable of recognizing recombinant SARS-CoV-2 genomes (or lineages) with one or two breakpoints with high accuracy and within reduced turn-around times. ReconbinHunt shows high specificity and sensitivity, compares favorably with other state-of-the-art methods, and faithfully confirms manual analyses by experts. RecombinHunt identifies recombinant viral genomes from the recent monkeypox epidemic in high concordance with manually curated analyses by experts, suggesting that our approach is robust and can be applied to any epidemic/pandemic virus.
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Affiliation(s)
- Tommaso Alfonsi
- Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Via Ponzio 34/5, 20133, Milan, Italy
| | - Anna Bernasconi
- Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Via Ponzio 34/5, 20133, Milan, Italy.
| | - Matteo Chiara
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Stefano Ceri
- Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Via Ponzio 34/5, 20133, Milan, Italy
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10
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Luong QXT, Hoang PT, Lee Y, Ayun RQ, Na K, Park S, Lin C, Ho PT, Lee TK, Lee S. An RNA-hydrolyzing recombinant minibody prevents both influenza A virus and coronavirus in co-infection models. Sci Rep 2024; 14:8472. [PMID: 38605110 PMCID: PMC11009316 DOI: 10.1038/s41598-024-52810-0] [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: 08/17/2023] [Accepted: 01/23/2024] [Indexed: 04/13/2024] Open
Abstract
With the lifting of COVID-19 non-pharmaceutical interventions, the resurgence of common viral respiratory infections was recorded in several countries worldwide. It facilitates viral co-infection, further burdens the already over-stretched healthcare systems. Racing to find co-infection-associated efficacy therapeutic agents need to be rapidly established. However, it has encountered numerous challenges that necessitate careful investigation. Here, we introduce a potential recombinant minibody-associated treatment, 3D8 single chain variable fragment (scFv), which has been developed as a broad-spectrum antiviral drug that acts via its nucleic acid catalytic and cell penetration abilities. In this research, we demonstrated that 3D8 scFv exerted antiviral activity simultaneously against both influenza A viruses (IAVs) and coronaviruses in three established co-infection models comprising two types of coronaviruses [beta coronavirus-human coronavirus OC43 (hCoV-OC43) and alpha coronavirus-porcine epidemic diarrhea virus (PEDV)] in Vero E6 cells, two IAVs [A/Puerto Rico/8/1934 H1N1 (H1N1/PR8) and A/X-31 (H3N2/X-31)] in MDCK cells, and a combination of coronavirus and IAV (hCoV-OC43 and adapted-H1N1) in Vero E6 cells by a statistically significant reduction in viral gene expression, proteins level, and approximately around 85%, 65%, and 80% of the progeny of 'hCoV-OC43-PEDV', 'H1N1/PR8-H3N2/X-31', and 'hCoV-OC43-adapted-H1N1', respectively, were decimated in the presence of 3D8 scFv. Taken together, we propose that 3D8 scFv is a promising broad-spectrum drug for treatment against RNA viruses in co-infection.
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Affiliation(s)
- Quynh Xuan Thi Luong
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Korea
| | - Phuong Thi Hoang
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Korea
| | - Yongjun Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Korea
| | | | - Kyungho Na
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Korea
| | - Seonhyeon Park
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Korea
| | - Chengmin Lin
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Korea
| | - Phuong Thi Ho
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Korea
| | - Taek-Kyun Lee
- Ecological Risk Research Department, Korea Institute of Ocean Science & Technology, Geoje, 53201, Korea.
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Korea.
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11
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Connor R, Shakya M, Yarmosh DA, Maier W, Martin R, Bradford R, Brister JR, Chain PSG, Copeland CA, di Iulio J, Hu B, Ebert P, Gunti J, Jin Y, Katz KS, Kochergin A, LaRosa T, Li J, Li PE, Lo CC, Rashid S, Maiorova ES, Xiao C, Zalunin V, Purcell L, Pruitt KD. Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows. Viruses 2024; 16:430. [PMID: 38543795 PMCID: PMC10975397 DOI: 10.3390/v16030430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/12/2024] [Accepted: 02/16/2024] [Indexed: 04/01/2024] Open
Abstract
Genomic sequencing of clinical samples to identify emerging variants of SARS-CoV-2 has been a key public health tool for curbing the spread of the virus. As a result, an unprecedented number of SARS-CoV-2 genomes were sequenced during the COVID-19 pandemic, which allowed for rapid identification of genetic variants, enabling the timely design and testing of therapies and deployment of new vaccine formulations to combat the new variants. However, despite the technological advances of deep sequencing, the analysis of the raw sequence data generated globally is neither standardized nor consistent, leading to vastly disparate sequences that may impact identification of variants. Here, we show that for both Illumina and Oxford Nanopore sequencing platforms, downstream bioinformatic protocols used by industry, government, and academic groups resulted in different virus sequences from same sample. These bioinformatic workflows produced consensus genomes with differences in single nucleotide polymorphisms, inclusion and exclusion of insertions, and/or deletions, despite using the same raw sequence as input datasets. Here, we compared and characterized such discrepancies and propose a specific suite of parameters and protocols that should be adopted across the field. Consistent results from bioinformatic workflows are fundamental to SARS-CoV-2 and future pathogen surveillance efforts, including pandemic preparation, to allow for a data-driven and timely public health response.
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Affiliation(s)
- Ryan Connor
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (R.C.); (J.R.B.); (J.G.); (Y.J.); (K.S.K.); (A.K.); (C.X.); (V.Z.)
| | - Migun Shakya
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (M.S.); (P.S.G.C.); (B.H.); (P.-E.L.); (C.-C.L.)
| | - David A. Yarmosh
- American Type Culture Collection, Manassas, VA 20110, USA; (D.A.Y.); (R.B.); (S.R.)
- BEI Resources, Manassas, VA 20110, USA
| | - Wolfgang Maier
- Galaxy Europe Team, University of Freiburg, 79085 Freiburg, Germany;
| | - Ross Martin
- Clinical Virology Department, Gilead Sciences, Foster City, CA 94404, USA; (R.M.); (J.L.); (E.S.M.)
| | - Rebecca Bradford
- American Type Culture Collection, Manassas, VA 20110, USA; (D.A.Y.); (R.B.); (S.R.)
- BEI Resources, Manassas, VA 20110, USA
| | - J. Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (R.C.); (J.R.B.); (J.G.); (Y.J.); (K.S.K.); (A.K.); (C.X.); (V.Z.)
| | - Patrick S. G. Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (M.S.); (P.S.G.C.); (B.H.); (P.-E.L.); (C.-C.L.)
| | | | - Julia di Iulio
- Vir Biotechnology Inc., San Francisco, CA 94158, USA; (J.d.I.); (L.P.)
| | - Bin Hu
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (M.S.); (P.S.G.C.); (B.H.); (P.-E.L.); (C.-C.L.)
| | - Philip Ebert
- Eli Lilly and Company, Indianapolis, IN 46225, USA;
| | - Jonathan Gunti
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (R.C.); (J.R.B.); (J.G.); (Y.J.); (K.S.K.); (A.K.); (C.X.); (V.Z.)
| | - Yumi Jin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (R.C.); (J.R.B.); (J.G.); (Y.J.); (K.S.K.); (A.K.); (C.X.); (V.Z.)
| | - Kenneth S. Katz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (R.C.); (J.R.B.); (J.G.); (Y.J.); (K.S.K.); (A.K.); (C.X.); (V.Z.)
| | - Andrey Kochergin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (R.C.); (J.R.B.); (J.G.); (Y.J.); (K.S.K.); (A.K.); (C.X.); (V.Z.)
| | - Tré LaRosa
- Deloitte Consulting LLP, Rosslyn, VA 22209, USA; (C.A.C.); (T.L.)
| | - Jiani Li
- Clinical Virology Department, Gilead Sciences, Foster City, CA 94404, USA; (R.M.); (J.L.); (E.S.M.)
| | - Po-E Li
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (M.S.); (P.S.G.C.); (B.H.); (P.-E.L.); (C.-C.L.)
| | - Chien-Chi Lo
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (M.S.); (P.S.G.C.); (B.H.); (P.-E.L.); (C.-C.L.)
| | - Sujatha Rashid
- American Type Culture Collection, Manassas, VA 20110, USA; (D.A.Y.); (R.B.); (S.R.)
| | - Evguenia S. Maiorova
- Clinical Virology Department, Gilead Sciences, Foster City, CA 94404, USA; (R.M.); (J.L.); (E.S.M.)
| | - Chunlin Xiao
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (R.C.); (J.R.B.); (J.G.); (Y.J.); (K.S.K.); (A.K.); (C.X.); (V.Z.)
| | - Vadim Zalunin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (R.C.); (J.R.B.); (J.G.); (Y.J.); (K.S.K.); (A.K.); (C.X.); (V.Z.)
| | - Lisa Purcell
- Vir Biotechnology Inc., San Francisco, CA 94158, USA; (J.d.I.); (L.P.)
| | - Kim D. Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (R.C.); (J.R.B.); (J.G.); (Y.J.); (K.S.K.); (A.K.); (C.X.); (V.Z.)
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12
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Pipek OA, Medgyes-Horváth A, Stéger J, Papp K, Visontai D, Koopmans M, Nieuwenhuijse D, Oude Munnink BB, Csabai I. Systematic detection of co-infection and intra-host recombination in more than 2 million global SARS-CoV-2 samples. Nat Commun 2024; 15:517. [PMID: 38225254 PMCID: PMC10789779 DOI: 10.1038/s41467-023-43391-z] [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: 07/11/2023] [Accepted: 11/06/2023] [Indexed: 01/17/2024] Open
Abstract
Systematic monitoring of SARS-CoV-2 co-infections between different lineages and assessing the risk of intra-host recombinant emergence are crucial for forecasting viral evolution. Here we present a comprehensive analysis of more than 2 million SARS-CoV-2 raw read datasets submitted to the European COVID-19 Data Portal to identify co-infections and intra-host recombination. Co-infection was observed in 0.35% of the investigated cases. Two independent procedures were implemented to detect intra-host recombination. We show that sensitivity is predominantly determined by the density of lineage-defining mutations along the genome, thus we used an expanded list of mutually exclusive defining mutations of specific variant combinations to increase statistical power. We call attention to multiple challenges rendering recombinant detection difficult and provide guidelines for the reduction of false positives arising from chimeric sequences produced during PCR amplification. Additionally, we identify three recombination hotspots of Delta - Omicron BA.1 intra-host recombinants.
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Affiliation(s)
- Orsolya Anna Pipek
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
| | - Anna Medgyes-Horváth
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary.
| | - József Stéger
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
| | - Krisztián Papp
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
| | - Dávid Visontai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
| | - Marion Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - David Nieuwenhuijse
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - István Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
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13
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Kandeel A, Fahim M, Deghedy O, BahaaEldin H, Roshdy WH, Khalifa MK, Kandeil A, El Shesheny R, Naguib A, AbdelFatah M, Afifi S, Abdel Ghaffar K. Comparative analysis of COVID-19 and influenza prevalence among Egyptian pilgrims returning from Hajj and Umrah in 2022: epidemiology, clinical characteristics, and genomic sequencing. Arch Public Health 2024; 82:6. [PMID: 38216978 PMCID: PMC10785524 DOI: 10.1186/s13690-023-01229-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 12/14/2023] [Indexed: 01/14/2024] Open
Abstract
PURPOSE To describe the changes that occurred in the SARS-CoV-2 and influenza Prevalence, epidemiology, clinical picture, and prevalent genotypes among the Egyptian pilgrims returning from Hajj and Umrah 2022 seasons. METHODS Pilgrims were contacted at the airport and invited to participate in the survey. Pilgrims who consented were interviewed using a standardized line list that included participant demographics, respiratory symptoms if any, previous COVID-19 infection, influenza vaccination whereas COVID-19 vaccination information were collected from vaccination cards. Participants were asked to provide throat and nasopharyngeal swabs for SARS-CoV-2 and influenza testing using RT-PCR and a subset of isolates were sequenced. Descriptive data analysis was performed to describe the epidemiology and clinical symptoms of SARS-CoV-2 and influenza. Prevalence rates of SARS-CoV-2 and influenza during Hajj were calculated and compared to Umrah surveys using chi2 and t-test with a significance level < 0.05. RESULTS Overall, 3,862 Egyptian pilgrims enrolled, their mean age was 50.5 ± 47 years, half of them were > 50 years of age and 58.2% were males. Of them, 384 (9.9%) tested positive for SARS-CoV-2 and 51 (1.3%) for influenza viruses. Prevalence of SARS-CoV-2 infections (vaccine breakthrough) increased significantly between the Umrah and Hajj surveys (6.7% vs. 9.9%, p < 0.001), and variants of the virus varied considerably. Whereas no significant difference was found in influenza prevalence, vaccine coverage and vaccine breakthrough infection rates (11.7 vs. 9.2%, 26.9 vs. 26.8%, and 1.4 vs. 1.1% respectively). CONCLUSIONS SARS-CoV-2 prevalence among Egyptian pilgrims returning from Hajj in July increased with reduced vaccine effectiveness compared to Umrah in March 2022 suggesting a possible wave of SARS-CoV-2 in the upcoming winter.
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Affiliation(s)
- Amr Kandeel
- Preventive Sector, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Manal Fahim
- Department of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Ola Deghedy
- Department of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Hala BahaaEldin
- Department of Epidemiology and Surveillance, Preventive Sector, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt.
| | - Wael H Roshdy
- Central Public Health Laboratory, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Mohamed Kamal Khalifa
- Central Public Health Laboratory, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Ahmed Kandeil
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, 12622 Dokki, Giza, Egypt
| | - Rabeh El Shesheny
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, 12622 Dokki, Giza, Egypt
| | - Amel Naguib
- Central Public Health Laboratory, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Mohamad AbdelFatah
- Preventive Sector, Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Salma Afifi
- Ministry of Health and Population Consultant, Governmental District, New Administrative Capital, Cairo, Egypt
| | - Khaled Abdel Ghaffar
- Ministry of Health and Population, Governmental District, New Administrative Capital, Cairo, Egypt
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14
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Lam C, Johnson-Mackinnon J, Basile K, Fong W, Suster CJ, Gall M, Agius J, Chandra S, Draper J, Martinez E, Drew A, Wang Q, Chen SC, Kok J, Dwyer DE, Sintchenko V, Rockett RJ. A laboratory framework for ongoing optimization of amplification-based genomic surveillance programs. Microbiol Spectr 2023; 11:e0220223. [PMID: 37966271 PMCID: PMC10715188 DOI: 10.1128/spectrum.02202-23] [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: 05/24/2023] [Accepted: 10/13/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE This study provides a laboratory framework to ensure ongoing relevance and performance of amplification-based whole genome sequencing to strengthen public health surveillance during extended outbreaks or pandemics. The framework integrates regular reviews of the performance of a genomic surveillance system and highlights the importance of ongoing monitoring and the identification and implementation of improvements to whole genome sequencing methods to enhance public health responses to pathogen outbreaks.
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Affiliation(s)
- Connie Lam
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Jessica Johnson-Mackinnon
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Kerri Basile
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
| | - Winkie Fong
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Carl J.E. Suster
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Mailie Gall
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Jessica Agius
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Shona Chandra
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Jenny Draper
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Elena Martinez
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Alexander Drew
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Sharon C. Chen
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Dominic E. Dwyer
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Rebecca J. Rockett
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
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15
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Diotallevi A, Buffi G, Barocci S, Ceccarelli M, Bencardino D, Andreoni F, Orlandi C, Ferri M, Vandini D, Menzo S, Carlotti E, Casabianca A, Magnani M, Galluzzi L. Rapid monitoring of SARS-CoV-2 variants of concern through high-resolution melt analysis. Sci Rep 2023; 13:21598. [PMID: 38062105 PMCID: PMC10703772 DOI: 10.1038/s41598-023-48929-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
The current global pandemic of COVID-19 is characterized by waves of infection due to the emergence of new SARS-CoV-2 variants carrying mutations on the Spike (S) protein gene. Since autumn 2020 many Variants of Concern (VOC) have been reported: Alpha/B.1.1.7, Beta/B.1.351, Gamma/P.1, Delta/B.1.617.2, Omicron/B.1.1.529, and sublineages. Surveillance of genomic variants is currently based on whole-genome sequencing (WGS) of viral genomes on a random fraction of samples positive to molecular tests. WGS involves high costs, extended analysis time, specialized staff, and expensive instruments compared to a PCR-based test. To rapidly identify the VOCs in positive samples, six assays based on real-time PCR and high-resolution melting (HRM) were designed on the S gene and applied to 120 oro/nasopharyngeal swab samples collected from October 2020 to June 2022 (106 positive and 14 negative samples). Overall, the assays showed 100% specificity and sensitivity compared with commercial PCR tests for COVID-19. Moreover, 104 samples out of 106 (98.1%) were correctly identified as follows: 8 Wuhan (wild type), 12 Alpha, 23 Delta, 46 Omicron BA.1/BA.1.1, 15 Omicron BA.2/BA.4/BA.5. With our lab equipment, about 10 samples can be processed every 3 h at the cost of less than € 10 ($ 10.60) per sample, including RNA extraction. The implementation of this approach could help local epidemiological surveillance and clinical decision-making.
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Affiliation(s)
- Aurora Diotallevi
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy.
| | - Gloria Buffi
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
| | - Simone Barocci
- Department of Clinical Pathology, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino, Marche, 61029, Urbino, PU, Italy
| | - Marcello Ceccarelli
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
- Department of Clinical Pathology, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino, Marche, 61029, Urbino, PU, Italy
| | - Daniela Bencardino
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
| | - Francesca Andreoni
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
- Department of Clinical Pathology, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino, Marche, 61029, Urbino, PU, Italy
| | - Chiara Orlandi
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
| | - Marilisa Ferri
- Department of Clinical Pathology, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino, Marche, 61029, Urbino, PU, Italy
| | - Daniela Vandini
- Department of Clinical Pathology, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino, Marche, 61029, Urbino, PU, Italy
| | - Stefano Menzo
- Virology Laboratory, Azienda Ospedaliero Universitaria delle Marche, 60126, Ancona, AN, Italy
| | - Eugenio Carlotti
- Department of Prevention, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino Marche, 61029, Urbino, PU, Italy
| | - Anna Casabianca
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
| | - Mauro Magnani
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
| | - Luca Galluzzi
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
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Ramos-Mandujano G, Grünberg R, Zhang Y, Bi C, Guzmán-Vega FJ, Shuaib M, Gorchakov RV, Xu J, Tehseen M, Takahashi M, Takahashi E, Dada A, Ahmad AN, Hamdan SM, Pain A, Arold ST, Li M. An open-source, automated, and cost-effective platform for COVID-19 diagnosis and rapid portable genomic surveillance using nanopore sequencing. Sci Rep 2023; 13:20349. [PMID: 37990068 PMCID: PMC10663496 DOI: 10.1038/s41598-023-47190-w] [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: 05/09/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023] Open
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, has emphasized the necessity for scalable diagnostic workflows using locally produced reagents and basic laboratory equipment with minimal dependence on global supply chains. We introduce an open-source automated platform for high-throughput RNA extraction and pathogen diagnosis, which uses reagents almost entirely produced in-house. This platform integrates our methods for self-manufacturing magnetic nanoparticles and qRT-PCR reagents-both of which have received regulatory approval for clinical use-with an in-house, open-source robotic extraction protocol. It also incorporates our "Nanopore Sequencing of Isothermal Rapid Viral Amplification for Near Real-time Analysis" (NIRVANA) technology, designed for tracking SARS-CoV-2 mutations and variants. The platform exhibits high reproducibility and consistency without cross-contamination, and its limit of detection, sensitivity, and specificity are comparable to commercial assays. Automated NIRVANA effectively identifies circulating SARS-CoV-2 variants. Our in-house, cost-effective reagents, automated diagnostic workflows, and portable genomic surveillance strategies provide a scalable and rapid solution for COVID-19 diagnosis and variant tracking, essential for current and future pandemic responses.
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Affiliation(s)
- Gerardo Ramos-Mandujano
- Stem Cell and Regeneration Laboratory, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Raik Grünberg
- Structural Biology and Engineering, Computational Biology Research Center. Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Yingzi Zhang
- Stem Cell and Regeneration Laboratory, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Chongwei Bi
- Stem Cell and Regeneration Laboratory, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Francisco J Guzmán-Vega
- Structural Biology and Engineering, Computational Biology Research Center. Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Muhammad Shuaib
- Pathogen Genomics Laboratory, Bioscience Program, Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Rodion V Gorchakov
- Health, Safety and Environment Department, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Jinna Xu
- Stem Cell and Regeneration Laboratory, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Muhammad Tehseen
- Laboratory of DNA Replication and Recombination, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Masateru Takahashi
- Laboratory of DNA Replication and Recombination, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Etsuko Takahashi
- Laboratory of DNA Replication and Recombination, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Ashraf Dada
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Kingdom of Saudi Arabia
- College of Medicine, Al Faisal University, Riyadh, Kingdom of Saudi Arabia
| | - Adeel Nazir Ahmad
- KAUST Health, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Samir M Hamdan
- Laboratory of DNA Replication and Recombination, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Arnab Pain
- Pathogen Genomics Laboratory, Bioscience Program, Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Stefan T Arold
- Structural Biology and Engineering, Computational Biology Research Center. Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia.
| | - Mo Li
- Stem Cell and Regeneration Laboratory, Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia.
- Bioengineering Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia.
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17
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Alisoltani A, Simons LM, Agnes MFR, Heald-Sargent TA, Muller WJ, Kociolek LK, Hultquist JF, Lorenzo-Redondo R, Ozer EA. Resurgence of SARS-CoV-2 Delta after Omicron variant superinfection in an immunocompromised pediatric patient. Virol J 2023; 20:246. [PMID: 37891657 PMCID: PMC10604949 DOI: 10.1186/s12985-023-02186-w] [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: 06/30/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Persistent SARS-CoV-2 infection in immunocompromised hosts is thought to contribute to viral evolution by facilitating long-term natural selection and viral recombination in cases of viral co-infection or superinfection. However, there are limited data on the longitudinal intra-host population dynamics of SARS-CoV-2 co-infection/superinfection, especially in pediatric populations. Here, we report a case of Delta-Omicron superinfection in a hospitalized, immunocompromised pediatric patient. METHODS We conducted Illumina whole genome sequencing (WGS) for longitudinal specimens to investigate intra-host dynamics of SARS-CoV-2 strains. Topoisomerase PCR cloning of Spike open-reading frame and Sanger sequencing of samples was performed for four specimens to validate the findings. Analysis of publicly available SARS-CoV-2 sequence data was performed to investigate the co-circulation and persistence of SARS-CoV-2 variants. RESULTS Results of WGS indicate the patient was initially infected with the SARS-CoV-2 Delta variant before developing a SARS-CoV-2 Omicron variant superinfection, which became predominant. Shortly thereafter, viral loads decreased below the level of detection before resurgence of the original Delta variant with no residual trace of Omicron. After 54 days of persistent infection, the patient tested negative for SARS-CoV-2 but ultimately succumbed to a COVID-19-related death. Despite protracted treatment with remdesivir, no antiviral resistance mutations emerged. These results indicate a unique case of persistent SARS-CoV-2 infection with the Delta variant interposed by a transient superinfection with the Omicron variant. Analysis of publicly available sequence data suggests the persistence and ongoing evolution of Delta subvariants despite the global predominance of Omicron, potentially indicative of continued transmission in an unknown population or niche. CONCLUSION A better understanding of SARS-CoV-2 intra-host population dynamics, persistence, and evolution during co-infections and/or superinfections will be required to continue optimizing patient care and to better predict the emergence of new variants of concern.
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Affiliation(s)
- Arghavan Alisoltani
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | - Lacy M Simons
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | - Maria Francesca Reyes Agnes
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | | | - William J Muller
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA
| | - Larry K Kociolek
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA
| | - Judd F Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA
| | - Egon A Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA.
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18
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Basak S, Kayet P, Ghosh M, Chatterjee J, Dutta S. Emergence of Genomic Diversity in the Spike Protein of the "Omicron" Variant. Viruses 2023; 15:2132. [PMID: 37896909 PMCID: PMC10612054 DOI: 10.3390/v15102132] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus) has constantly been evolving into different forms throughout its spread in the population. Emerging SARS-CoV-2 variants, predominantly the variants of concern (VOCs), could have an impact on the virus spread, pathogenicity, and diagnosis. The recently emerged "Omicron" variant has exhibited rapid transmission and divergence. The spike protein of SARS-CoV-2 has consistently been appearing as the mutational hotspot of all these VOCs. In order to determine a deeper understanding of the recently emerged and extremely divergent "Omicron", a study of amino acid usage patterns and their substitution patterns was performed and compared with those of the other four successful variants of concern ("Alpha", "Beta", "Gamma", and "Delta"). We observed that the amino acid usage of "Omicron" has a distinct pattern that distinguishes it from other VOCs and is significantly correlated with the increased hydrophobicity in spike proteins. We observed an increase in the non-synonymous substitution rate compared with the other four VOCs. Considering the phylogenetic relationship, we hypothesized about the functional interdependence between recombination and the mutation rate that might have resulted in a shift in the optimum of the mutation rate for the evolution of the "Omicron" variant. The results suggest that for improved disease prevention and control, more attention should be given to the significant genetic differentiation and diversity of newly emerging variants.
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Affiliation(s)
- Surajit Basak
- Division of Bioinformatics, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Pratanu Kayet
- Division of Bioinformatics, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Manisha Ghosh
- Division of Bioinformatics, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Joyeeta Chatterjee
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry 605014, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
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Cecchetto R, Tonon E, Medaina N, Turri G, Diani E, Piccaluga PP, Salomoni A, Conti M, Tacconelli E, Lagni A, Lotti V, Favarato M, Gibellini D. Detection of SARS-CoV-2 Δ426 ORF8 Deletion Mutant Cluster in NGS Screening. Microorganisms 2023; 11:2378. [PMID: 37894036 PMCID: PMC10609088 DOI: 10.3390/microorganisms11102378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/14/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
Next-generation sequencing (NGS) from SARS-CoV-2-positive swabs collected during the last months of 2022 revealed a large deletion spanning ORF7b and ORF8 (426 nt) in six patients infected with the BA.5.1 Omicron variant. This extensive genome loss removed a large part of these two genes, maintaining in frame the first 22 aminoacids of ORF7b and the last three aminoacids of ORF8. Interestingly, the deleted region was flanked by two small repeats, which were likely involved in the formation of a hairpin structure. Similar rearrangements, comparable in size and location to the deletion, were also identified in 15 sequences in the NCBI database. In this group, seven out of 15 cases from the USA and Switzerland presented both the BA.5.1 variant and the same 426 nucleotides deletion. It is noteworthy that three out of six cases were detected in patients with immunodeficiency, and it is conceivable that this clinical condition could promote the replication and selection of these mutations.
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Affiliation(s)
- Riccardo Cecchetto
- Microbiology Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy; (R.C.); (E.T.); (A.L.); (V.L.); (D.G.)
- UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy; (N.M.); (G.T.)
| | - Emil Tonon
- Microbiology Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy; (R.C.); (E.T.); (A.L.); (V.L.); (D.G.)
- UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy; (N.M.); (G.T.)
| | - Nicoletta Medaina
- UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy; (N.M.); (G.T.)
| | - Giona Turri
- UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy; (N.M.); (G.T.)
| | - Erica Diani
- Microbiology Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy; (R.C.); (E.T.); (A.L.); (V.L.); (D.G.)
| | - Pier Paolo Piccaluga
- Hematopathology Section, Department of Experimental, Diagnostic, and Experimental Medicine, Bologna University, 40126 Bologna, Italy;
| | - Angela Salomoni
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, 35020 Padua, Italy;
| | - Michela Conti
- Infectious Diseases Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy; (M.C.); (E.T.)
| | - Evelina Tacconelli
- Infectious Diseases Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy; (M.C.); (E.T.)
| | - Anna Lagni
- Microbiology Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy; (R.C.); (E.T.); (A.L.); (V.L.); (D.G.)
| | - Virginia Lotti
- Microbiology Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy; (R.C.); (E.T.); (A.L.); (V.L.); (D.G.)
| | - Mosé Favarato
- Molecular Diagnostics and Genetics, AULSS 3 Serenissima, 30174 Venice, Italy;
| | - Davide Gibellini
- Microbiology Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy; (R.C.); (E.T.); (A.L.); (V.L.); (D.G.)
- UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy; (N.M.); (G.T.)
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20
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Sim EM, Wang Q, Howard P, Kim R, Lim L, Hope K, Sintchenko V. Persistent Salmonella enterica serovar Typhi sub-populations within host interrogated by whole genome sequencing and metagenomics. PLoS One 2023; 18:e0289070. [PMID: 37611017 PMCID: PMC10446203 DOI: 10.1371/journal.pone.0289070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/10/2023] [Indexed: 08/25/2023] Open
Abstract
Salmonella enterica serovar Typhi (S. Typhi) causes typhoid fever and, in some cases, chronic carriage after resolution of acute disease. This study examined sequential isolates of S. Typhi from a single host with persistent asymptomatic infection. These isolates, along with another S. Typhi isolate recovered from a household contact with typhoid fever, were subjected to whole genome sequencing and analysis. In addition, direct sequencing of the bile fluid from the host with persistent infection was also performed. Comparative analysis of isolates revealed three sub-populations of S. Typhi with distinct genetic patterns. Metagenomic sequencing recognised only two of the three sub-populations within the bile fluid. The detection and investigation of insertion sequences IS10R and associated deletions complemented analysis of single nucleotide polymorphisms. These findings improve our understanding of within-host dynamics of S. Typhi in cases of persistent infection and inform epidemiological investigations of transmission events associated with chronic carriers.
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Affiliation(s)
- Eby M. Sim
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, New South Wales, Australia
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology- Public Health, Westmead Hospital, Westmead, New South Wales, Australia
| | - Qinning Wang
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales, Australia
| | - Peter Howard
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales, Australia
| | - Rady Kim
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales, Australia
| | - Ling Lim
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales, Australia
| | - Kirsty Hope
- Health Protection, New South Wales Ministry of Health, North Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, New South Wales, Australia
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology- Public Health, Westmead Hospital, Westmead, New South Wales, Australia
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21
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Trémeaux P, Latour J, Ranger N, Ferrer V, Harter A, Carcenac R, Boyer P, Demmou S, Nicot F, Raymond S, Izopet J. SARS-CoV-2 Co-Infections and Recombinations Identified by Long-Read Single-Molecule Real-Time Sequencing. Microbiol Spectr 2023; 11:e0049323. [PMID: 37260377 PMCID: PMC10434069 DOI: 10.1128/spectrum.00493-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/09/2023] [Indexed: 06/02/2023] Open
Abstract
Co-infection with at least 2 strains of virus is the prerequisite for recombination, one of the means of genetic diversification. Little is known about the prevalence of these events in SARS-CoV-2, partly because it is difficult to detect them. We used long-read PacBio single-molecule real-time (SMRT) sequencing technology to sequence whole genomes and targeted regions for haplotyping. We identified 17 co-infections with SARS-CoV-2 strains belonging to different clades in 6829 samples sequenced between January and October, 2022 (prevalence 0.25%). There were 3 Delta/Omicron co-infections and 14 Omicron/Omicron co-infections (4 cases of 21K/21L, 1 case of 21L/22A, 2 cases of 21L/22B, 4 cases of 22A/22B, 2 cases of 22B/22C and 1 case of 22B/22E). Four of these patients (24%) also harbored recombinant minor haplotypes, including one with a recombinant virus that was selected in the viral quasispecies over the course of his chronic infection. While co-infections remain rare among SARS-CoV-2-infected individuals, long-read SMRT sequencing is a useful tool for detecting them as well as recombinant events, providing the basis for assessing their clinical impact, and a precise indicator of epidemic evolution. IMPORTANCE SARS-CoV-2 variants have been responsible for the successive waves of infection over the 3 years of pandemic. While co-infection followed by recombination is one driver of virus evolution, there have been few reports of co-infections, mainly between Delta and Omicron variants or between the first 2 Omicron variants 21K_BA.1 and 21L_BA.2. The 17 co-infections we detected during 2022 included cases with the recent clades of Omicron 22A, 22B, 22C, and 22E; 24% harbored recombinant variants. This study shows that long-read SMRT sequencing is well suited to SARS-CoV-2 genomic surveillance.
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Affiliation(s)
- Pauline Trémeaux
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Justine Latour
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Noémie Ranger
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Vénicia Ferrer
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Agnès Harter
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Romain Carcenac
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Pauline Boyer
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Sofia Demmou
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Florence Nicot
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Stéphanie Raymond
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291 – CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
| | - Jacques Izopet
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291 – CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
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22
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Reichmuth ML, Hodcroft EB, Althaus CL. Importation of Alpha and Delta variants during the SARS-CoV-2 epidemic in Switzerland: Phylogenetic analysis and intervention scenarios. PLoS Pathog 2023; 19:e1011553. [PMID: 37561788 PMCID: PMC10443857 DOI: 10.1371/journal.ppat.1011553] [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: 08/22/2023] [Accepted: 07/11/2023] [Indexed: 08/12/2023] Open
Abstract
The SARS-CoV-2 pandemic has led to the emergence of various variants of concern (VoCs) that are associated with increased transmissibility, immune evasion, or differences in disease severity. The emergence of VoCs fueled interest in understanding the potential impact of travel restrictions and surveillance strategies to prevent or delay the early spread of VoCs. We performed phylogenetic analyses and mathematical modeling to study the importation and spread of the VoCs Alpha and Delta in Switzerland in 2020 and 2021. Using a phylogenetic approach, we estimated between 383-1,038 imports of Alpha and 455-1,347 imports of Delta into Switzerland. We then used the results from the phylogenetic analysis to parameterize a dynamic transmission model that accurately described the subsequent spread of Alpha and Delta. We modeled different counterfactual intervention scenarios to quantify the potential impact of border closures and surveillance of travelers on the spread of Alpha and Delta. We found that implementing border closures after the announcement of VoCs would have been of limited impact to mitigate the spread of VoCs. In contrast, increased surveillance of travelers could prove to be an effective measure for delaying the spread of VoCs in situations where their severity remains unclear. Our study shows how phylogenetic analysis in combination with dynamic transmission models can be used to estimate the number of imported SARS-CoV-2 variants and the potential impact of different intervention scenarios to inform the public health response during the pandemic.
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Affiliation(s)
- Martina L. Reichmuth
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Emma B. Hodcroft
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Christian L. Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
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23
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Deroche L, Bellecave P, David R, Ouattara E, Garcia M, Roblot F, Boinot L, Faucher JF, Rejasse A, Gschwind G, Malvy D, Filleul L, Rogez S, Lévêque N, Lafon ME. One year of SARS-CoV-2 circulation in the Nouvelle-Aquitaine region, February 2021-2022, France. Front Microbiol 2023; 14:1176575. [PMID: 37577437 PMCID: PMC10420073 DOI: 10.3389/fmicb.2023.1176575] [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: 02/28/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023] Open
Abstract
Background Since 2021, 3 variants of concern (VOC) have spread to France, causing successive epidemic waves. Objectives To describe the features of Alpha, Delta and Omicron VOC circulation in the Nouvelle-Aquitaine region, France, between February 2021 and February 2022. Study design Data from the three university hospitals (UH) of Nouvelle-Aquitaine were used to describe regional SARS-CoV-2 circulation (RT-PCR positive rates and identified VOC) as well as its consequences (total number of hospitalizations and admissions in intensive care unit). They were analyzed according to the predominant variant and compared with national data. Results A total of 611,106 SARS-CoV-2 RT-PCR tests were performed in the 3 Nouvelle-Aquitaine UH during the study period. The 37,750 positive samples were analyzed by variant-specific RT-PCR or whole-genome sequencing. In 2021, Alpha VOC was detected from week 5 until week 35. Delta became the most prevalent variant (77.3%) in week 26, reaching 100% in week 35. It was replaced by Omicron, which was initially detected week 48, represented 77% of positive samples in week 52 and was still predominant in February 2022. The RT-PCR positive rates were 4.3, 4.2, and 21.9% during the Alpha, Delta and Omicron waves, respectively. The ratio between intensive care unit admissions and total hospitalizations was lower during the Omicron wave than during the two previous waves due to the Alpha and Delta variants. Conclusion This study highlighted the need for strong regional cooperation to achieve effective SARS-CoV-2 epidemiological surveillance, in close association with the public health authorities.
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Affiliation(s)
- Luc Deroche
- Virology Laboratory, CHU Poitiers, Poitiers, France
| | | | - Romain David
- Virology Laboratory, CHU Bordeaux, Bordeaux, France
| | - Eric Ouattara
- Medical Information Analysis and Coordination Unit (UCAIM-DIM), Medical Information Department, Bordeaux University Hospital, Bordeaux, France
| | - Magali Garcia
- Virology Laboratory, CHU Poitiers, Poitiers, France
- LITEC UR15560, Université de Poitiers, Poitiers, France
| | - France Roblot
- Tropical Infectious Diseases Department, Poitiers University Hospital, Poitiers, France
- INSERM U1070, Université de Poitiers, Poitiers, France
| | - Laurence Boinot
- Service d’Information Médicale, CHU Poitiers, Poitiers, France
| | - Jean-François Faucher
- Tropical Infectious Diseases Department, Limoges University Hospital, Limoges, France
| | - Aurélie Rejasse
- Medical Information Department, Limoges University Hospital, Limoges, France
| | - Guillaume Gschwind
- Medical Information Department, Limoges University Hospital, Limoges, France
| | - Denis Malvy
- Department of Infectious and Tropical Diseases, CHU Bordeaux, Bordeaux, France
- UMR Inserm 1219/IRD, University of Bordeaux, Bordeaux, France
| | - Laurent Filleul
- Regional Office-Nouvelle Aquitaine, Santé publique France, Bordeaux, France
| | - Sylvie Rogez
- Virology Laboratory, CHU Limoges, Limoges, France
| | - Nicolas Lévêque
- Virology Laboratory, CHU Poitiers, Poitiers, France
- LITEC UR15560, Université de Poitiers, Poitiers, France
| | - Marie-Edith Lafon
- Virology Laboratory, CHU Bordeaux, Bordeaux, France
- CNRS UMR 5234, University of Bordeaux, Bordeaux, France
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24
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Fang L, Xu J, Zhao Y, Fan J, Shen J, Liu W, Cao G. The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2. Front Microbiol 2023; 14:1228128. [PMID: 37560529 PMCID: PMC10409611 DOI: 10.3389/fmicb.2023.1228128] [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: 05/24/2023] [Accepted: 07/03/2023] [Indexed: 08/11/2023] Open
Abstract
Over three years' pandemic of 2019 novel coronavirus disease (COVID-19), multiple variants and novel subvariants have emerged successively, outcompeted earlier variants and become predominant. The sequential emergence of variants reflects the evolutionary process of mutation-selection-adaption of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Amino acid substitution/insertion/deletion in the spike protein causes altered viral antigenicity, transmissibility, and pathogenicity of SARS-CoV-2. Early in the pandemic, D614G mutation conferred virus with advantages over previous variants and increased transmissibility, and it also laid a conservative background for subsequent substantial mutations. The role of genomic recombination in the evolution of SARS-CoV-2 raised increasing concern with the occurrence of novel recombinants such as Deltacron, XBB.1.5, XBB.1.9.1, and XBB.1.16 in the late phase of pandemic. Co-circulation of different variants and co-infection in immunocompromised patients accelerate the emergence of recombinants. Surveillance for SARS-CoV-2 genomic variations, particularly spike protein mutation and recombination, is essential to identify ongoing changes in the viral genome and antigenic epitopes and thus leads to the development of new vaccine strategies and interventions.
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Affiliation(s)
- Letian Fang
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Jie Xu
- Department of Foreign Languages, International Exchange Center for Military Medicine, Second Military Medical University, Shanghai, China
| | - Yue Zhao
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Junyan Fan
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Jiaying Shen
- School of Medicine, Tongji University, Shanghai, China
| | - Wenbin Liu
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Guangwen Cao
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
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25
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Peñas-Utrilla D, Pérez-Lago L, Molero-Salinas A, Estévez A, Sanz A, Herranz M, Martínez-Laperche C, Andrés-Zayas C, Veintimilla C, Catalán P, Alonso R, Muñoz P, García de Viedma D. Systematic genomic analysis of SARS-CoV-2 co-infections throughout the pandemic and segregation of the strains involved. Genome Med 2023; 15:57. [PMID: 37488638 PMCID: PMC10367318 DOI: 10.1186/s13073-023-01198-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 05/30/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND SARS-CoV-2 recombinants involving the divergent Delta and Omicron lineages have been described, and one of them, "Kraken" (XBB.1.5), has recently been a matter of concern. Recombination requires the coexistence of two SARS-CoV-2 strains in the same individual. Only a limited number of studies have focused on the identification of co-infections and are restricted to co-infections involving the Delta/Omicron lineages. METHODS We performed a systematic identification of SARS-CoV-2 co-infections throughout the pandemic (7609 different patients sequenced), not biassed towards the involvement of highly divergent lineages. Through a comprehensive set of validations based on the distribution of allelic frequencies, phylogenetic consistency, re-sequencing, host genetic analysis and contextual epidemiological analysis, these co-infections were robustly assigned. RESULTS Fourteen (0.18%) co-infections with ≥ 8 heterozygous calls (8-85 HZs) were identified. Co-infections were identified throughout the pandemic and involved an equal proportion of strains from different lineages/sublineages (including pre-Alpha variants, Delta and Omicron) or strains from the same lineage. Co-infected cases were mainly unvaccinated, with mild or asymptomatic clinical presentation, and most were at risk of overexposure associated with the healthcare environment. Strain segregation enabled integration of sequences to clarify nosocomial outbreaks where analysis had been impaired due to co-infection. CONCLUSIONS Co-infection cases were identified throughout the pandemic, not just in the time periods when highly divergent lineages were co-circulating. Co-infections involving different lineages or strains from the same lineage were occurring in the same proportion. Most cases were mild, did not require medical assistance and were not vaccinated, and a large proportion were associated with the hospital environment.
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Affiliation(s)
- Daniel Peñas-Utrilla
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Escuela de Doctorado, Universidad de Alcalá, Plaza de San Diego, S/N, Alcalá de Henares, Madrid, 28801, Spain
| | - Laura Pérez-Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain.
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain.
| | - Andrea Molero-Salinas
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Agustín Estévez
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Amadeo Sanz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Marta Herranz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Carolina Martínez-Laperche
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Servicio de Oncohematología, Gregorio Marañón General University Hospital, Madrid, Spain
| | - Cristina Andrés-Zayas
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Genomics Unit, Gregorio Marañón General University Hospital, Madrid, Spain
| | - Cristina Veintimilla
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Pilar Catalán
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Roberto Alonso
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Patricia Muñoz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Departamento de Medicina, Universidad Complutense, Madrid, Spain
| | - Darío García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Dr. Esquerdo 46, Madrid, 28007, Spain.
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain.
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
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26
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Pandit R, Matthews QL. A SARS-CoV-2: Companion Animal Transmission and Variants Classification. Pathogens 2023; 12:775. [PMID: 37375465 DOI: 10.3390/pathogens12060775] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
The continuous emergence of novel viruses and their diseases are a threat to global public health as there have been three outbreaks of coronaviruses that are highly pathogenic to humans in the span of the last two decades, severe acute respiratory syndrome (SARS)-CoV in 2002, Middle East respiratory syndrome (MERS)-CoV in 2012, and novel SARS-CoV-2 which emerged in 2019. The unprecedented spread of SARS-CoV-2 worldwide has given rise to multiple SARS-CoV-2 variants that have either altered transmissibility, infectivity, or immune escaping ability, causing diseases in a broad range of animals including human and non-human hosts such as companion, farm, zoo, or wild animals. In this review, we have discussed the recent SARS-CoV-2 outbreak, potential animal reservoirs, and natural infections in companion and farm animals, with a particular focus on SARS-CoV-2 variants. The expeditious development of COVID-19 vaccines and the advancements in antiviral therapeutics have contained the COVID-19 pandemic to some extent; however, extensive research and surveillance concerning viral epidemiology, animal transmission, variants, or seroprevalence in diverse hosts are essential for the future eradication of COVID-19.
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Affiliation(s)
- Rachana Pandit
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
| | - Qiana L Matthews
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
- Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
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27
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Scendoni R, Bury E, Lima Arrais Ribeiro I, Cingolani M, Cameriere R, De Benedictis A, De Micco F. Leading Pathogens Involved in Co-Infection and Super-Infection with COVID-19: Forensic Medicine Considerations after a Systematic Review and Meta-Analysis. Pathogens 2023; 12:pathogens12050646. [PMID: 37242315 DOI: 10.3390/pathogens12050646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
The COVID-19 pandemic raised concerns about the potential for co-infection or over-infection with other respiratory infections, as they can complicate the diagnosis, treatment and prognosis of the disease. This is also a challenge for forensic pathologists, who may come across cases where the presence of co-infection or over-infection is suspected or confirmed, and it is important that they take this into account when determining the cause of death. The aim of this systematic review is to analyse the prevalence of each specific pathogen co-infecting or over-infecting patients with SARS-CoV-2 infection. In total, 575 studies were selected from the Scopus and Pub-Med online databases and 8 studies were included in a meta-analysis. Male gender, advanced age and nursing home care are risk factors associated with the development of co-infection, whereas age, tachypnoea, hypoxaemia and bacterial infection are predictors of mortality. Overall, however, having a SARS-CoV-2 infection does not represent a real risk for the development of co-infections/super-infections.
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Affiliation(s)
- Roberto Scendoni
- Department of Law, University of Macerata, 62100 Macerata, Italy
| | - Emanuele Bury
- Department of Law, University of Macerata, 62100 Macerata, Italy
| | | | | | - Roberto Cameriere
- Department of Medicine and Health Sciences, University of Molise, 86100 Campobasso, Italy
| | - Anna De Benedictis
- Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Roma, Italy
- Research Unit of Nursing Science, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, 00128 Roma, Italy
| | - Francesco De Micco
- Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Roma, Italy
- Research Unit of Bioethics and Humanities, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, 00128 Roma, Italy
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28
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Saade C, Pozzetto B, Yaugel-Novoa M, Oriol G, Josset L, Lina B, Paul S, Bal A, Trouillet-Assant S. Long-term humoral response following Delta and Omicron BA.1 co-infection. NPJ Vaccines 2023; 8:57. [PMID: 37080996 PMCID: PMC10116110 DOI: 10.1038/s41541-023-00652-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/23/2023] [Indexed: 04/22/2023] Open
Abstract
This study reports the 6-month humoral immune response in vaccinated patients concomitantly infected with Delta and Omicron BA.1 variants of SARS-CoV-2. Interestingly, the simultaneous exposure to the Delta and BA.1 S proteins does not confer an additional immune advantage compared to exposure to the BA.1 S protein alone.
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Affiliation(s)
- Carla Saade
- CIRI-Centre International de Recherche en Infectiologie, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, Université Jean Monnet de Saint-Etienne, Lyon, 69007, France
| | - Bruno Pozzetto
- CIRI-Centre International de Recherche en Infectiologie, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, Université Jean Monnet de Saint-Etienne, Lyon, 69007, France
- Immunology Laboratory, CIC1408, CHU Saint-Etienne, Saint-Etienne, 42055, France
| | - Melyssa Yaugel-Novoa
- CIRI-Centre International de Recherche en Infectiologie, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, Université Jean Monnet de Saint-Etienne, Lyon, 69007, France
| | - Guy Oriol
- Joint Research Unit Civils Hospices of Lyon-bioMérieux, Hospices Civils de Lyon, Hôpital Lyon Sud, Pierre-Bénite, 69310, France
| | - Laurence Josset
- CIRI-Centre International de Recherche en Infectiologie, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, Université Jean Monnet de Saint-Etienne, Lyon, 69007, France
- Laboratoire de Virologie, Institut des Agents Infectieux, Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France
- GenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Bruno Lina
- CIRI-Centre International de Recherche en Infectiologie, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, Université Jean Monnet de Saint-Etienne, Lyon, 69007, France
- Laboratoire de Virologie, Institut des Agents Infectieux, Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Stéphane Paul
- CIRI-Centre International de Recherche en Infectiologie, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, Université Jean Monnet de Saint-Etienne, Lyon, 69007, France
- Immunology Laboratory, CIC1408, CHU Saint-Etienne, Saint-Etienne, 42055, France
| | - Antonin Bal
- CIRI-Centre International de Recherche en Infectiologie, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, Université Jean Monnet de Saint-Etienne, Lyon, 69007, France
- Laboratoire de Virologie, Institut des Agents Infectieux, Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France
- GenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Sophie Trouillet-Assant
- CIRI-Centre International de Recherche en Infectiologie, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, Université Jean Monnet de Saint-Etienne, Lyon, 69007, France.
- Joint Research Unit Civils Hospices of Lyon-bioMérieux, Hospices Civils de Lyon, Hôpital Lyon Sud, Pierre-Bénite, 69310, France.
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29
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Pacchiarini N, Cronin M, Sawyer C, Williams C, Beazer A, Cottrell S, Morgan M, Saunders V, Moore C, Connor TR, Williams C. Novel recombinant SARS-CoV-2 lineage detected through genomic surveillance in Wales, UK. Microb Genom 2023; 9. [PMID: 37052600 DOI: 10.1099/mgen.0.000984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Recombination, the process whereby a segment of genetic material from one genome is inserted into another, producing a new chimeric genome, is an important evolutionary mechanism frequently observed in coronaviruses. The risks posed by recombination include the shuffling of advantageous mutations that may increase transmissibility, severity or vaccine escape. We present a genomic and epidemiological description of a new recombinant lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), XR, first identified in Wales. The Pathogen Genomics Unit (Public Health Wales, UK) sequences positive SARS-CoV-2 PCR tests using the ARTIC SARS-CoV-2 sequencing protocol. Recombinants were detected using an in-house pipeline and the epidemiological data analysed in R. Nosocomial cases were defined as those with samples taken after >7 days in hospital. Between February and March 2022, we identified 78 samples with highly similar genomes, comprising a BA.1-like 5' end, a BA.2-like 3' end and a BA.2-like spike protein. This signature is consistent with recombination and was defined as XR by Pangolin (PANGO v1.8). A total of 50 % of cases had a sample collected whilst in hospital and the first three cases were immunocompromised patients. The patient median age was 58 years (range: 4-95 years) and most of the patients were fully vaccinated against SARS-CoV-2 (74 % third dose/booster). Three patients died within 28 days of their sample collection date, one of whom had COVID-19 listed amongst ICD10 (International Classification of Diseases 10) coded causes of death. Our integrated system enabled real-time monitoring of recombinant SARS-CoV-2 for early detection, in order to rapidly risk assess and respond. This work highlights the importance of setting-based surveillance of recombinant SARS-CoV-2, as well as the need to monitor immunocompromised populations through repeat testing and sequencing.
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Affiliation(s)
- Nicole Pacchiarini
- Communicable Disease Surveillance Centre (CDSC), Public Health Wales, Cardiff, Wales, UK
| | - Michelle Cronin
- Communicable Disease Surveillance Centre (CDSC), Public Health Wales, Cardiff, Wales, UK
| | - Clare Sawyer
- Communicable Disease Surveillance Centre (CDSC), Public Health Wales, Cardiff, Wales, UK
| | - Catie Williams
- Pathogen Genomics Unit, Public Health Wales, Cardiff, Wales, UK
| | - Andrew Beazer
- Pathogen Genomics Unit, Public Health Wales, Cardiff, Wales, UK
| | - Simon Cottrell
- Communicable Disease Surveillance Centre (CDSC), Public Health Wales, Cardiff, Wales, UK
| | - Mari Morgan
- Communicable Disease Surveillance Centre (CDSC), Public Health Wales, Cardiff, Wales, UK
| | - Vince Saunders
- Cardiff and Vale University Health Board, Cardiff, Wales, UK
| | - Catherine Moore
- Wales Specialist Virology Centre, Microbiology, Public Health Wales, Cardiff, Wales, UK
| | - Thomas R Connor
- Pathogen Genomics Unit, Public Health Wales, Cardiff, Wales, UK
- Cardiff University School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Christopher Williams
- Communicable Disease Surveillance Centre (CDSC), Public Health Wales, Cardiff, Wales, UK
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30
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Kun Á, Hubai AG, Král A, Mokos J, Mikulecz BÁ, Radványi Á. Do pathogens always evolve to be less virulent? The virulence–transmission trade-off in light of the COVID-19 pandemic. Biol Futur 2023:10.1007/s42977-023-00159-2. [PMID: 37002448 PMCID: PMC10066022 DOI: 10.1007/s42977-023-00159-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/09/2023] [Indexed: 04/03/2023]
Abstract
AbstractThe direction the evolution of virulence takes in connection with any pathogen is a long-standing question. Formerly, it was theorized that pathogens should always evolve to be less virulent. As observations were not in line with this theoretical outcome, new theories emerged, chief among them the transmission–virulence trade-off hypotheses, which predicts an intermediate level of virulence as the endpoint of evolution. At the moment, we are very much interested in the future evolution of COVID-19’s virulence. Here, we show that the disease does not fulfill all the assumptions of the hypothesis. In the case of COVID-19, a higher viral load does not mean a higher risk of death; immunity is not long-lasting; other hosts can act as reservoirs for the virus; and death as a consequence of viral infection does not shorten the infectious period. Consequently, we cannot predict the short- or long-term evolution of the virulence of COVID-19.
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Deng F, Pan J, Liu Z, Zeng L, Chen J. Programmable DNA biocomputing circuits for rapid and intelligent screening of SARS-CoV-2 variants. Biosens Bioelectron 2023; 223:115025. [PMID: 36542937 PMCID: PMC9759469 DOI: 10.1016/j.bios.2022.115025] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/05/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022]
Abstract
The frequent emergence of SARS-CoV-2 variants increased viral transmissibility and reduced protection afforded by vaccines. The rapid, multichannel, and intelligent screening of variants is critical to minimizing community transmissions. DNA molecular logic gates have attracted wide attention in recent years due to the powerful information processing capabilities and molecular data biocomputing functions. In this work, some molecular switches (MSs) were connected with each other to implement arbitrary binary functions by emulating the threshold switching of MOS transistors and the decision tree model. Using specific sequences of different SARS-CoV-2 variants as inputs, the MSs net was used to build several molecular biocomputing circuits, including NOT, AND, OR, INHIBIT, XOR, half adder, half subtractor, full adder, and full subtractor. Four fluorophores (FAM, Cy3, ROX, and Cy5) were employed in the logic systems to realize the multichannel monitoring of the logic operation results. The logic response is fast and can be finished with 10 min, which facilitates the rapid wide-population screening for SARS-CoV-2 variants. Importantly, the logic results can be directly observed by the naked eye under a portable UV lamp, thus providing a simple and intelligent method to enable high-frequency point-of-care diagnostics, particularly in low-resource communities.
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Affiliation(s)
- Fang Deng
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China; College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Jiafeng Pan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China; College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Zhi Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Lingwen Zeng
- Guangdong Langyuan Biotechnology Co., LTD, Foshan, 528313, China; School of Food Science and Engineering, Foshan University, Foshan, 528231, China
| | - Junhua Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.
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Emergent Omicron BR.2.1 sublineage of SARS-CoV-2 in New South Wales, Australia: a subvariant with high fitness but without increased disease severity. Int J Infect Dis 2023; 130:38-41. [PMID: 36842755 PMCID: PMC9957655 DOI: 10.1016/j.ijid.2023.02.019] [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: 01/07/2023] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 02/28/2023] Open
Abstract
OBJECTIVES To describe the epidemiology and impact of Omicron BR.2.1, an emergent SARS-CoV-2 Omicron BA.2.75 sublineage displaying high fitness compared to other cocirculating subvariants in New South Wales, Australia. METHODS From September 01 to November 26, 2022, 4971 SARS-CoV-2 consensus genomes from unique patients were generated, and correlated with international travel and reinfection history, and admission to the intensive care unit. RESULTS BR.2.1 became the predominant variant by late November, and was responsible for a significantly higher proportion of community-acquired cases during the study period (55.1% vs 38.4%, P < 0.001). Reinfections (defined as occurring between 6 and 24 weeks after a prior diagnosis of COVID-19) were significantly higher among BR.2.1 compared to non-BR.2.1 infected persons (17.0% vs 6.0%, P < 0.001). BR.2.1 cases were also significantly younger compared to non-BR.2.1 (median age 48 years (interquartile range [IQR] 32) vs 53 years (IQR 32), P = 0.004). The proportion of patients admitted to the intensive care unit with BR.2.1 was not significantly higher than other subvariants (2.3% vs 2.0%, P = 0.717). CONCLUSION Having emerged locally within New South Wales, BR.2.1 caused a significant number of SARS-CoV-2 reinfections, but with disease severity comparable with other currently circulating lineages. Given its rapid rise in prevalence, BR.2.1 has the potential to become established internationally.
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Duerr R, Zhou H, Tada T, Dimartino D, Marier C, Zappile P, Wang G, Plitnick J, Griesemer SB, Girardin R, Machowski J, Bialosuknia S, Lasek-Nesselquist E, Hong SL, Baele G, Dittmann M, Ortigoza MB, Prasad PJ, McDonough K, Landau NR, St George K, Heguy A. Delta-Omicron recombinant escapes therapeutic antibody neutralization. iScience 2023; 26:106075. [PMID: 36844451 PMCID: PMC9937133 DOI: 10.1016/j.isci.2023.106075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/29/2022] [Accepted: 01/24/2023] [Indexed: 02/16/2023] Open
Abstract
The emergence of recombinant viruses is a threat to public health, as recombination may integrate variant-specific features that together result in escape from treatment or immunity. The selective advantages of recombinant SARS-CoV-2 isolates over their parental lineages remain unknown. We identified a Delta-Omicron (AY.45-BA.1) recombinant in an immunosuppressed transplant recipient treated with monoclonal antibody Sotrovimab. The single recombination breakpoint is located in the spike N-terminal domain adjacent to the Sotrovimab binding site. While Delta and BA.1 are sensitive to Sotrovimab neutralization, the Delta-Omicron recombinant is highly resistant. To our knowledge, this is the first described instance of recombination between circulating SARS-CoV-2 variants as a functional mechanism of resistance to treatment and immune escape.
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Affiliation(s)
- Ralf Duerr
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
- Vaccine Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Hao Zhou
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Takuya Tada
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Dacia Dimartino
- Genome Technology Center, Office of Science and Research, NYU Langone Health, New York, NY 10016, USA
| | - Christian Marier
- Genome Technology Center, Office of Science and Research, NYU Langone Health, New York, NY 10016, USA
| | - Paul Zappile
- Genome Technology Center, Office of Science and Research, NYU Langone Health, New York, NY 10016, USA
| | - Guiqing Wang
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jonathan Plitnick
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Sara B Griesemer
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Roxanne Girardin
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Jessica Machowski
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Sean Bialosuknia
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Erica Lasek-Nesselquist
- Bioinformatics Core, Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
- Biomedical Sciences Department, School of Public Health, University at Albany, SUNY, Albany, NY 12144, USA
| | - Samuel L Hong
- Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Meike Dittmann
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Mila B Ortigoza
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Prithiv J Prasad
- Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Kathleen McDonough
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
- Biomedical Sciences Department, School of Public Health, University at Albany, SUNY, Albany, NY 12144, USA
| | - Nathaniel R Landau
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Kirsten St George
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
- Biomedical Sciences Department, School of Public Health, University at Albany, SUNY, Albany, NY 12144, USA
| | - Adriana Heguy
- Genome Technology Center, Office of Science and Research, NYU Langone Health, New York, NY 10016, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
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Wacharapluesadee S, Hirunpatrawong P, Petcharat S, Torvorapanit P, Jitsatja A, Thippamom N, Ninwattana S, Phanlop C, Buathong R, Tangwangvivat R, Klungthong C, Chinnawirotpisan P, Hunsawong T, Suthum K, Komolsiri S, Jones AR, Fernandez S, Putcharoen O. Simultaneous detection of omicron and other SARS-CoV-2 variants by multiplex PCR MassARRAY technology. Sci Rep 2023; 13:2089. [PMID: 36747014 PMCID: PMC9900542 DOI: 10.1038/s41598-023-28715-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 01/23/2023] [Indexed: 02/08/2023] Open
Abstract
The rapid emergence of SARS-CoV-2 variants with high severity and transmutability adds further urgency for rapid and multiplex molecular testing to identify the variants. A nucleotide matrix-assisted laser-desorption-ionization time-of-flight mass spectrophotometry (MALDI-TOF MS)-based assay was developed (called point mutation array, PMA) to identify four major SARS-CoV-2 variants of concern (VOCs) including Alpha, Beta, Delta, and Omicron (namely PMA-ABDO) and differentiate Omicron subvariant (namely PMA-Omicron). PMA-ABDO and PMA-Omicron consist of 24 and 28 mutation sites of the spike gene. Both PMA panels specifically identified VOCs with as low as 10 viral copies/µl. The panel has shown a 100% concordant with the Next Generation Sequencing (NGS) results testing on 256 clinical specimens with real-time PCR cycle threshold (Ct) values less than 26. It showed a higher sensitivity over NGS; 25/28 samples were positive by PMA but not NGS in the clinical samples with PCR Ct higher than 26. Due to the mass of nucleotide used to differentiate between wild-type and mutation strains, the co-infection or recombination of multiple variants can be determined by the PMA method. This method is flexible in adding a new primer set to identify a new emerging mutation site among the current circulating VOCs and the turnaround time is less than 8 h. However, the spike gene sequencing or NGS retains the advantage of detecting newly emerged variants.
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Affiliation(s)
- Supaporn Wacharapluesadee
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Piyapha Hirunpatrawong
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Sininat Petcharat
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Pattama Torvorapanit
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand.,Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Anusara Jitsatja
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Nattakarn Thippamom
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Sasiprapa Ninwattana
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Chanchanit Phanlop
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Rome Buathong
- Division of International Communicable Disease Control Ports and Quarantine, Department of Diseases Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Ratanaporn Tangwangvivat
- Division of Communicable Diseases, Department of Diseases Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Chonticha Klungthong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | - Taweewun Hunsawong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Krairerk Suthum
- Office of Disease Prevention and Control, Region 5, Department of Diseases Control, Ministry of Public Health, Ratchaburi, Thailand
| | - Suparerk Komolsiri
- Office of Disease Prevention and Control, Region 5, Department of Diseases Control, Ministry of Public Health, Ratchaburi, Thailand
| | - Anthony R Jones
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Opass Putcharoen
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand. .,Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
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Perez-Florido J, Casimiro-Soriguer CS, Ortuño F, Fernandez-Rueda JL, Aguado A, Lara M, Riazzo C, Rodriguez-Iglesias MA, Camacho-Martinez P, Merino-Diaz L, Pupo-Ledo I, de Salazar A, Viñuela L, Fuentes A, Chueca N, García F, Dopazo J, Lepe JA. Detection of High Level of Co-Infection and the Emergence of Novel SARS CoV-2 Delta-Omicron and Omicron-Omicron Recombinants in the Epidemiological Surveillance of Andalusia. Int J Mol Sci 2023; 24:2419. [PMID: 36768752 PMCID: PMC9916856 DOI: 10.3390/ijms24032419] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
Recombination is an evolutionary strategy to quickly acquire new viral properties inherited from the parental lineages. The systematic survey of the SARS-CoV-2 genome sequences of the Andalusian genomic surveillance strategy has allowed the detection of an unexpectedly high number of co-infections, which constitute the ideal scenario for the emergence of new recombinants. Whole genome sequence of SARS-CoV-2 has been carried out as part of the genomic surveillance programme. Sample sources included the main hospitals in the Andalusia region. In addition to the increase of co-infections and known recombinants, three novel SARS-CoV-2 delta-omicron and omicron-omicron recombinant variants with two break points have been detected. Our observations document an epidemiological scenario in which co-infection and recombination are detected more frequently. Finally, we describe a family case in which co-infection is followed by the detection of a recombinant made from the two co-infecting variants. This increased number of recombinants raises the risk of emergence of recombinant variants with increased transmissibility and pathogenicity.
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Affiliation(s)
- Javier Perez-Florido
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Sevilla, 41013 Sevilla, Spain
| | - Carlos S. Casimiro-Soriguer
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Sevilla, 41013 Sevilla, Spain
| | - Francisco Ortuño
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Department of Computer Architecture and Computer Technology, University of Granada, 18071 Granada, Spain
| | - Jose L. Fernandez-Rueda
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
| | - Andrea Aguado
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
| | - María Lara
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
| | - Cristina Riazzo
- Unit of Microbiology, University Hospital Reina Sofia, 14004 Cordoba, Spain
| | - Manuel A. Rodriguez-Iglesias
- Servicio de Microbiología, Hospital Universitario Puerta del Mar, INIBICA, Universidad de Cádiz, 11003 Cádiz, Spain
| | - Pedro Camacho-Martinez
- Servicio de Microbiología, Unidad Clínica Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain
| | - Laura Merino-Diaz
- Servicio de Microbiología, Unidad Clínica Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain
| | - Inmaculada Pupo-Ledo
- Servicio de Microbiología, Unidad Clínica Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain
| | - Adolfo de Salazar
- Servicio de Microbiología, Hospital Universitario San Cecilio, 18016 Granada, Spain
| | - Laura Viñuela
- Servicio de Microbiología, Hospital Universitario San Cecilio, 18016 Granada, Spain
| | - Ana Fuentes
- Servicio de Microbiología, Hospital Universitario San Cecilio, 18016 Granada, Spain
| | - Natalia Chueca
- Servicio de Microbiología, Hospital Universitario San Cecilio, 18016 Granada, Spain
| | | | - Federico García
- Servicio de Microbiología, Hospital Universitario San Cecilio, 18016 Granada, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIII, 28046 Madrid, Spain
- Instituto de Investigación Biosanitaria, ibs.GRANADA, 18012 Granada, Spain
| | - Joaquín Dopazo
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013 Sevilla, Spain
- Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Sevilla, 41013 Sevilla, Spain
- FPS/ELIXIR-ES, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, 41013 Sevilla, Spain
| | - Jose A. Lepe
- Servicio de Microbiología, Unidad Clínica Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain
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Sant’Anna FH, Finger Andreis T, Salvato RS, Muterle Varela AP, Comerlato J, Gregianini TS, Barcellos RB, de Souza Godinho FM, Resende PC, da Luz Wallau G, y Castro TR, Casarin BC, de Almeida Vieira A, Schwarzbold AV, de Arruda Trindade P, Tumioto Giannini GL, Freese L, Bristot G, Brasil CS, de Oliveira Rocha B, Martins PB, de Oliveira FH, van Oosterhout C, Wendland E. Incipient Parallel Evolution of SARS-CoV-2 Deltacron Variant in South Brazil. Vaccines (Basel) 2023; 11:vaccines11020212. [PMID: 36851091 PMCID: PMC9961971 DOI: 10.3390/vaccines11020212] [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: 12/26/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
With the coexistence of multiple lineages and increased international travel, recombination and gene flow are likely to become increasingly important in the adaptive evolution of SARS-CoV-2. These processes could result in genetic introgression and the incipient parallel evolution of multiple recombinant lineages. However, identifying recombinant lineages is challenging, and the true extent of recombinant evolution in SARS-CoV-2 may be underestimated. This study describes the first SARS-CoV-2 Deltacron recombinant case identified in Brazil. We demonstrate that the recombination breakpoint is at the beginning of the Spike gene. The 5' genome portion (circa 22 kb) resembles the AY.101 (Delta), and the 3' genome portion (circa 8 kb nucleotides) is most similar to the BA.1.1 (Omicron). Furthermore, evolutionary genomic analyses indicate that the new strain emerged after a single recombination event between lineages of diverse geographical locations in December 2021 in South Brazil. This Deltacron, AYBA-RS, is one of the dozens of recombinants described in 2022. The submission of only four sequences in the GISAID database suggests that this lineage had a minor epidemiological impact. However, the recent emergence of this and other Deltacron recombinant lineages (XD, XF, and XS) suggests that gene flow and recombination may play an increasingly important role in the COVID-19 pandemic. We explain the evolutionary and population genetic theory that supports this assertion, concluding that this stresses the need for continued genomic surveillance. This monitoring is vital for countries where multiple variants are present, as well as for countries that receive significant inbound international travel.
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Affiliation(s)
| | | | - Richard Steiner Salvato
- Centro de Desenvolvimento Científico e Tecnológico, Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (CDCT/CEVS/SES-RS), Porto Alegre 90450-190, RS, Brazil
| | | | | | - Tatiana Schäffer Gregianini
- Laboratório Central de Saúde Pública, Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (LACEN/CEVS/SES-RS), Porto Alegre 90450-190, RS, Brazil
| | - Regina Bones Barcellos
- Centro de Desenvolvimento Científico e Tecnológico, Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (CDCT/CEVS/SES-RS), Porto Alegre 90450-190, RS, Brazil
| | - Fernanda Marques de Souza Godinho
- Centro de Desenvolvimento Científico e Tecnológico, Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (CDCT/CEVS/SES-RS), Porto Alegre 90450-190, RS, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
| | - Gabriel da Luz Wallau
- Departamento de Entomologia e Núcleo de Bioinformática, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz Pernambuco (FIOCRUZ-PE), Recife 50740-465, PE, Brazil
| | - Thaís Regina y Castro
- Departamento de Análises Clínicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil
| | - Bruna Campestrini Casarin
- Departamento de Análises Clínicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil
| | - Andressa de Almeida Vieira
- Departamento de Análises Clínicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil
| | | | | | | | - Luana Freese
- Hospital Moinhos de Vento, Porto Alegre 90035-000, RS, Brazil
| | - Giovana Bristot
- Hospital Moinhos de Vento, Porto Alegre 90035-000, RS, Brazil
| | | | | | | | | | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- Correspondence:
| | - Eliana Wendland
- Hospital Moinhos de Vento, Porto Alegre 90035-000, RS, Brazil
- Graduate Program in Biosciences, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil
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37
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Wacharapluesadee S, Hirunpatrawong P, Petcharat S, Torvorapanit P, Jitsatja A, Thippamom N, Ninwattana S, Phanlop C, Buathong R, Tangwangvivat R, Klungthong C, Chinnawirotpisan P, Hunsawong T, Suthum K, Komolsiri S, Jones AR, Fernandez S, Putcharoen O. Simultaneous Detection of Omicron and Other SARS-CoV-2 Variants by Multiplex PCR MassARRAY Technology. RESEARCH SQUARE 2023:rs.3.rs-2482226. [PMID: 36711810 PMCID: PMC9882655 DOI: 10.21203/rs.3.rs-2482226/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The rapid emergence of SARS-CoV-2 variants with high severity and transmutability adds further urgency for rapid and multiplex molecular testing to identify the variants. A nucleotide matrix-assisted laser-desorption-ionization time-of-flight mass spectrophotometry (MALDI-TOF MS)-based assay was developed (called point mutation array, PMA) to identify four major SARS-CoV-2 variants of concern (VOCs) including Alpha, Beta, Delta, and Omicron (namely PMA-ABDO) and differentiate Omicron subvariant (namely PMA-Omicron). PMA-ABDO and PMA-Omicron consist of 24 and 28 mutation sites of the spike gene. Both PMA panels specifically identified VOCs with as low as 10 viral copies/ µl. The panel has shown a 100% concordant with the Next Generation Sequencing (NGS) results testing on 256 clinical specimens with real-time PCR cycle threshold (Ct) values less than 26. It showed a higher sensitivity over NGS; 25/28 samples were positive by PMA but not NGS in the clinical samples with PCR Ct higher than 26. Due to the mass of nucleotide used to differentiate between wild-type and mutation strains, the co-infection or recombination of multiple variants can be determined by the PMA method. This method is flexible in adding a new primer set to identify a new emerging mutation site among the current circulating VOCs and the turnaround time is less than 8 hours. However, the spike gene sequencing or NGS retains the advantage of detecting newly emerged variants.
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Affiliation(s)
- Supaporn Wacharapluesadee
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Piyapha Hirunpatrawong
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Sininat Petcharat
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Pattama Torvorapanit
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Anusara Jitsatja
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Nattakarn Thippamom
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Sasiprapa Ninwattana
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Chanchanit Phanlop
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Rome Buathong
- Division of International Communicable Disease Control Ports and Quarantine, Department of Diseases Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Ratanaporn Tangwangvivat
- Division of Communicable Diseases, Department of Diseases Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Chonticha Klungthong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | - Taweewun Hunsawong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Krairerk Suthum
- Office of Disease Prevention and Control, Region 5, Department of Diseases Control, Ministry of Public Health, Ratchaburi, Thailand
| | - Suparerk Komolsiri
- Office of Disease Prevention and Control, Region 5, Department of Diseases Control, Ministry of Public Health, Ratchaburi, Thailand
| | - Anthony R Jones
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Opass Putcharoen
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Pérez-Vargas J, Shapira T, Olmstead AD, Villanueva I, Thompson CAH, Ennis S, Gao G, De Guzman J, Williams DE, Wang M, Chin A, Bautista-Sánchez D, Agafitei O, Levett P, Xie X, Nuzzo G, Freire VF, Quintana-Bulla JI, Bernardi DI, Gubiani JR, Suthiphasilp V, Raksat A, Meesakul P, Polbuppha I, Cheenpracha S, Jaidee W, Kanokmedhakul K, Yenjai C, Chaiyosang B, Teles HL, Manzo E, Fontana A, Leduc R, Boudreault PL, Berlinck RGS, Laphookhieo S, Kanokmedhakul S, Tietjen I, Cherkasov A, Krajden M, Nabi IR, Niikura M, Shi PY, Andersen RJ, Jean F. Discovery of lead natural products for developing pan-SARS-CoV-2 therapeutics. Antiviral Res 2023; 209:105484. [PMID: 36503013 PMCID: PMC9729583 DOI: 10.1016/j.antiviral.2022.105484] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/26/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains a global public health crisis. The reduced efficacy of therapeutic monoclonal antibodies against emerging SARS-CoV-2 variants of concern (VOCs), such as omicron BA.5 subvariants, has underlined the need to explore a novel spectrum of antivirals that are effective against existing and evolving SARS-CoV-2 VOCs. To address the need for novel therapeutic options, we applied cell-based high-content screening to a library of natural products (NPs) obtained from plants, fungi, bacteria, and marine sponges, which represent a considerable diversity of chemical scaffolds. The antiviral effect of 373 NPs was evaluated using the mNeonGreen (mNG) reporter SARS-CoV-2 virus in a lung epithelial cell line (Calu-3). The screening identified 26 NPs with half-maximal effective concentrations (EC50) below 50 μM against mNG-SARS-CoV-2; 16 of these had EC50 values below 10 μM and three NPs (holyrine A, alotaketal C, and bafilomycin D) had EC50 values in the nanomolar range. We demonstrated the pan-SARS-CoV-2 activity of these three lead antivirals against SARS-CoV-2 highly transmissible Omicron subvariants (BA.5, BA.2 and BA.1) and highly pathogenic Delta VOCs in human Calu-3 lung cells. Notably, holyrine A, alotaketal C, and bafilomycin D, are potent nanomolar inhibitors of SARS-CoV-2 Omicron subvariants BA.5 and BA.2. The pan-SARS-CoV-2 activity of alotaketal C [protein kinase C (PKC) activator] and bafilomycin D (V-ATPase inhibitor) suggest that these two NPs are acting as host-directed antivirals (HDAs). Future research should explore whether PKC regulation impacts human susceptibility to and the severity of SARS-CoV-2 infection, and it should confirm the important role of human V-ATPase in the VOC lifecycle. Interestingly, we observed a synergistic action of bafilomycin D and N-0385 (a highly potent inhibitor of human TMPRSS2 protease) against Omicron subvariant BA.2 in human Calu-3 lung cells, which suggests that these two highly potent HDAs are targeting two different mechanisms of SARS-CoV-2 entry. Overall, our study provides insight into the potential of NPs with highly diverse chemical structures as valuable inspirational starting points for developing pan-SARS-CoV-2 therapeutics and for unravelling potential host factors and pathways regulating SARS-CoV-2 VOC infection including emerging omicron BA.5 subvariants.
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Affiliation(s)
- Jimena Pérez-Vargas
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Tirosh Shapira
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Andrea D Olmstead
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Ivan Villanueva
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Connor A H Thompson
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Siobhan Ennis
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Guang Gao
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Joshua De Guzman
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - David E Williams
- Departments of Chemistry and Earth, Ocean & Atmospheric Science, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Meng Wang
- Departments of Chemistry and Earth, Ocean & Atmospheric Science, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Aaleigha Chin
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Diana Bautista-Sánchez
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Olga Agafitei
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Paul Levett
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, V5Z 4R4, Canada
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Genoveffa Nuzzo
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry, National Research Council, Via Campi Flegrei 34, 80078, Pozzuoli, Italy
| | - Vitor F Freire
- Instituto de Química de São Carlos, Universidade de São Paulo, CP780, CEP13560-970, São Carlos, SP, Brazil
| | - Jairo I Quintana-Bulla
- Instituto de Química de São Carlos, Universidade de São Paulo, CP780, CEP13560-970, São Carlos, SP, Brazil
| | - Darlon I Bernardi
- Instituto de Química de São Carlos, Universidade de São Paulo, CP780, CEP13560-970, São Carlos, SP, Brazil
| | - Juliana R Gubiani
- Instituto de Química de São Carlos, Universidade de São Paulo, CP780, CEP13560-970, São Carlos, SP, Brazil
| | - Virayu Suthiphasilp
- Center of Chemical Innovation for Sustainability (CIS), School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Achara Raksat
- Center of Chemical Innovation for Sustainability (CIS), School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Pornphimol Meesakul
- Center of Chemical Innovation for Sustainability (CIS), School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Isaraporn Polbuppha
- Center of Chemical Innovation for Sustainability (CIS), School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | | | - Wuttichai Jaidee
- Medicinal Plants Innovation Center of Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Kwanjai Kanokmedhakul
- Natural Products Research Unit, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Chavi Yenjai
- Natural Products Research Unit, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Boonyanoot Chaiyosang
- Natural Products Research Unit, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Helder Lopes Teles
- Instituto de Ciências Exatas e Naturais, Universidade Federal de Rondonópolis, CEP 78736-900, Rondonópolis, MT, Brazil
| | - Emiliano Manzo
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry, National Research Council, Via Campi Flegrei 34, 80078, Pozzuoli, Italy
| | - Angelo Fontana
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry, National Research Council, Via Campi Flegrei 34, 80078, Pozzuoli, Italy; Department of Biology, Università di Napoli "Federico II", Via Cupa Nuova Cinthia 21, 80126, Napoli, Italy
| | - Richard Leduc
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
| | - Pierre-Luc Boudreault
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
| | - Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, CP780, CEP13560-970, São Carlos, SP, Brazil
| | - Surat Laphookhieo
- Center of Chemical Innovation for Sustainability (CIS), School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Somdej Kanokmedhakul
- Natural Products Research Unit, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Ian Tietjen
- Departments of Chemistry and Earth, Ocean & Atmospheric Science, University of British Columbia, Vancouver, BC V6T 1Z1, Canada; The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
| | - Mel Krajden
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, V5Z 4R4, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Ivan Robert Nabi
- Department of Cellular and Physiological Sciences, School of Biomedical Engineering, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Raymond J Andersen
- Departments of Chemistry and Earth, Ocean & Atmospheric Science, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.
| | - François Jean
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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The case for including microbial sequences in the electronic health record. Nat Med 2023; 29:22-25. [PMID: 36646805 DOI: 10.1038/s41591-022-02157-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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40
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Singh P, Sharma K, Shaw D, Bhargava A, Negi SS. Mosaic Recombination Inflicted Various SARS-CoV-2 Lineages to Emerge into Novel Virus Variants: a Review Update. Indian J Clin Biochem 2022; 38:1-8. [PMID: 36569378 PMCID: PMC9759274 DOI: 10.1007/s12291-022-01109-w] [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: 10/21/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Human Coronaviruses (hCoVs) belongs to the enormous and dissimilar family of positive-sense, non-segmented, single-stranded RNA viruses. The RNA viruses are prone to high rates of mutational recombination resulting in emergence of evolutionary variant to alter various features including transmissibility and severity. The evolutionary changes affect the immune escape and reduce effectiveness of diagnostic and therapeutic measures by becoming undetectable by the currently available diagnostics and refractory to therapeutics and vaccines. Whole genome sequencing studies from various countries have adequately reported mosaic recombination between different lineage strain of SARS-CoV-2 whereby RNA dependent RNA polymerase (RdRp) gene reconnects with a homologous RNA strand at diverse position. This all lead to evolutionary emergence of new variant/ lineage as evident with the emergence of XBB in India at the time of writing this review. The continuous periodical genomic surveillance is utmost required for understanding the various lineages involved in recombination to emerge into hybrid variant. This may further help in assessing virus transmission dynamics, virulence and severity factor to help health authorities take appropriate timely action for prevention and control of any future COVID-19 outbreak.
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Affiliation(s)
- Pushpendra Singh
- Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh India
| | - Kuldeep Sharma
- Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh India
| | - Dipika Shaw
- Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh India
| | - Anudita Bhargava
- Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh India
| | - Sanjay Singh Negi
- Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh India
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Bolze A, Basler T, White S, Dei Rossi A, Wyman D, Dai H, Roychoudhury P, Greninger AL, Hayashibara K, Beatty M, Shah S, Stous S, McCrone JT, Kil E, Cassens T, Tsan K, Nguyen J, Ramirez J, Carter S, Cirulli ET, Schiabor Barrett K, Washington NL, Belda-Ferre P, Jacobs S, Sandoval E, Becker D, Lu JT, Isaksson M, Lee W, Luo S. Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination. MED (NEW YORK, N.Y.) 2022; 3:848-859.e4. [PMID: 36332633 PMCID: PMC9581791 DOI: 10.1016/j.medj.2022.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/14/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Between November 2021 and February 2022, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta and Omicron variants co-circulated in the United States, allowing for co-infections and possible recombination events. METHODS We sequenced 29,719 positive samples during this period and analyzed the presence and fraction of reads supporting mutations specific to either the Delta or Omicron variant. FINDINGS We identified 18 co-infections, one of which displayed evidence of a low Delta-Omicron recombinant viral population. We also identified two independent cases of infection by a Delta-Omicron recombinant virus, where 100% of the viral RNA came from one clonal recombinant. In the three cases, the 5' end of the viral genome was from the Delta genome and the 3' end from Omicron, including the majority of the spike protein gene, though the breakpoints were different. CONCLUSIONS Delta-Omicron recombinant viruses were rare, and there is currently no evidence that Delta-Omicron recombinant viruses are more transmissible between hosts compared with the circulating Omicron lineages. FUNDING This research was supported by the NIH RADx initiative and by the Centers for Disease Control Contract 75D30121C12730 (Helix).
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Affiliation(s)
| | | | | | | | | | | | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA 98195, USA
| | | | - Mark Beatty
- County of San Diego Health and Human Services, San Diego, CA 92110, USA
| | - Seema Shah
- County of San Diego Health and Human Services, San Diego, CA 92110, USA
| | - Sarah Stous
- County of San Diego Health and Human Services, San Diego, CA 92110, USA
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42
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Farahat RA, Abdelaal A, Umar TP, El-Sakka AA, Benmelouka AY, Albakri K, Ali I, Al-Ahdal T, Abdelazeem B, Sah R, Rodriguez-Morales AJ. The emergence of SARS-CoV-2 Omicron subvariants: current situation and future trends. LE INFEZIONI IN MEDICINA 2022; 30:480-494. [PMID: 36482957 PMCID: PMC9714996 DOI: 10.53854/liim-3004-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/03/2022] [Indexed: 12/12/2022]
Abstract
The SARS-CoV-2 Omicron variant (B.1.1.529) has been the most recent variant of concern (VOC) established by the World Health Organization (WHO). Because of its greater infectivity and immune evasion, this variant quickly became the dominant type of circulating SARS-CoV-2 worldwide. Our literature review thoroughly explains the current state of Omicron emergence, particularly by comparing different omicron subvariants, including BA.2, BA.1, and BA.3. Such elaboration would be based on structural variations, mutations, clinical manifestation, transmissibility, pathogenicity, and vaccination effectiveness. The most notable difference between the three subvariants is the insufficiency of deletion (Δ69-70) in the spike protein, which results in a lower detection rate of the spike (S) gene target known as (S) gene target failure (SGTF). Furthermore, BA.2 had a stronger affinity to the human Angiotensin-converting Enzyme (hACE2) receptor than other Omicron sub-lineages. Regarding the number of mutations, BA.1.1 has the most (40), followed by BA.1, BA.3, and BA.3 with 39, 34, and 31 mutations, respectively. In addition, BA.2 and BA.3 have greater transmissibility than other sub-lineages (BA.1 and BA.1.1). These characteristics are primarily responsible for Omicron's vast geographical spread and high contagiousness rates, particularly BA.2 sub-lineages.
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Affiliation(s)
| | - Abdelaziz Abdelaal
- Harvard Medical School, Boston, MA,
USA,Boston University, MA,
USA,General Practitioner, Tanta University Hospitals,
Egypt
| | | | | | | | - Khaled Albakri
- Faculty of Medicine, The Hashemite University, Zarqa,
Jordan
| | - Iftikhar Ali
- Department of Pharmacy, Paraplegic Center, Peshawar,
Pakistan
| | - Tareq Al-Ahdal
- Institute of Global Health (HIGH), Heidelberg University, Heidelberg,
Germany
| | - Basel Abdelazeem
- Department of Internal Medicine, McLaren Health Care, Flint, Michigan,
USA,Department of Internal Medicine, Michigan State University, East Lansing, Michigan,
USA
| | - Ranjit Sah
- Department of Microbiology, Tribhuvan University Teaching Hospital, Institute of Medicine, Kathmandu,
Nepal,Dr. D.Y Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra,
India
| | - Alfonso J. Rodriguez-Morales
- Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de Las Américas, Pereira, Risaralda,
Colombia,Faculty of Medicine, Institución Universitaria Vision de Las Americas, Pereira, Risaralda,
Colombia,Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut P.O. Box 36,
Lebanon,Master of Clinical Epidemiology and Biostatistics, Universidad Científica del Sur, Lima,
Perú
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43
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Venugopala KN. Progress Update on the Epidemiology of COVID-19 Variants and the Assessment Status of Developed Vaccines. J Pharmacol Pharmacother 2022. [DOI: 10.1177/0976500x221138393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has spread rapidly and diffused to more than 180 countries at varying severities. This pandemic has accounted for increased mortality and morbidity in developed as well as developing nations. The WHO has announced that there is a persistent need for the evaluation of the COVID-19 vaccine effectiveness (VE) against major outcomes, which include severe diseases, symptomatic COVID-19, and mortalities related to COVID-19. Therefore, mass vaccination programs using vaccines of high effectiveness are among the strategies that have been used by governments worldwide to impede the COVID-19 pandemic transmission. In this regard, massive efforts were made by governments, scientists, biomedical researchers, and healthcare professionals leading to the successful development of various vaccines to bring this pandemic under control. This editorial aims to shed light on the epidemiological status of COVID-19 variants, namely, Delta, Omicron, and Deltacron variants as well as discuss the effectiveness of the currently available COVID-19 vaccines.
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Affiliation(s)
- Katharigatta N. Venugopala
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
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Ciupeanu AS, Varughese M, Roda WC, Han D, Cheng Q, Li MY. Mathematical modeling of the dynamics of COVID-19 variants of concern: Asymptotic and finite-time perspectives. Infect Dis Model 2022; 7:581-596. [PMID: 36097594 PMCID: PMC9454204 DOI: 10.1016/j.idm.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/23/2022] Open
Abstract
The COVID-19 pandemic has seen multiple waves, in part due to the implementation and relaxation of social distancing measures by the public health authorities around the world, and also caused by the emergence of new variants of concern (VOCs) of the SARS-Cov-2 virus. As the COVID-19 pandemic is expected to transition into an endemic state, how to manage outbreaks caused by newly emerging VOCs has become one of the primary public health issues. Using mathematical modeling tools, we investigated the dynamics of VOCs, both in a general theoretical framework and based on observations from public health data of past COVID-19 waves, with the objective of understanding key factors that determine the dominance and coexistence of VOCs. Our results show that the transmissibility advantage of a new VOC is a main factor for it to become dominant. Additionally, our modeling study indicates that the initial number of people infected with the new VOC plays an important role in determining the size of the epidemic. Our results also support the evidence that public health measures targeting the newly emerging VOC taken in the early phase of its spread can limit the size of the epidemic caused by the new VOC (Wu et al., 2139Wu, Scarabel, Majeed, Bragazzi, & Orbinski, ; Wu et al., 2021).
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Affiliation(s)
- Adriana-Stefania Ciupeanu
- Department of Mathematics and Department of Statistics, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Marie Varughese
- Analytics and Performance Reporting Branch, Alberta Health, Edmonton, Alberta, Canada
| | - Weston C. Roda
- Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, Alberta, T6G 2G1, Canada
| | - Donglin Han
- Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, Alberta, T6G 2G1, Canada
| | - Qun Cheng
- Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, Alberta, T6G 2G1, Canada
| | - Michael Y. Li
- Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, Alberta, T6G 2G1, Canada
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Salimović-Bešić I, Dedeić-Ljubović A, Zahirović E, Hasanović M, Šehić M, Vukovikj M, Boshevska G, Vegar-Zubović S, Mehmedika-Suljić E, Izetbegović S. The SARS-CoV-2 Delta (B.1.617.2) variant with spike N501Y mutation in the shadow of Omicron emergence. Heliyon 2022; 8:e12650. [PMID: 36590492 PMCID: PMC9789543 DOI: 10.1016/j.heliyon.2022.e12650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 10/05/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
Circulation of the Omicron variant with the reemergence of the N501Y mutation along with many others in the spike protein has once again stirred the academic community. Interestingly, tracing the genetic diversity of SARS-CoV-2 shed light on a less frequent N501Y + Delta variant which has been in the global circulation for some time before the Omicron appearance. This paper aims to present the molecular characteristics of the SARS-CoV-2 Spike_N501Y + Delta variant detected in Bosnia and Herzegovina. The study was conducted during November and December 2021. All patients were tested using real-time RT-PCR for detection of SARS-CoV-2. A representative number of SARS-CoV-2 positive samples was pre-screened using VirSNiP SARS-CoV-2 Spike N501Y kit. The characterization of the viruses was carried out with Illumina RNA Prep with enrichment and the Respiratory Virus Oligo Panel kit. Among the analyzed sequences, we found two isolates of the Delta variant that differ from their most related clade- GK AY.4.3 in additional mutations N501Y and L54F. In this study, we described the presence of a rare form of Delta variant with Spike_N501Y mutation in the shadow of the Omicron emergence. Despite the set of mutations in the Spike protein, this form of Delta variant does not indicate the large-scale consequences for the general population. Further functional studies of this form could provide more information about its antigenicity and infectivity.
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Affiliation(s)
- Irma Salimović-Bešić
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina
| | - Amela Dedeić-Ljubović
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina
| | - Edina Zahirović
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina
| | - Medina Hasanović
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina
| | - Merima Šehić
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina
| | - Maja Vukovikj
- Institute of Public Health of Republic of North Macedonia, 50-ta Divizija 6, 1000, Skopje, Macedonia
| | - Golubinka Boshevska
- Faculty for Medical Sciences, University Goce Delchev, Krste Misirkov No.10-A P.O. Box 201, 2000, Shtip, Macedonia
| | - Sandra Vegar-Zubović
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina
| | - Enra Mehmedika-Suljić
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina
| | - Sebija Izetbegović
- Clinical Center of the University of Sarajevo, Bolnička 25, 71000, Sarajevo, Bosnia and Herzegovina
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Sarkar P, Banerjee S, Chakrabarti S, Chakrabarti P, Bandyopadhyay A, Mitra AG, Saha S, Roy A, Sarkar S. Genome characterization, phylogenomic assessment and spatio-temporal dynamics study of highly mutated BA variants from India. Indian J Med Microbiol 2022; 43:66-72. [PMID: 36400646 PMCID: PMC9664238 DOI: 10.1016/j.ijmmb.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/08/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022]
Abstract
Purpose The emergence of highly mutated and transmissible BA variants has caused an unprecedented surge in COVID-19 infections worldwide. Thorough analysis of its genome structure and phylogenomic evolutionary details will serve as scientific reference for future research. Method Here, we have analyzed the BA variants from India using whole-genome sequencing, spike protein mutation study, spatio-temporal surveillance, phylogenomic assessment and epitope mapping. Results The predominance of BA.2/BA.2-like was observed in India during COVID-19 third wave. Genome analysis and mutation study highlighted the existence of 2128 amino acid changes within BA as compared to NC_045512.2. Presence of 23 unknown mutation sites (spanning region 61–831) were observed among the Indian BA variants as compared to the global BA strains. Unassigned probable Omicron showed the highest number of mutations (370) followed by BA.1 (104), BA.2.3 (56), and BA.2 (27). Presence of mutations ‘Q493R + Q498R + N501Y’, and ‘K417 N + E484A + N501Y’ remained exclusive to BA.2 as well as unassigned probable Omicron. The time-tree and phylogenomic network assessed the evolutionary relationship of the BA variants. Existence of 424 segregating sites and 113 parsimony informative sites within BA genomes were observed through haplotype network analysis. Epitope mapping depicted the presence of unique antigenic sites within the receptor binding domain of the BA variants that could be exploited for robust vaccine development. Conclusion These findings provide important scientific insights about the nature, diversity, and evolution of Indian BA variants. The study further divulges in the avenues of therapeutic upgradation for better management and eventual eradication of COVID-19.
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Affiliation(s)
- Poulomi Sarkar
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India,IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India
| | - Sarthak Banerjee
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India,IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India
| | - Saikat Chakrabarti
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India,IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India
| | - Partha Chakrabarti
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India
| | - Arun Bandyopadhyay
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India,IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India
| | | | - Soumen Saha
- MEDICA Super-specialty Hospital, Kolkata, India
| | - Aviral Roy
- MEDICA Super-specialty Hospital, Kolkata, India
| | - Siddik Sarkar
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India,IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India,Corresponding author. CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB-700032, India
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Combes P, Bisseux M, Bal A, Marin P, Latour J, Archimbaud C, Brebion A, Chabrolles H, Regagnon C, Lafolie J, Destras G, Simon B, Izopet J, Laurence Josset, Henquell C, Mirand A. Evidence of co-infections during Delta and Omicron SARS-CoV-2 variants co-circulation through prospective screening and sequencing. Clin Microbiol Infect 2022; 28:1503.e5-1503.e8. [PMID: 35792280 PMCID: PMC9250411 DOI: 10.1016/j.cmi.2022.06.030] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/17/2022] [Accepted: 06/28/2022] [Indexed: 12/13/2022]
Abstract
OBJECTIVES To describe Delta/Omicron SARS-CoV-2 variants co-infection detection and confirmation during the fifth wave of COVID-19 pandemics in France in 7 immunocompetent and epidemiologically unrelated patients. METHODS Since December 2021, the surveillance of Delta/Omicron SARS-CoV-2 variants of concern (VOC) circulation was performed through prospective screening of positive-samples using single nucleotide polymorphism (SNP) PCR assays targeting SARS-CoV-2 S-gene mutations K417N (Omicron specific) and L452R (Delta specific). Samples showing unexpected mutational profiles were further submitted to whole genome sequencing (WGS) using three different primer sets. RESULTS Between weeks 49-2021 and 02-2022, SARS-CoV-2 genome was detected in 3831 respiratory samples, of which 3237 (84.5%) were screened for VOC specific SNPs. Unexpected mutation profiles suggesting a dual Delta/Omicron population were observed in 7 nasopharyngeal samples (0.2%). These co-infections were confirmed by WGS. For 2 patients, the sequence analyses of longitudinal samples collected 7 to 11 days apart showed that Delta or Omicron can outcompete the other variant during dual infection. Additionally, for one of these samples, a recombination event between Delta and Omicron was detected. CONCLUSIONS This work demonstrates that SARS-CoV-2 Delta/Omicron co-infections are not rare in high virus co-circulation periods. Moreover, co-infections can further lead to genetic recombination which may generate new chimeric variants with unpredictable epidemic or pathogenic properties that could represent a serious health threat.
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Affiliation(s)
- Patricia Combes
- CHU Clermont-Ferrand, pôle BMAP, F-63003 Clermont-Ferrand, France
| | - Maxime Bisseux
- CHU Clermont-Ferrand, 3IHP, Virology Laboratory, National Reference Centre for Enteroviruses and parechoviruses-associated laboratory, F-63003 Clermont-Ferrand, France; Université Clermont Auvergne, CNRS 6023-LMGE, EPIE, F-63001 Clermont-Ferrand, France
| | - Antonin Bal
- GenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004 Lyon, France; CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Pierre Marin
- CHU Clermont-Ferrand, 3IHP, Virology Laboratory, National Reference Centre for Enteroviruses and parechoviruses-associated laboratory, F-63003 Clermont-Ferrand, France
| | - Justine Latour
- CHU de Toulouse, Virology Laboratory, F-31300 Toulouse, France
| | - Christine Archimbaud
- CHU Clermont-Ferrand, 3IHP, Virology Laboratory, National Reference Centre for Enteroviruses and parechoviruses-associated laboratory, F-63003 Clermont-Ferrand, France; Université Clermont Auvergne, CNRS 6023-LMGE, EPIE, F-63001 Clermont-Ferrand, France
| | - Amélie Brebion
- CHU Clermont-Ferrand, 3IHP, Virology Laboratory, National Reference Centre for Enteroviruses and parechoviruses-associated laboratory, F-63003 Clermont-Ferrand, France
| | - Hélène Chabrolles
- CHU Clermont-Ferrand, 3IHP, Virology Laboratory, National Reference Centre for Enteroviruses and parechoviruses-associated laboratory, F-63003 Clermont-Ferrand, France; Université Clermont Auvergne, CNRS 6023-LMGE, EPIE, F-63001 Clermont-Ferrand, France
| | - Christel Regagnon
- CHU Clermont-Ferrand, 3IHP, Virology Laboratory, National Reference Centre for Enteroviruses and parechoviruses-associated laboratory, F-63003 Clermont-Ferrand, France
| | | | - Gregory Destras
- GenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004 Lyon, France; CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Bruno Simon
- GenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004 Lyon, France; CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Jacques Izopet
- CHU de Toulouse, Virology Laboratory, F-31300 Toulouse, France; INFINITY, INSERM UMR291-CNRS UMR5051-Toulouse University, F-31300 Toulouse, France; Université Toulouse III Paul Sabatier, F-31300 Toulouse, France
| | - Laurence Josset
- GenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004 Lyon, France; CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Cécile Henquell
- CHU Clermont-Ferrand, 3IHP, Virology Laboratory, National Reference Centre for Enteroviruses and parechoviruses-associated laboratory, F-63003 Clermont-Ferrand, France; Université Clermont Auvergne, CNRS 6023-LMGE, EPIE, F-63001 Clermont-Ferrand, France
| | - Audrey Mirand
- CHU Clermont-Ferrand, 3IHP, Virology Laboratory, National Reference Centre for Enteroviruses and parechoviruses-associated laboratory, F-63003 Clermont-Ferrand, France; Université Clermont Auvergne, CNRS 6023-LMGE, EPIE, F-63001 Clermont-Ferrand, France.
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Cai D, Shang J, Sun Y. HaploDMF: viral haplotype reconstruction from long reads via deep matrix factorization. Bioinformatics 2022; 38:5360-5367. [PMID: 36308467 PMCID: PMC9750122 DOI: 10.1093/bioinformatics/btac708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/06/2022] [Accepted: 10/25/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Lacking strict proofreading mechanisms, many RNA viruses can generate progeny with slightly changed genomes. Being able to characterize highly similar genomes (i.e. haplotypes) in one virus population helps study the viruses' evolution and their interactions with the host/other microbes. High-throughput sequencing data has become the major source for characterizing viral populations. However, the inherent limitation on read length by next-generation sequencing makes complete haplotype reconstruction difficult. RESULTS In this work, we present a new tool named HaploDMF that can construct complete haplotypes using third-generation sequencing (TGS) data. HaploDMF utilizes a deep matrix factorization model with an adapted loss function to learn latent features from aligned reads automatically. The latent features are then used to cluster reads of the same haplotype. Unlike existing tools whose performance can be affected by the overlap size between reads, HaploDMF is able to achieve highly robust performance on data with different coverage, haplotype number and error rates. In particular, it can generate more complete haplotypes even when the sequencing coverage drops in the middle. We benchmark HaploDMF against the state-of-the-art tools on simulated and real sequencing TGS data on different viruses. The results show that HaploDMF competes favorably against all others. AVAILABILITY AND IMPLEMENTATION The source code and the documentation of HaploDMF are available at https://github.com/dhcai21/HaploDMF. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Dehan Cai
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Jiayu Shang
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Yanni Sun
- To whom correspondence should be addressed.
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Bal A, Simon B, Destras G, Chalvignac R, Semanas Q, Oblette A, Quéromès G, Fanget R, Regue H, Morfin F, Valette M, Lina B, Josset L. Detection and prevalence of SARS-CoV-2 co-infections during the Omicron variant circulation in France. Nat Commun 2022; 13:6316. [PMID: 36274062 PMCID: PMC9588762 DOI: 10.1038/s41467-022-33910-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 10/07/2022] [Indexed: 12/25/2022] Open
Abstract
From December 2021-February 2022, an intense and unprecedented co-circulation of SARS-CoV-2 variants with high genetic diversity raised the question of possible co-infections between variants and how to detect them. Using 11 mixes of Delta:Omicron isolates at different ratios, we evaluated the performance of 4 different sets of primers used for whole-genome sequencing and developed an unbiased bioinformatics method for the detection of co-infections involving genetically distinct SARS-CoV-2 lineages. Applied on 21,387 samples collected between December 6, 2021 to February 27, 2022 from random genomic surveillance in France, we detected 53 co-infections between different lineages. The prevalence of Delta and Omicron (BA.1) co-infections and Omicron lineages BA.1 and BA.2 co-infections were estimated at 0.18% and 0.26%, respectively. Among 6,242 hospitalized patients, the intensive care unit (ICU) admission rates were 1.64%, 4.81% and 15.38% in Omicron, Delta and Delta/Omicron patients, respectively. No BA.1/BA.2 co-infections were reported among ICU admitted patients. Among the 53 co-infected patients, a total of 21 patients (39.6%) were not vaccinated. Although SARS-CoV-2 co-infections were rare in this study, their proper detection is crucial to evaluate their clinical impact and the risk of the emergence of potential recombinants.
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Affiliation(s)
- Antonin Bal
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France
- GenEPII sequencing platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm,U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Bruno Simon
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France
- GenEPII sequencing platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Gregory Destras
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France
- GenEPII sequencing platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm,U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Richard Chalvignac
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France
- GenEPII sequencing platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Quentin Semanas
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France
- GenEPII sequencing platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Antoine Oblette
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France
- GenEPII sequencing platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Grégory Quéromès
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm,U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Remi Fanget
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Hadrien Regue
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France
- GenEPII sequencing platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Florence Morfin
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France
- GenEPII sequencing platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm,U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Martine Valette
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Bruno Lina
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France
- GenEPII sequencing platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm,U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Laurence Josset
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France.
- GenEPII sequencing platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France.
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm,U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France.
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50
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Silva TDS, Salvato RS, Gregianini TS, Gomes IA, Pereira EC, de Oliveira E, de Menezes AL, Barcellos RB, Godinho FM, Riediger I, Debur MDC, de Oliveira CM, Ribeiro-Rodrigues R, Miyajima F, Dias FS, Abbud A, do Monte-Neto R, Calzavara-Silva CE, Siqueira MM, Wallau GL, Resende PC, Fernandes GDR, Alves P. Molecular characterization of a new SARS-CoV-2 recombinant cluster XAG identified in Brazil. Front Med (Lausanne) 2022; 9:1008600. [PMID: 36250091 PMCID: PMC9554242 DOI: 10.3389/fmed.2022.1008600] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
Recombination events have been described in the Coronaviridae family. Since the beginning of the SARS-CoV-2 pandemic, a variable degree of selection pressure has acted upon the virus, generating new strains with increased fitness in terms of viral transmission and antibody scape. Most of the SC2 variants of concern (VOC) detected so far carry a combination of key amino acid changes and indels. Recombination may also reshuffle existing genetic profiles of distinct strains, potentially giving origin to recombinant strains with altered phenotypes. However, co-infection and recombination events are challenging to detect and require in-depth curation of assembled genomes and sequencing reds. Here, we present the molecular characterization of a new SARS-CoV-2 recombinant between BA.1.1 and BA.2.23 Omicron lineages identified in Brazil. We characterized four mutations that had not been previously described in any of the recombinants already identified worldwide and described the likely breaking points. Moreover, through phylogenetic analysis, we showed that the newly named XAG lineage groups in a highly supported monophyletic clade confirmed its common evolutionary history from parental Omicron lineages and other recombinants already described. These observations were only possible thanks to the joint effort of bioinformatics tools auxiliary in genomic surveillance and the manual curation of experienced personnel, demonstrating the importance of genetic, and bioinformatic knowledge in genomics.
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Affiliation(s)
| | | | | | | | | | - Eneida de Oliveira
- Laboratório Municipal de Referência, Setor de Biologia Molecular, Belo Horizonte, Brazil
| | - André Luiz de Menezes
- Laboratório Municipal de Referência, Setor de Biologia Molecular, Belo Horizonte, Brazil
| | | | | | - Irina Riediger
- Laboratório Central de Saúde Pública do Estado do Paraná, Curitiba, Brazil
| | | | | | | | | | | | | | | | | | | | - Gabriel Luz Wallau
- Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | | | - Pedro Alves
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
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