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Kung YA, Chuang CH, Chen YC, Yang HP, Li HC, Chen CL, Janapatla RP, Chen CJ, Shih SR, Chiu CH. Worldwide SARS-CoV-2 Omicron variant infection: Emerging sub-variants and future vaccination perspectives. J Formos Med Assoc 2024:S0929-6646(24)00389-9. [PMID: 39179492 DOI: 10.1016/j.jfma.2024.08.021] [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: 02/06/2024] [Revised: 08/13/2024] [Accepted: 08/16/2024] [Indexed: 08/26/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has sparked widespread concern globally, particularly with the Omicron variant and its sub-lineages emerging as the predominant cause of infection for nearly two years. Taiwan's successful containment of COVID-19, underscored by broad vaccine coverage, the utilization of anti-viral therapeutics, and timely response strategies, has resulted in reduced excess mortality. Moreover, there is a crucial need for a phased exit strategy, balancing efforts to curtail disease transmission with the mitigation of socioeconomic impacts from rigorous measures. In this review, we examined the evolution and the epidemiological landscape of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sub-variants in Taiwan as well as other countries of the world. We also critically evaluated the effectiveness of COVID-19 vaccines against various SARS-CoV-2 variants. Additionally, we addressed the advantages of heterologous immunization strategies, fluctuations in neutralizing antibody titers, and complexities in establishing protective correlates among swiftly mutating viral variants.
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Affiliation(s)
- Yu-An Kung
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Hsien Chuang
- Department of Pediatrics, St. Paul's Hospital, Taoyuan, Taiwan; Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; School of Medicine, College of Medicine, Fu-Jen Catholic University, New Taipei, Taiwan
| | - Yi-Ching Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Hsin-Ping Yang
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Hsin-Chieh Li
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chyi-Liang Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | | | - Chin-Jung Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan.
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Nwokorogu VC, Pillai S, San JE, Pillay C, Nyaga MM, Sabiu S. A metagenomic investigation of the faecal RNA virome structure of asymptomatic chickens obtained from a commercial farm in Durban, KwaZulu-Natal province, South Africa. BMC Genomics 2024; 25:629. [PMID: 38914944 PMCID: PMC11194887 DOI: 10.1186/s12864-024-10517-6] [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: 01/13/2024] [Accepted: 06/12/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND Virome studies on birds, including chickens are relatively scarce, particularly from the African continent. Despite the continuous evolution of RNA viruses and severe losses recorded in poultry from seasonal viral outbreaks, the information on RNA virome composition is even scantier as a result of their highly unstable nature, genetic diversity, and difficulties associated with characterization. Also, information on factors that may modulate the occurrence of some viruses in birds is limited, particularly for domesticated birds. Viral metagenomics through advancements in sequencing technologies, has enabled the characterization of the entire virome of diverse host species using various samples. METHODS The complex RNA viral constituents present in 27 faecal samples of asymptomatic chickens from a South African farm collected at 3-time points from two independent seasons were determined, and the impact of the chicken's age and collection season on viral abundance and diversity was further investigated. The study utilized the non-invasive faecal sampling method, mRNA viral targeted enrichment steps, a whole transcriptome amplification strategy, Illumina sequencing, and bioinformatics tools. RESULTS The results obtained revealed a total of 48 viral species spanning across 11 orders, 15 families and 21 genera. Viral RNA families such as Coronaviridae, Picornaviridae, Reoviridae, Astroviridae, Caliciviridae, Picorbirnaviridae and Retroviridae were abundant, among which picornaviruses, demonstrated a 100% prevalence across the three age groups (2, 4 and 7 weeks) and two seasons (summer and winter) of the 27 faecal samples investigated. A further probe into the extent of variation between the different chicken groups investigated indicated that viral diversity and abundance were significantly influenced by age (P = 0.01099) and season (P = 0.00099) between chicken groups, while there was no effect on viral shedding within samples in a group (alpha diversity) for age (P = 0.146) and season (P = 0.242). CONCLUSION The presence of an exceedingly varied chicken RNA virome, encompassing avian, mammalian, fungal, and dietary-associated viruses, underscores the complexities inherent in comprehending the causation, dynamics, and interspecies transmission of RNA viruses within the investigated chicken population. Hence, chickens, even in the absence of discernible symptoms, can harbour viruses that may exhibit opportunistic, commensal, or pathogenic characteristics.
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Affiliation(s)
- Vivian C Nwokorogu
- Department of Biotechnology and Food Science, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Santhosh Pillai
- Department of Biotechnology and Food Science, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - James E San
- Nelson Mandela School of Medicine, KwaZulu-Natal Research Innovation and Sequencing platform unit, University of KwaZulu- Natal, 719 Umbilo Road, Durban, 4001, South Africa
| | - Charlene Pillay
- Department of Biotechnology and Food Science, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Martin M Nyaga
- Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa.
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Rogozin IB, Saura A, Poliakov E, Bykova A, Roche-Lima A, Pavlov YI, Yurchenko V. Properties and Mechanisms of Deletions, Insertions, and Substitutions in the Evolutionary History of SARS-CoV-2. Int J Mol Sci 2024; 25:3696. [PMID: 38612505 PMCID: PMC11011937 DOI: 10.3390/ijms25073696] [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: 02/25/2024] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024] Open
Abstract
SARS-CoV-2 has accumulated many mutations since its emergence in late 2019. Nucleotide substitutions leading to amino acid replacements constitute the primary material for natural selection. Insertions, deletions, and substitutions appear to be critical for coronavirus's macro- and microevolution. Understanding the molecular mechanisms of mutations in the mutational hotspots (positions, loci with recurrent mutations, and nucleotide context) is important for disentangling roles of mutagenesis and selection. In the SARS-CoV-2 genome, deletions and insertions are frequently associated with repetitive sequences, whereas C>U substitutions are often surrounded by nucleotides resembling the APOBEC mutable motifs. We describe various approaches to mutation spectra analyses, including the context features of RNAs that are likely to be involved in the generation of recurrent mutations. We also discuss the interplay between mutations and natural selection as a complex evolutionary trend. The substantial variability and complexity of pipelines for the reconstruction of mutations and the huge number of genomic sequences are major problems for the analyses of mutations in the SARS-CoV-2 genome. As a solution, we advocate for the development of a centralized database of predicted mutations, which needs to be updated on a regular basis.
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Affiliation(s)
- Igor B. Rogozin
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Andreu Saura
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Eugenia Poliakov
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anastassia Bykova
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Abiel Roche-Lima
- Center for Collaborative Research in Health Disparities—RCMI Program, Medical Sciences Campus, University of Puerto Rico, San Juan 00936, Puerto Rico
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
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4
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Scarpa F, Branda F, Petrosillo N, Ciccozzi M. On the SARS-CoV-2 Variants. Infect Dis Rep 2024; 16:289-297. [PMID: 38667750 PMCID: PMC11050187 DOI: 10.3390/idr16020024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/09/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
The evolutionary dynamics of viruses, particularly exemplified by SARS-CoV-2 during the ongoing COVID-19 pandemic, underscore the intricate interplay between genetics, host adaptation, and viral spread. This paper delves into the genetic evolution of SARS-CoV-2, emphasizing the implications of viral variants on global health. Initially emerging from the Wuhan-Hu-1 lineage, SARS-CoV-2 rapidly diversified into numerous variants, each characterized by distinct mutations in the spike protein and other genomic regions. Notable variants such as B.1.1.7 (α), B.1.351 (β), P.1 (γ), B.1.617.2 (δ), and the Omicron variant have garnered significant attention due to their heightened transmissibility and immune evasion capabilities. In particular, the Omicron variant has presented a myriad of subvariants, raising concerns about its potential impact on public health. Despite the emergence of numerous variants, the vast majority have exhibited limited expansion capabilities and have not posed significant threats akin to early pandemic strains. Continued genomic surveillance is imperative to identify emerging variants of concern promptly. While genetic adaptation is intrinsic to viral evolution, effective public health responses must be grounded in empirical evidence to navigate the evolving landscape of the pandemic with resilience and precision.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy
| | - Francesco Branda
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, 00128 Rome, Italy; (F.B.); (M.C.)
| | - Nicola Petrosillo
- Infection Prevention Control/Infectious Disease Service, Fondazione Policlinico Universitario Campus Bio-Medico, 00127 Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, 00128 Rome, Italy; (F.B.); (M.C.)
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5
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Karim F, Riou C, Bernstein M, Jule Z, Lustig G, van Graan S, Keeton RS, Upton JL, Ganga Y, Khan K, Reedoy K, Mazibuko M, Govender K, Thambu K, Ngcobo N, Venter E, Makhado Z, Hanekom W, von Gottberg A, Hoque M, Karim QA, Abdool Karim SS, Manickchund N, Magula N, Gosnell BI, Lessells RJ, Moore PL, Burgers WA, de Oliveira T, Moosa MYS, Sigal A. Clearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation. Nat Commun 2024; 15:2360. [PMID: 38491050 PMCID: PMC10943233 DOI: 10.1038/s41467-024-46673-2] [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: 08/10/2023] [Accepted: 02/27/2024] [Indexed: 03/18/2024] Open
Abstract
SARS-CoV-2 clearance requires adaptive immunity but the contribution of neutralizing antibodies and T cells in different immune states is unclear. Here we ask which adaptive immune responses associate with clearance of long-term SARS-CoV-2 infection in HIV-mediated immunosuppression after suppressive antiretroviral therapy (ART) initiation. We assembled a cohort of SARS-CoV-2 infected people in South Africa (n = 994) including participants with advanced HIV disease characterized by immunosuppression due to T cell depletion. Fifty-four percent of participants with advanced HIV disease had prolonged SARS-CoV-2 infection (>1 month). In the five vaccinated participants with advanced HIV disease tested, SARS-CoV-2 clearance associates with emergence of neutralizing antibodies but not SARS-CoV-2 specific CD8 T cells, while CD4 T cell responses were not determined due to low cell numbers. Further, complete HIV suppression is not required for clearance, although it is necessary for an effective vaccine response. Persistent SARS-CoV-2 infection led to SARS-CoV-2 evolution, including virus with extensive neutralization escape in a Delta variant infected participant. The results provide evidence that neutralizing antibodies are required for SARS-CoV-2 clearance in HIV-mediated immunosuppression recovery, and that suppressive ART is necessary to curtail evolution of co-infecting pathogens to reduce individual health consequences as well as public health risk linked with generation of escape mutants.
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Affiliation(s)
- Farina Karim
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | | | - Zesuliwe Jule
- Africa Health Research Institute, Durban, South Africa
| | - Gila Lustig
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Strauss van Graan
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Roanne S Keeton
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | | | - Yashica Ganga
- Africa Health Research Institute, Durban, South Africa
| | - Khadija Khan
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Kajal Reedoy
- Africa Health Research Institute, Durban, South Africa
| | | | | | | | | | - Elizabeth Venter
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Zanele Makhado
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Willem Hanekom
- Africa Health Research Institute, Durban, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Monjurul Hoque
- KwaDabeka Community Health Centre, KwaDabeka, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nithendra Manickchund
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nombulelo Magula
- Department of Internal Medicine, Nelson R. Mandela School of Medicine, University of Kwa-Zulu Natal, Durban, South Africa
| | - Bernadett I Gosnell
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard J Lessells
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Penny L Moore
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Wendy A Burgers
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Tulio de Oliveira
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
- Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Mahomed-Yunus S Moosa
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa.
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa.
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6
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Punacha G, Adiga R. Feature selection for effective prediction of SARS-COV-2 using machine learning. Genes Genomics 2024; 46:341-354. [PMID: 37985549 DOI: 10.1007/s13258-023-01467-6] [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: 05/06/2023] [Accepted: 10/01/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND With rise in variants of SARS-CoV-2, it is necessary to classify the emerging SARS-CoV-2 for early detection and thereby reduce human transmission. Genomic and proteomic information have less frequently been used for classifying in a machine learning (ML) approach for detection of SARS-CoV-2. OBJECTIVE With this aim we used nucleoprotein and viral proteomic evolutionary information of SARS-CoV-2 along with the charge and basicity distribution of amino acids from various strains of SARS-CoV-2 to generate a disease severity model based on ML. METHODS All sequence and clinical data were obtained from GISAID. Proteomic level calculations were added to comprise the dataset. The training set was used for feature selection. Select K- Best feature selection method was employed which was cross validated with testing set and performance evaluated. Delong's test was also done. We also employed BIRCH clustering on SARS-CoV-2 for clustering the strains. RESULTS Out of six ML models four were successful in training and testing. Extra Trees algorithm generated a micro-averaged F1-score of 74.2% and a weighted averaged area under the receiver operating characteristic curve (AUC-ROC) score of 73.7% with multi-class option. The feature selection set to 5, enhanced the ROC AUC from 73.7 to 76.4%. Accuracy of the selected model of 86.9% was achieved. CONCLUSION The unique features identified in the ML approach was able to classify disease severity into classes and had potential for predicting risk in newer variants.
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Affiliation(s)
- Gagan Punacha
- Nitte (Deemed to be University), Department of Molecular Genetics & Cancer, Nitte University Centre for Science Education & Research (NUCSER), Mangalore, Karnataka, India
| | - Rama Adiga
- Nitte (Deemed to be University), Department of Molecular Genetics & Cancer, Nitte University Centre for Science Education & Research (NUCSER), Mangalore, Karnataka, India.
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Hakim MS, Gunadi, Rahayu A, Wibawa H, Eryvinka LS, Supriyati E, Vujira KA, Iskandar K, Afiahayati, Daniwijaya EW, Oktoviani FN, Annisa L, Utami FDT, Amadeus VC, Nurhidayah SS, Leksono TP, Halim FV, Arguni E, Nuryastuti T, Wibawa T. Sequence analysis of the Spike, RNA-dependent RNA polymerase, and protease genes reveals a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia. Virus Genes 2024:10.1007/s11262-023-02048-1. [PMID: 38244104 DOI: 10.1007/s11262-023-02048-1] [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: 06/25/2023] [Accepted: 12/22/2023] [Indexed: 01/22/2024]
Abstract
During the Covid-19 pandemic, the resurgence of SARS-CoV-2 was due to the development of novel variants of concern (VOC). Thus, genomic surveillance is essential to monitor continuing evolution of SARS-CoV-2 and to track the emergence of novel variants. In this study, we performed phylogenetic, mutation, and selection pressure analyses of the Spike, nsp12, nsp3, and nsp5 genes of SARS-CoV-2 isolates circulating in Yogyakarta and Central Java provinces, Indonesia from May 2021 to February 2022. Various bioinformatics tools were employed to investigate the evolutionary dynamics of distinct SARS-CoV-2 isolates. During the study period, 213 and 139 isolates of Omicron and Delta variants were identified, respectively. Particularly in the Spike gene, mutations were significantly more abundant in Omicron than in Delta variants. Consistently, in all of four genes studied, the substitution rates of Omicron were higher than that of Delta variants, especially in the Spike and nsp12 genes. In addition, selective pressure analysis revealed several sites that were positively selected in particular genes, implying that these sites were functionally essential for virus evolution. In conclusion, our study demonstrated a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia.
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Affiliation(s)
- Mohamad Saifudin Hakim
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.
| | - Gunadi
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ayu Rahayu
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hendra Wibawa
- Disease Investigation Center Wates, Directorate General of Livestok Services, Ministry of Agriculture, Yogyakarta, Indonesia
| | - Laudria Stella Eryvinka
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Khanza Adzkia Vujira
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Kristy Iskandar
- Department of Child Health and Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Afiahayati
- Department of Computer Science and Electronics, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Edwin Widyanto Daniwijaya
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Farida Nur Oktoviani
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Luthvia Annisa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Fadila Dyah Trie Utami
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Verrell Christopher Amadeus
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Setiani Silvy Nurhidayah
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tiara Putri Leksono
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Fiqih Vidiantoro Halim
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
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Ferrareze PAG, Cybis GB, de Oliveira LFV, Zimerman RA, Schiavon DEB, Peter C, Thompson CE. Intense P.1 (Gamma) diversification followed by rapid Delta substitution in Southern Brazil: a SARS-CoV-2 genomic epidemiology study. Microbes Infect 2024; 26:105216. [PMID: 37827275 DOI: 10.1016/j.micinf.2023.105216] [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: 07/04/2023] [Revised: 08/30/2023] [Accepted: 09/03/2023] [Indexed: 10/14/2023]
Abstract
The analyses of genetic traits, dispersion patterns and phylogenomics are essential for understanding the evolutionary forces driving SARS-CoV-2 viruses in these three years of COVID-19 pandemics. Brazil is one of the most affected countries in the world and not sufficient genomic studies have been performed. The emergence of P.1 lineage led to one of the most serious public health crises on record. Our study presents the genomic sequencing and characterization of 412 samples from Rio Grande do Sul state, in the Brazilian Southern region, during Gamma and Delta epidemic waves, in 2021. Additionally, molecular evolution tests were performed to identify positively selected sites in Brazil between 2020 and 2022, as well as offer some evolutionary perspective about the maintenance of multiple spike mutations in Omicron lineages. Genomic epidemiology analysis has indicated an intense P.1 (Gamma) diversification followed by rapid Delta substitution in Southern Brazil.
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Affiliation(s)
- Patrícia Aline Gröhs Ferrareze
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Gabriela Betella Cybis
- Department of Statistics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | | | - Dieine Estela Bernieri Schiavon
- Undergraduate Program in Biomedical Informatics, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Claudia Elizabeth Thompson
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil; Department of Pharmacosciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil.
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9
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Lustig G, Ganga Y, Rodel HE, Tegally H, Khairallah A, Jackson L, Cele S, Khan K, Jule Z, Reedoy K, Karim F, Bernstein M, Ndung’u T, Moosa MYS, Archary D, de Oliveira T, Lessells R, Neher RA, Abdool Karim SS, Sigal A. SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations. Virus Evol 2023; 10:vead075. [PMID: 38361824 PMCID: PMC10868398 DOI: 10.1093/ve/vead075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/11/2023] [Accepted: 12/21/2023] [Indexed: 02/17/2024] Open
Abstract
One mechanism of variant formation may be evolution during long-term infection in immunosuppressed people. To understand the viral phenotypes evolved during such infection, we tested SARS-CoV-2 viruses evolved from an ancestral B.1 lineage infection lasting over 190 days post-diagnosis in an advanced HIV disease immunosuppressed individual. Sequence and phylogenetic analysis showed two evolving sub-lineages, with the second sub-lineage replacing the first sub-lineage in a seeming evolutionary sweep. Each sub-lineage independently evolved escape from neutralizing antibodies. The most evolved virus for the first sub-lineage (isolated day 34) and the second sub-lineage (isolated day 190) showed similar escape from ancestral SARS-CoV-2 and Delta-variant infection elicited neutralizing immunity despite having no spike mutations in common relative to the B.1 lineage. The day 190 isolate also evolved higher cell-cell fusion and faster viral replication and caused more cell death relative to virus isolated soon after diagnosis, though cell death was similar to day 34 first sub-lineage virus. These data show that SARS-CoV-2 strains in prolonged infection in a single individual can follow independent evolutionary trajectories which lead to neutralization escape and other changes in viral properties.
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Affiliation(s)
- Gila Lustig
- Centre for the AIDS Programme of Research in South Africa, 719 Umbilo Road, Durban 4001, South Africa
| | - Yashica Ganga
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Hylton E Rodel
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- Division of Infection and Immunity, University College London, UCL Cruciform Building Gower Street, London WC1E 6BT, UK
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform, 719 Umbilo Road, Durban 4001, South Africa
- Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Francie Van Zijl Drive, Cape Town 7505, South Africa
| | - Afrah Khairallah
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Laurelle Jackson
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Sandile Cele
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
| | - Khadija Khan
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
| | - Zesuliwe Jule
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Kajal Reedoy
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Farina Karim
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
| | - Mallory Bernstein
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Thumbi Ndung’u
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- Division of Infection and Immunity, University College London, UCL Cruciform Building Gower Street, London WC1E 6BT, UK
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
- HIV Pathogenesis Programme, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
- Ragon Institute of MGH, MIT and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Mahomed-Yunus S Moosa
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
| | - Derseree Archary
- Centre for the AIDS Programme of Research in South Africa, 719 Umbilo Road, Durban 4001, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform, 719 Umbilo Road, Durban 4001, South Africa
- Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Francie Van Zijl Drive, Cape Town 7505, South Africa
- Department of Global Health, University of Washington, 3980 15th Avenue NE, Seattle, WA 98105, USA
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform, 719 Umbilo Road, Durban 4001, South Africa
| | - Richard A Neher
- SIB Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, Lausanne 1015, Switzerland
- Biozentrum, University of Basel, Spitalstrasse 41 4056, Basel, Switzerland
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, 719 Umbilo Road, Durban 4001, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY 10032, United States
| | - Alex Sigal
- Centre for the AIDS Programme of Research in South Africa, 719 Umbilo Road, Durban 4001, South Africa
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
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10
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Khan K, Lustig G, Römer C, Reedoy K, Jule Z, Karim F, Ganga Y, Bernstein M, Baig Z, Jackson L, Mahlangu B, Mnguni A, Nzimande A, Stock N, Kekana D, Ntozini B, van Deventer C, Marshall T, Manickchund N, Gosnell BI, Lessells RJ, Karim QA, Abdool Karim SS, Moosa MYS, de Oliveira T, von Gottberg A, Wolter N, Neher RA, Sigal A. Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariant. Nat Commun 2023; 14:8078. [PMID: 38057313 PMCID: PMC10700484 DOI: 10.1038/s41467-023-43703-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023] Open
Abstract
Omicron BA.2.86 subvariant differs from Omicron BA.2 as well as recently circulating variants by over 30 mutations in the spike protein alone. Here we report on the isolation of the live BA.2.86 subvariant from a diagnostic swab collected in South Africa which we tested for escape from neutralizing antibodies and viral replication properties in cell culture. We found that BA.2.86 does not have significantly more escape relative to Omicron XBB.1.5 from neutralizing immunity elicited by either Omicron XBB-family subvariant infection or from residual neutralizing immunity of recently collected sera from the South African population. BA.2.86 does have extensive escape relative to ancestral virus with the D614G substitution (B.1 lineage) when neutralized by sera from pre-Omicron vaccinated individuals and relative to Omicron BA.1 when neutralized by sera from Omicron BA.1 infected individuals. BA.2.86 and XBB.1.5 show similar viral infection dynamics in the VeroE6-TMPRSS2 and H1299-ACE2 cell lines. We also investigate the relationship of BA.2.86 to BA.2 sequences. The closest BA.2 sequences are BA.2 samples from Southern Africa circulating in early 2022. Similarly, many basal BA.2.86 sequences were sampled in Southern Africa. This suggests that BA.2.86 potentially evolved in this region, and that unobserved evolution led to escape from neutralizing antibodies similar in scale to recently circulating strains of SARS-CoV-2.
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Affiliation(s)
- Khadija Khan
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Gila Lustig
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Cornelius Römer
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kajal Reedoy
- Africa Health Research Institute, Durban, South Africa
| | - Zesuliwe Jule
- Africa Health Research Institute, Durban, South Africa
| | - Farina Karim
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Yashica Ganga
- Africa Health Research Institute, Durban, South Africa
| | | | - Zainab Baig
- Africa Health Research Institute, Durban, South Africa
| | | | - Boitshoko Mahlangu
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Anele Mnguni
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Ayanda Nzimande
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nadine Stock
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Dikeledi Kekana
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Buhle Ntozini
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | | | | | - Nithendra Manickchund
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Bernadett I Gosnell
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard J Lessells
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Mahomed-Yunus S Moosa
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Tulio de Oliveira
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
- Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Richard A Neher
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa.
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa.
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11
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Mena J, Hidalgo C, Estay-Olea D, Sallaberry-Pincheira N, Bacigalupo A, Rubio AV, Peñaloza D, Sánchez C, Gómez-Adaros J, Olmos V, Cabello J, Ivelic K, Abarca MJ, Ramírez-Álvarez D, Torregrosa Rocabado M, Durán Castro N, Carreño M, Gómez G, Cattan PE, Ramírez-Toloza G, Robbiano S, Marchese C, Raffo E, Stowhas P, Medina-Vogel G, Landaeta-Aqueveque C, Ortega R, Waleckx E, Gónzalez-Acuña D, Rojo G. Molecular surveillance of potential SARS-CoV-2 reservoir hosts in wildlife rehabilitation centers. Vet Q 2023; 43:1-10. [PMID: 36594266 PMCID: PMC9858396 DOI: 10.1080/01652176.2023.2164909] [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: 04/22/2022] [Accepted: 12/31/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The COVID-19 pandemic, caused by SARS-CoV-2 infection, has become the most devastating zoonotic event in recent times, with negative impacts on both human and animal welfare as well as on the global economy. Although SARS-CoV-2 is considered a human virus, it likely emerged from animals, and it can infect both domestic and wild animals. This constitutes a risk for human and animal health including wildlife with evidence of SARS-CoV-2 horizontal transmission back and forth between humans and wild animals. AIM Molecular surveillance in different wildlife rehabilitation centers and wildlife associated institutions in Chile, which are critical points of animal-human interaction and wildlife conservation, especially since the aim of wildlife rehabilitation centers is to reintroduce animals to their original habitat. MATERIALS AND METHODS The survey was conducted in six WRCs and three wildlife associated institutions. A total of 185 samples were obtained from 83 individuals belonging to 15 different species, including vulnerable and endangered species. Each specimen was sampled with two different swabs: one oropharyngeal or nasopharyngeal according to the nostril diameter, and/or a second rectal sample. RNA was extracted from the samples and two different molecular assays were performed: first, a conventional RT-PCR with pan-coronavirus primers and a second SARS-CoV-2 qPCR targeting the N and S genes. RESULTS All 185 samples were negative for SARS-CoV-2. CLINICAL RELEVANCE This study constitutes the first report on the surveillance of SARS-CoV-2 from wildlife treated in rehabilitation centers in Chile, and supports the biosafety procedures adopted in those centers.
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Affiliation(s)
- Juan Mena
- Instituto de Ciencias Agroalimentarias, Animales y Ambientales (ICA3), Universidad de O'Higgins, San Fernando, Chile
| | - Christian Hidalgo
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas (NIAVA), Universidad de Las Américas, Chile
| | - Daniela Estay-Olea
- Instituto de Ciencias Agroalimentarias, Animales y Ambientales (ICA3), Universidad de O'Higgins, San Fernando, Chile
| | - Nicole Sallaberry-Pincheira
- Unidad de Rehabilitación de Fauna Silvestre (UFAS), Escuela de Medicina Veterinaria, Universidad Andres Bello, Santiago, Chile
| | - Antonella Bacigalupo
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - André V. Rubio
- Departamento de Ciencias Biológicas Animales, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Diego Peñaloza
- Departamento de Áreas Silvestres Protegidas, Corporación Nacional Forestal (CONAF), Región del Libertador General Bernardo O’Higgins, Rancagua, Chile
| | - Carolina Sánchez
- Unidad de Rehabilitación de Fauna Silvestre (UFAS), Escuela de Medicina Veterinaria, Universidad Andres Bello, Santiago, Chile
| | | | - Valeria Olmos
- Centro de Rehabilitación y Exhibición de Fauna Silvestre, Rancagua, Chile
| | - Javier Cabello
- Centro de Conservación de la Biodiversidad, Ancud, Chile
| | - Kendra Ivelic
- Refugio Animal Cascada, Centro de Rehabilitación y Exhibición de fauna nativa de la Fundación Acción Fauna, Santiago, Chile
| | - María José Abarca
- Comité Nacional Pro Defensa de la Fauna y Flora (CODEFF), Santiago, Chile
| | - Diego Ramírez-Álvarez
- Servicio Agrícola y Ganadero de Chile (SAG), Unidad de Vida Silvestre, Rancagua, Chile
| | - Marisol Torregrosa Rocabado
- Médico Veterinaria Encargada Sección Salud Animal, Zoológico Nacional del Parque Metropolitano, Santiago, Chile
| | - Natalia Durán Castro
- Médico Veterinaria Sección Salud Animal, Zoológico Nacional del Parque Metropolitano, Santiago, Chile
| | | | - Gabriela Gómez
- Departamento de Áreas Silvestres Protegidas, Corporación Nacional Forestal (CONAF), Región de Aysén, Chile
| | - Pedro E. Cattan
- Departamento de Ciencias Biológicas Animales, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Galia Ramírez-Toloza
- Departamento de Medicina Preventiva, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Sofía Robbiano
- Centro de Rehabilitación de Fauna Silvestre, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Carla Marchese
- Servicio Agrícola y Ganadero de Chile (SAG), Unidad de Vida Silvestre, Valdivia, Chile
| | - Eduardo Raffo
- Servicio Agrícola y Ganadero de Chile (SAG), Unidad de Vida Silvestre, Valdivia, Chile
| | - Paulina Stowhas
- Programa Nacional Integrado de Gestión de Especies Exóticas Invasoras, Ministerio del Medio Ambiente, Santiago, Chile
| | - Gonzalo Medina-Vogel
- Centro de Investigación para la Sustentabilidad (CIS), Universidad Andres Bello, Santiago, Chile
| | - Carlos Landaeta-Aqueveque
- Departamento Patología y Medicina Preventiva, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - René Ortega
- Departamento Patología y Medicina Preventiva, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Etienne Waleckx
- Institut de Recherche pour le Développement, UMR INTERTRYP IRD, CIRAD, Université de Montpellier, Montpellier, France
- Laboratorio de Parasitología, Centro de Investigaciones Regionales “Dr Hideyo Noguchi”, Universidad Autónoma de Yucatán, Mérida, México
| | - Daniel Gónzalez-Acuña
- Departamento Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Gemma Rojo
- Instituto de Ciencias Agroalimentarias, Animales y Ambientales (ICA3), Universidad de O'Higgins, San Fernando, Chile
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12
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Alruwaili M, Armstrong S, Prince T, Erdmann M, Matthews DA, Luu L, Davidson A, Aljabr W, Hiscox JA. SARS-CoV-2 NSP12 associates with TRiC and the P323L substitution acts as a host adaption. J Virol 2023; 97:e0042423. [PMID: 37929963 PMCID: PMC10688337 DOI: 10.1128/jvi.00424-23] [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: 03/19/2023] [Accepted: 08/29/2023] [Indexed: 11/07/2023] Open
Abstract
IMPORTANCE SARS-CoV-2 has caused a worldwide health and economic crisis. During the course of the pandemic, genetic changes occurred in the virus, which have resulted in new properties of the virus-particularly around gains in transmission and the ability to partially evade either natural or vaccine-acquired immunity. Some of these viruses have been labeled Variants of Concern (VoCs). At the root of all VoCs are two mutations, one in the viral spike protein that has been very well characterized and the other in the virus polymerase (NSP12). This is the viral protein responsible for replicating the genome. We show that NSP12 associates with host cell proteins that act as a scaffold to facilitate the function of this protein. Furthermore, we found that different variants of NSP12 interact with host cell proteins in subtle and different ways, which affect function.
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Affiliation(s)
- Muhannad Alruwaili
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Medical Laboratory Technology Department, Northern Border University, Arar City, Saudi Arabia
| | - Stuart Armstrong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Tessa Prince
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Maximillian Erdmann
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - David A. Matthews
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Lisa Luu
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Andrew Davidson
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | | | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
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13
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Nakagawa S, Katayama T, Jin L, Wu J, Kryukov K, Oyachi R, Takeuchi JS, Fujisawa T, Asano S, Komatsu M, Onami JI, Abe T, Arita M. SARS-CoV-2 HaploGraph: visualization of SARS-CoV-2 haplotype spread in Japan. Genes Genet Syst 2023; 98:221-237. [PMID: 37839865 DOI: 10.1266/ggs.23-00085] [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] [Indexed: 10/17/2023] Open
Abstract
Since the early phase of the coronavirus disease 2019 (COVID-19) pandemic, a number of research institutes have been sequencing and sharing high-quality severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes to trace the route of infection in Japan. To provide insight into the spread of COVID-19, we developed a web platform named SARS-CoV-2 HaploGraph to visualize the emergence timing and geographical transmission of SARS-CoV-2 haplotypes. Using data from the GISAID EpiCoV database as of June 4, 2022, we created a haplotype naming system by determining the ancestral haplotype for each epidemic wave and showed prefecture- or region-specific haplotypes in each of four waves in Japan. The SARS-CoV-2 HaploGraph allows for interactive tracking of virus evolution and of geographical prevalence of haplotypes, and aids in developing effective public health control strategies during the global pandemic. The code and the data used for this study are publicly available at: https://github.com/ktym/covid19/.
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Affiliation(s)
- So Nakagawa
- Bioinformation and DDBJ Center, National Institute of Genetics
- Department of Molecular Life Science, Tokai University School of Medicine
- Micro/Nano Technology Center, Tokai University
- Institute of Medical Sciences, Tokai University
| | | | | | - Jiaqi Wu
- Department of Molecular Life Science, Tokai University School of Medicine
| | - Kirill Kryukov
- Bioinformation and DDBJ Center, National Institute of Genetics
- Department of Informatics, National Institute of Genetics
| | - Rise Oyachi
- Department of Molecular Life Science, Tokai University School of Medicine
| | - Junko S Takeuchi
- Center for Clinical Sciences, National Center for Global Health and Medicine
| | | | - Satomi Asano
- Department of Informatics, National Institute of Genetics
| | - Momoka Komatsu
- Smart Information Systems, Faculty of Engineering, Niigata University
| | - Jun-Ichi Onami
- Research Center for Open Science and Data Platform, National Institute of Informatics
| | - Takashi Abe
- Bioinformation and DDBJ Center, National Institute of Genetics
- Smart Information Systems, Faculty of Engineering, Niigata University
| | - Masanori Arita
- Bioinformation and DDBJ Center, National Institute of Genetics
- Department of Informatics, National Institute of Genetics
- RIKEN Center for Sustainable Resource Science
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14
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Gilliland T, Dunn M, Liu Y, Alcorn MD, Terada Y, Vasilatos S, Lundy J, Li R, Nambulli S, Larson D, Duprex P, Wu H, Luke T, Bausch C, Egland K, Sullivan E, Wang Z, Klimstra WB. Transchromosomic bovine-derived anti-SARS-CoV-2 polyclonal human antibodies protects hACE2 transgenic hamsters against multiple variants. iScience 2023; 26:107764. [PMID: 37736038 PMCID: PMC10509298 DOI: 10.1016/j.isci.2023.107764] [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: 04/18/2023] [Revised: 07/24/2023] [Accepted: 08/25/2023] [Indexed: 09/23/2023] Open
Abstract
Pandemic SARS-CoV-2 has undergone rapid evolution resulting in the emergence of many variants with mutations in the spike protein, some of which appear to evade antibody neutralization, transmit more efficiently, and/or exhibit altered virulence. This raises significant concerns regarding the efficacy of anti-S monoclonal antibody-based therapeutics which have failed against variant SARS-CoV-2 viruses. To address this concern, SAB-185, a human anti-SARS-CoV-2 polyclonal antibody was generated in the DiversitAb platform. SAB-185 exhibited equivalent, robust in vitro neutralization for Munich, Alpha, Beta, Gamma, and Δ144-146 variants and, although diminished, retained PRNT50 and PRNT80 neutralization endpoints for Delta and Omicron variants. Human ACE2 transgenic Syrian hamsters, which exhibit lethal SARS-CoV-2 disease, were protected from mortality after challenge with the Munich, Alpha, Beta, Delta, and Δ144-146 variants and clinical signs after non-lethal Omicron BA.1 infection. This suggests that SAB-185 may be an effective immunotherapy even in the presence of ongoing viral mutation.
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Affiliation(s)
- Theron Gilliland
- Center for Vaccine Research and Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Matthew Dunn
- Center for Vaccine Research and Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yanan Liu
- Department of Animal Dairy, Veterinary Sciences, Utah State University, Logan, UT 84341, USA
| | - Maria D.H. Alcorn
- Center for Vaccine Research and Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yutaka Terada
- Center for Vaccine Research and Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Shauna Vasilatos
- Center for Vaccine Research and Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jeneveve Lundy
- Center for Vaccine Research and Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Rong Li
- Department of Animal Dairy, Veterinary Sciences, Utah State University, Logan, UT 84341, USA
| | - Sham Nambulli
- Center for Vaccine Research and Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Deanna Larson
- Department of Animal Dairy, Veterinary Sciences, Utah State University, Logan, UT 84341, USA
| | - Paul Duprex
- Center for Vaccine Research and Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Hua Wu
- SAb Biotherapeutics, Inc, Sioux Falls, SD 57104, USA
| | - Thomas Luke
- SAb Biotherapeutics, Inc, Sioux Falls, SD 57104, USA
| | | | - Kristi Egland
- SAb Biotherapeutics, Inc, Sioux Falls, SD 57104, USA
| | | | - Zhongde Wang
- Department of Animal Dairy, Veterinary Sciences, Utah State University, Logan, UT 84341, USA
| | - William B. Klimstra
- Center for Vaccine Research and Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
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15
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Wu M, Liu J, Wang X, Zhang X, Liang T, Chen L, Huang T, Li Y, Zheng C, Yang Y, Wang J, Yu X, Guo L, Yang J, Ren L. Profiling of SARS-CoV-2 neutralizing antibody-associated antigenic peptides signature using proteome microarray. MedComm (Beijing) 2023; 4:e361. [PMID: 37667740 PMCID: PMC10475218 DOI: 10.1002/mco2.361] [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: 11/24/2022] [Revised: 08/02/2023] [Accepted: 08/06/2023] [Indexed: 09/06/2023] Open
Abstract
The profile of antibodies against antigenic epitopes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during neutralizing antibody (NAb) decay has not been clarified. Using a SARS-CoV-2 proteome microarray that contained viral antigenic peptides, we analyzed the characteristics of the humoral response in patients with coronavirus disease 19 (COVID-19) in a longitudinal study. A total of 89 patients were recruited, and 226 plasma samples were serially collected in 2020. In the antigenic peptide microarray, the level of immunoglobulin G (IgG) antibodies against peptides within the S2 subunit (S-82) and a conserved gene region in variants of interest, open reading frame protein 10 (ORF10-3), were closely associated with the presence of SARS-CoV-2 NAbs. In an independent evaluation cohort of 232 plasma samples collected from 116 COVID-19 cases in 2020, S82-IgG titers were higher in NAbs-positive samples (p = 0.002) than in NAbs-negative samples using enzyme-linked immunosorbent assay. We further collected 66 plasma samples from another cohort infected by Omicron BA.1 virus in 2022. Compared with the samples with lower S82-IgG titers, NAb titers were significantly higher in the samples with higher S82-IgG titers (p = 0.04). Our findings provide insights into the understanding of the decay-associated signatures of SARS-CoV-2 NAbs.
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Affiliation(s)
- Mingkun Wu
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux LaboratoryInstitute of Pathogen BiologyChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
| | - Jiangfeng Liu
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
| | - Xinming Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux LaboratoryInstitute of Pathogen BiologyChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
| | - Xiaomei Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research CenterNational Center for Protein Sciences‐Beijing (PHOENIX Center)Beijing Institute of LifeomicsBeijingChina
| | - Te Liang
- State Key Laboratory of Proteomics, Beijing Proteome Research CenterNational Center for Protein Sciences‐Beijing (PHOENIX Center)Beijing Institute of LifeomicsBeijingChina
| | - Lan Chen
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux LaboratoryInstitute of Pathogen BiologyChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
| | - Tingxuan Huang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux LaboratoryInstitute of Pathogen BiologyChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
| | - Yanan Li
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux LaboratoryInstitute of Pathogen BiologyChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
| | - Chang Zheng
- State Key Laboratory of Proteomics, Beijing Proteome Research CenterNational Center for Protein Sciences‐Beijing (PHOENIX Center)Beijing Institute of LifeomicsBeijingChina
| | - Yehong Yang
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
| | - Jianwei Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux LaboratoryInstitute of Pathogen BiologyChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
- Key Laboratory of Respiratory Disease PathogenomicsChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research CenterNational Center for Protein Sciences‐Beijing (PHOENIX Center)Beijing Institute of LifeomicsBeijingChina
| | - Li Guo
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux LaboratoryInstitute of Pathogen BiologyChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
- Key Laboratory of Respiratory Disease PathogenomicsChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Juntao Yang
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
| | - Lili Ren
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux LaboratoryInstitute of Pathogen BiologyChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
- Key Laboratory of Respiratory Disease PathogenomicsChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
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16
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Jose-Abrego A, Roman S, Laguna-Meraz S, Panduro A. Host and HBV Interactions and Their Potential Impact on Clinical Outcomes. Pathogens 2023; 12:1146. [PMID: 37764954 PMCID: PMC10535809 DOI: 10.3390/pathogens12091146] [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: 08/09/2023] [Revised: 08/27/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Hepatitis B virus (HBV) is a challenge for global health services, affecting millions and leading thousands to end-stage liver disease each year. This comprehensive review explores the interactions between HBV and the host, examining their impact on clinical outcomes. HBV infection encompasses a spectrum of severity, ranging from acute hepatitis B to chronic hepatitis B, which can potentially progress to cirrhosis and hepatocellular carcinoma (HCC). Occult hepatitis B infection (OBI), characterized by low HBV DNA levels in hepatitis B surface antigen-negative individuals, can reactivate and cause acute hepatitis B. HBV genotyping has revealed unique geographical patterns and relationships with clinical outcomes. Moreover, single nucleotide polymorphisms (SNPs) within the human host genome have been linked to several clinical outcomes, including cirrhosis, HCC, OBI, hepatitis B reactivation, and spontaneous clearance. The immune response plays a key role in controlling HBV infection by eliminating infected cells and neutralizing HBV in the bloodstream. Furthermore, HBV can modulate host metabolic pathways involved in glucose and lipid metabolism and bile acid absorption, influencing disease progression. HBV clinical outcomes correlate with three levels of viral adaptation. In conclusion, the clinical outcomes of HBV infection could result from complex immune and metabolic interactions between the host and HBV. These outcomes can vary among populations and are influenced by HBV genotypes, host genetics, environmental factors, and lifestyle. Understanding the degrees of HBV adaptation is essential for developing region-specific control and prevention measures.
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Affiliation(s)
- Alexis Jose-Abrego
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, “Fray Antonio Alcalde”, Guadalajara 44280, Mexico; (A.J.-A.); (S.R.); (S.L.-M.)
- Health Sciences Center, University of Guadalajara, Guadalajara 44340, Mexico
| | - Sonia Roman
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, “Fray Antonio Alcalde”, Guadalajara 44280, Mexico; (A.J.-A.); (S.R.); (S.L.-M.)
- Health Sciences Center, University of Guadalajara, Guadalajara 44340, Mexico
| | - Saul Laguna-Meraz
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, “Fray Antonio Alcalde”, Guadalajara 44280, Mexico; (A.J.-A.); (S.R.); (S.L.-M.)
- Health Sciences Center, University of Guadalajara, Guadalajara 44340, Mexico
| | - Arturo Panduro
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, “Fray Antonio Alcalde”, Guadalajara 44280, Mexico; (A.J.-A.); (S.R.); (S.L.-M.)
- Health Sciences Center, University of Guadalajara, Guadalajara 44340, Mexico
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17
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Burgos G, Ambuludí A, Morales-Jadán D, Garcia-Bereguiain MA, Muslin C, Armijos-Jaramillo V. A tool for the cheap and rapid screening of SARS-CoV-2 variants of concern (VoCs) by Sanger sequencing. Microbiol Spectr 2023; 11:e0506422. [PMID: 37676038 PMCID: PMC10586709 DOI: 10.1128/spectrum.05064-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 07/05/2023] [Indexed: 09/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging virus that, since March 2020, has been responsible for a global and ongoing pandemic. Its rapid spread over the past nearly 3 years has caused novel variants to arise. To monitor the circulation and emergence of SARS-CoV-2 variants, surveillance systems based on nucleotide mutations are required. In this regard, we searched in the spike, ORF8, and nucleocapsid genes to detect variable sites among SARS-CoV-2 variants. We describe polymorphic genetic regions that enable us to differentiate between the Alpha, Beta, Gamma, Delta, and Omicron variants of concern (VoCs). We found 21 relevant mutations, 13 of which are unique for Omicron lineages BA.1/BA.1.1, BA.2, BA.3, BA.4, and BA.5. This genetic profile enables the discrimination between VoCs using only four reverse transcription PCR fragments and Sanger sequencing, offering a cheaper and faster alternative to whole-genome sequencing for SARS-CoV-2 surveillance. IMPORTANCE Our work describes a new (Sanger sequencing-based) screening methodology for SARS-CoV-2, performing PCR amplifications of a few target regions to detect diagnostic mutations between virus variants. Using the methodology developed in this work, we were able to discriminate between the following VoCs: Alpha, Beta, Gamma, Delta, and Omicron (BA.1/BA.1.1, BA.2, BA.3, BA.4, and BA.5). This becomes important, especially in low-income countries where current methodologies like next-generation sequencing have prohibitive costs. Furthermore, rapid detection would allow sanitary authorities to take rapid measures to limit the spread of the virus and therefore reduce the probability of new virus dispersion. With this methodological approach, 13 previously unreported diagnostic mutations among several Omicron lineages were found.
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Affiliation(s)
- Germán Burgos
- Facultad de Medicina, Universidad de Las Américas (UDLA), Quito, Ecuador
- One Health Research Group, Faculty of Health Sciences, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - Andrés Ambuludí
- Carrera de Ingeniería en Biotecnología, Facultad de Ingenierías y Ciencias Aplicadas, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - USFQ SARS-CoV-2 Consortium
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales (COCIBA), Universidad San Francisco de Quito (USFQ), Cumbaya, Ecuador
| | - Diana Morales-Jadán
- One Health Research Group, Faculty of Health Sciences, Universidad de Las Américas (UDLA), Quito, Ecuador
| | | | - Claire Muslin
- One Health Research Group, Faculty of Health Sciences, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - Vinicio Armijos-Jaramillo
- Carrera de Ingeniería en Biotecnología, Facultad de Ingenierías y Ciencias Aplicadas, Universidad de Las Américas (UDLA), Quito, Ecuador
- Grupo de Bio-Quimioinformática, Universidad de Las Américas (UDLA), Quito, Ecuador
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18
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Bellocchi MC, Scutari R, Carioti L, Iannetta M, Marchegiani G, Piermatteo L, Coppola L, Tedde S, Duca L, Malagnino V, Ansaldo L, Braccialarghe N, D′Anna S, Santoro MM, Di Lorenzo A, Salpini R, Teti E, Svicher V, Andreoni M, Sarmati L, Ceccherini-Silberstein F. Frequency of Atypical Mutations in the Spike Glycoprotein in SARS-CoV-2 Circulating from July 2020 to July 2022 in Central Italy: A Refined Analysis by Next Generation Sequencing. Viruses 2023; 15:1711. [PMID: 37632054 PMCID: PMC10458583 DOI: 10.3390/v15081711] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
In this study, we provided a retrospective overview in order to better define SARS-CoV-2 variants circulating in Italy during the first two years of the pandemic, by characterizing the spike mutational profiles and their association with viral load (expressed as ct values), N-glycosylation pattern, hospitalization and vaccination. Next-generation sequencing (NGS) data were obtained from 607 individuals (among them, 298 vaccinated and/or 199 hospitalized). Different rates of hospitalization were observed over time and among variants of concern (VOCs), both in the overall population and in vaccinated individuals (Alpha: 40.7% and 31.3%, Beta: 0%, Gamma: 36.5% and 44.4%, Delta: 37.8% and 40.2% and Omicron: 11.2% and 7.1%, respectively, both p-values < 0.001). Approximately 32% of VOC-infected individuals showed at least one atypical major spike mutation (intra-prevalence > 90%), with a distribution differing among the strains (22.9% in Alpha, 14.3% in Beta, 41.8% in Gamma, 46.5% in Delta and 15.4% in Omicron, p-value < 0.001). Overall, significantly less atypical variability was observed in vaccinated individuals than unvaccinated individuals; nevertheless, vaccinated people who needed hospitalization showed an increase in atypical variability compared to vaccinated people that did not need hospitalization. Only 5/607 samples showed a different putative N-glycosylation pattern, four within the Delta VOC and one within the Omicron BA.2.52 sublineage. Interestingly, atypical minor mutations (intra-prevalence < 20%) were associated with higher Ct values and a longer duration of infection. Our study reports updated information on the temporal circulation of SARS-CoV-2 variants circulating in Central Italy and their association with hospitalization and vaccination. The results underline how SARS-CoV-2 has changed over time and how the vaccination strategy has contributed to reducing severity and hospitalization for this infection in Italy.
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Affiliation(s)
| | - Rossana Scutari
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Luca Carioti
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Marco Iannetta
- Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Greta Marchegiani
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Lorenzo Piermatteo
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Luigi Coppola
- Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Simona Tedde
- Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Leonardo Duca
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Vincenzo Malagnino
- Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Lorenzo Ansaldo
- Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Neva Braccialarghe
- Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Stefano D′Anna
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | | | - Andrea Di Lorenzo
- Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Romina Salpini
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Elisabetta Teti
- Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Valentina Svicher
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Massimo Andreoni
- Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Loredana Sarmati
- Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
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19
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Ghaemi A, Vakili-Azghandi M, Abnous K, Taghdisi SM, Ramezani M, Alibolandi M. Oral non-viral gene delivery platforms for therapeutic applications. Int J Pharm 2023; 642:123198. [PMID: 37406949 DOI: 10.1016/j.ijpharm.2023.123198] [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: 01/15/2023] [Revised: 06/18/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023]
Abstract
Since gene therapy can regulate gene and protein expression directly, it has a great potential to prevent or treat a variety of genetic or acquired diseases through vaccines such as viral infections, cystic fibrosis, and cancer. Owing to their high efficacy, in vivo gene therapy trials are usually conducted intravenously, which is usually costly and invasive. There are several advantages to oral drug administration over intravenous injections, such as better patient compliance, ease of use, and lower cost. However, gene therapy is successful if the oligonucleotides can cross the cell membrane easily and reach the nucleus after the endosomal escape. In order to accomplish this task and deliver the cargo to the intended location, appropriate delivery systems should be introduced. This review summarizes oral delivery systems developed for effective gene delivery, vaccination, and treatment of various diseases. Studies have also shown that oral delivery approaches are potentially applicable to treat various diseases, especially inflammatory bowel disease, stomach, and colorectal cancers. Also, the current review provides an update overview on the development of non-viral and oral gene delivery techniques for gene therapy and vaccination purposes.
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Affiliation(s)
- Asma Ghaemi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Masoume Vakili-Azghandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mohammad Taghdisi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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20
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Iannucci S, Harvey WT, Hughes J, Robertson DL, Poyade M, Hutchinson E. The SARS-CoV-2 Spike Protein Mutation Explorer: using an interactive application to improve the public understanding of SARS-CoV-2 variants of concern. J Vis Commun Med 2023; 46:122-132. [PMID: 37526402 PMCID: PMC10726978 DOI: 10.1080/17453054.2023.2237087] [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: 09/15/2022] [Accepted: 06/23/2023] [Indexed: 08/02/2023]
Abstract
Due to the COVID-19 pandemic the virus responsible, SARS-CoV-2, became a source of intense interest for non-expert audiences. The viral spike protein gained particular public interest as the main target for protective immune responses, including those elicited by vaccines. The rapid evolution of SARS-CoV-2 resulted in variations in the spike that enhanced transmissibility or weakened vaccine protection. This created new variants of concern (VOCs). The emergence of VOCs was studied using viral sequence data which was shared through portals such as the online Mutation Explorer of the COVID-19 Genomics UK consortium (COG-UK/ME). This was designed for an expert audience, but the information it contained could be of general interest if suitably communicated. Visualisations, interactivity and animation can improve engagement and understanding of molecular biology topics, and so we developed a graphical educational resource, the SARS-CoV-2 Spike Protein Mutation Explorer (SSPME), which used interactive 3D molecular models and animations to explain the molecular biology underpinning VOCs. User testing showed that the SSPME had better usability and improved participant knowledge confidence and knowledge acquisition compared to COG-UK/ME. This demonstrates how interactive visualisations can be used for effective molecular biology communication, as well as improving the public understanding of SARS-CoV-2 VOCs.
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Affiliation(s)
- Sarah Iannucci
- School of Simulation and Visualisation, The Glasgow School of Art, Glasgow, UK
| | | | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Matthieu Poyade
- School of Simulation and Visualisation, The Glasgow School of Art, Glasgow, UK
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21
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Dwivedi R, Farrag M, Sharma P, Shi D, Shami AA, Misra SK, Ray P, Shukla J, Zhang F, Linhardt RJ, Sharp JS, Tandon R, Pomin VH. The Sea Cucumber Thyonella gemmata Contains a Low Anticoagulant Sulfated Fucan with High Anti-SARS-CoV-2 Actions against Wild-Type and Delta Variants. JOURNAL OF NATURAL PRODUCTS 2023; 86:1463-1475. [PMID: 37306476 PMCID: PMC10401483 DOI: 10.1021/acs.jnatprod.3c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In this work, we isolated two new sulfated glycans from the body wall of the sea cucumber Thyonella gemmata: one fucosylated chondroitin sulfate (TgFucCS) (17.5 ± 3.5% kDa) and one sulfated fucan (TgSF) (383.3 ± 2.1% kDa). NMR results showed the TgFucCS backbone composed of [→3)-β-N-acetylgalactosamine-(1→4)-β-glucuronic acid-(1→] with 70% 4-sulfated and 30% 4,6-disulfated GalNAc units and one-third of the GlcA units decorated at the C3 position with branching α-fucose (Fuc) units either 4-sulfated (65%) or 2,4-disulfated (35%) and the TgSF structure composed of a tetrasaccharide repeating unit of [→3)-α-Fuc2,4S-(1→2)-α-Fuc4S-(1→3)-α-Fuc2S-(1→3)-α-Fuc2S-(1→]n. Inhibitory properties of TgFucCS and TgSF were investigated using SARS-CoV-2 pseudovirus coated with S-proteins of the wild-type (Wuhan-Hu-1) or the delta (B.1.617.2) strains and in four different anticoagulant assays, comparatively with unfractionated heparin. Molecular binding to coagulation (co)-factors and S-proteins was investigated by competitive surface plasmon resonance spectroscopy. Among the two sulfated glycans tested, TgSF showed significant anti-SARS-CoV-2 activity against both strains together with low anticoagulant properties, indicating a good candidate for future studies in drug development.
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Affiliation(s)
- Rohini Dwivedi
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
| | - Marwa Farrag
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut 71515, Egypt
| | - Poonam Sharma
- Center for Immunology and Microbial Research, Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi 39216, United States
| | - Deling Shi
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Anter A Shami
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
| | - Sandeep K Misra
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
| | - Priya Ray
- Center for Immunology and Microbial Research, Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi 39216, United States
| | - Jayanti Shukla
- Center for Immunology and Microbial Research, Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi 39216, United States
| | - Fuming Zhang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Robert J Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Joshua S Sharp
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
- Department of Chemistry and Biochemistry, University of Mississippi, Oxford, Mississippi 38677, United States
- Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, Oxford, Mississippi 38677, United States
| | - Ritesh Tandon
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
- Center for Immunology and Microbial Research, Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi 39216, United States
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi 39216, United States
| | - Vitor H Pomin
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
- Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, Oxford, Mississippi 38677, United States
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22
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Rosli SNZ, Dimeng SR, Shamsuddin F, Mohd Ali MR, Muhamad Hendri NA, Suppiah J, Mohd Zain R, Thayan R, Ahmad N. Vero CCL-81 and Calu-3 Cell Lines as Alternative Hosts for Isolation and Propagation of SARS-CoV-2 Isolated in Malaysia. Biomedicines 2023; 11:1658. [PMID: 37371753 DOI: 10.3390/biomedicines11061658] [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: 05/19/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been identified as the etiologic agent for the pneumonia outbreak that started in early December 2019 in Wuhan City, Hubei Province, China. To date, coronavirus disease (COVID-19) has caused almost 6 million deaths worldwide. The ability to propagate the virus into a customizable volume will enable better research on COVID-19 therapy, vaccine development, and many others. In the search for the most efficient replication host, we inoculated three (3) local SARS-CoV-2 isolates of different lineages (Clade L/Lineage B Wuhan, Clade GR/Lineage B.1.1.354, and Clade O/Lineage B.6.2) into various clinically important mammalian cell lines. The replication profile of these isolates was evaluated based on the formation of cytopathic effects (CPE), viral load (Ct value and plaque-forming unit (pfu)), as well as observation by electron microscopy (EM). Next-generation sequencing (NGS) was performed to examine the genomic stability of the propagated SARS-CoV-2 in these cell lines. Our study found that Vero E6 and Vero CCL-81 cell lines posed similar capacities in propagating the local isolates, with Vero CCL-81 demonstrating exceptional potency in conserving the genomic stability of the Lineage B Wuhan isolate. In addition, our study demonstrated the utility of Calu-3 cells as a replication host for SARS-CoV-2 without causing substantial cellular senescence. In conclusion, this study provides crucial information on the growth profile of Malaysian SARS-CoV-2 in various mammalian cell lines and thus will be a great source of reference for better isolation and propagation of the SARS-CoV-2 virus isolated in Malaysia.
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Affiliation(s)
- Siti Nur Zawani Rosli
- Bacteriology Unit, Infectious Disease Research Center, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170 Setia Alam, Malaysia
| | - Sitti Rahmawati Dimeng
- Bacteriology Unit, Infectious Disease Research Center, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170 Setia Alam, Malaysia
| | - Farah Shamsuddin
- Bacteriology Unit, Infectious Disease Research Center, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170 Setia Alam, Malaysia
| | - Mohammad Ridhuan Mohd Ali
- Bacteriology Unit, Infectious Disease Research Center, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170 Setia Alam, Malaysia
| | - Nur Afrina Muhamad Hendri
- Electron Microscopy Unit, Special Resource Center, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170 Setia Alam, Malaysia
| | - Jeyanthi Suppiah
- Virology Unit, Infectious Disease Research Center, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170 Setia Alam, Malaysia
| | - Rozainanee Mohd Zain
- Virology Unit, Infectious Disease Research Center, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170 Setia Alam, Malaysia
| | - Ravindran Thayan
- Virology Unit, Infectious Disease Research Center, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170 Setia Alam, Malaysia
| | - Norazah Ahmad
- Infectious Disease Research Center, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, 40170 Setia Alam, Malaysia
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23
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Lambrechts L. Does arbovirus emergence in humans require adaptation to domestic mosquitoes? Curr Opin Virol 2023; 60:101315. [PMID: 36996522 DOI: 10.1016/j.coviro.2023.101315] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/01/2023] [Accepted: 02/23/2023] [Indexed: 03/30/2023]
Abstract
In the last few decades, several mosquito-borne arboviruses of zoonotic origin have established large-scale epidemic transmission cycles in the human population. It is often considered that arbovirus emergence is driven by adaptive evolution, such as virus adaptation for transmission by 'domestic' mosquito vector species that live in close association with humans. Here, I argue that although arbovirus adaptation to domestic mosquito vectors has been observed for several emerging arboviruses, it was generally not directly responsible for their initial emergence. Secondary adaptation to domestic mosquitoes often amplified epidemic transmission, however, this was more likely a consequence than a cause of arbovirus emergence. Considering that emerging arboviruses are generally 'preadapted' for transmission by domestic mosquito vectors may help to enhance preparedness toward future arbovirus emergence events.
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24
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Subramoney K, Mtileni N, Giandhari J, Naidoo Y, Ramphal Y, Pillay S, Ramphal U, Maharaj A, Tshiabuila D, Tegally H, Wilkinson E, de Oliveira T, Fielding BC, Treurnicht FK. Molecular Epidemiology of SARS-CoV-2 during Five COVID-19 Waves and the Significance of Low-Frequency Lineages. Viruses 2023; 15:1194. [PMID: 37243279 PMCID: PMC10223853 DOI: 10.3390/v15051194] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
SARS-CoV-2 lineages and variants of concern (VOC) have gained more efficient transmission and immune evasion properties with time. We describe the circulation of VOCs in South Africa and the potential role of low-frequency lineages on the emergence of future lineages. Whole genome sequencing was performed on SARS-CoV-2 samples from South Africa. Sequences were analysed with Nextstrain pangolin tools and Stanford University Coronavirus Antiviral & Resistance Database. In 2020, 24 lineages were detected, with B.1 (3%; 8/278), B.1.1 (16%; 45/278), B.1.1.348 (3%; 8/278), B.1.1.52 (5%; 13/278), C.1 (13%; 37/278) and C.2 (2%; 6/278) circulating during the first wave. Beta emerged late in 2020, dominating the second wave of infection. B.1 and B.1.1 continued to circulate at low frequencies in 2021 and B.1.1 re-emerged in 2022. Beta was outcompeted by Delta in 2021, which was thereafter outcompeted by Omicron sub-lineages during the 4th and 5th waves in 2022. Several significant mutations identified in VOCs were also detected in low-frequency lineages, including S68F (E protein); I82T (M protein); P13L, R203K and G204R/K (N protein); R126S (ORF3a); P323L (RdRp); and N501Y, E484K, D614G, H655Y and N679K (S protein). Low-frequency variants, together with VOCs circulating, may lead to convergence and the emergence of future lineages that may increase transmissibility, infectivity and escape vaccine-induced or natural host immunity.
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Affiliation(s)
- Kathleen Subramoney
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa;
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg 2193, South Africa;
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, Johannesburg 2131, South Africa
| | - Nkhensani Mtileni
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg 2193, South Africa;
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa; (J.G.); (Y.R.); (S.P.); (U.R.); (A.M.); (H.T.); (T.d.O.)
| | - Yeshnee Naidoo
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa; (Y.N.); (D.T.); (E.W.)
| | - Yajna Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa; (J.G.); (Y.R.); (S.P.); (U.R.); (A.M.); (H.T.); (T.d.O.)
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa; (J.G.); (Y.R.); (S.P.); (U.R.); (A.M.); (H.T.); (T.d.O.)
| | - Upasana Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa; (J.G.); (Y.R.); (S.P.); (U.R.); (A.M.); (H.T.); (T.d.O.)
| | - Akhil Maharaj
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa; (J.G.); (Y.R.); (S.P.); (U.R.); (A.M.); (H.T.); (T.d.O.)
| | - Derek Tshiabuila
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa; (Y.N.); (D.T.); (E.W.)
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa; (J.G.); (Y.R.); (S.P.); (U.R.); (A.M.); (H.T.); (T.d.O.)
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa; (Y.N.); (D.T.); (E.W.)
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa; (J.G.); (Y.R.); (S.P.); (U.R.); (A.M.); (H.T.); (T.d.O.)
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa; (Y.N.); (D.T.); (E.W.)
| | - Burtram C. Fielding
- Molecular Biology and Virology Research Laboratory, Department of Medical BioSciences, University of the Western Cape, Cape Town 7535, South Africa;
| | - Florette K. Treurnicht
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa;
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg 2193, South Africa;
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25
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Cheng Y, Ji C, Zhou HY, Zheng H, Wu A. Web Resources for SARS-CoV-2 Genomic Database, Annotation, Analysis and Variant Tracking. Viruses 2023; 15:1158. [PMID: 37243244 PMCID: PMC10222785 DOI: 10.3390/v15051158] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
The SARS-CoV-2 genomic data continue to grow, providing valuable information for researchers and public health officials. Genomic analysis of these data sheds light on the transmission and evolution of the virus. To aid in SARS-CoV-2 genomic analysis, many web resources have been developed to store, collate, analyze, and visualize the genomic data. This review summarizes web resources used for the SARS-CoV-2 genomic epidemiology, covering data management and sharing, genomic annotation, analysis, and variant tracking. The challenges and further expectations for these web resources are also discussed. Finally, we highlight the importance and need for continued development and improvement of related web resources to effectively track the spread and understand the evolution of the virus.
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Affiliation(s)
- Yexiao Cheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 211100, China
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Chengyang Ji
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Hang-Yu Zhou
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Heng Zheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 211100, China
| | - Aiping Wu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
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26
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Bills C, Xie X, Shi PY. The multiple roles of nsp6 in the molecular pathogenesis of SARS-CoV-2. Antiviral Res 2023; 213:105590. [PMID: 37003304 PMCID: PMC10063458 DOI: 10.1016/j.antiviral.2023.105590] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/19/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve and adapt after its emergence in late 2019. As the causative agent of the coronavirus disease 2019 (COVID-19), the replication and pathogenesis of SARS-CoV-2 have been extensively studied by the research community for vaccine and therapeutics development. Given the importance of viral spike protein in viral infection/transmission and vaccine development, the scientific community has thus far primarily focused on studying the structure, function, and evolution of the spike protein. Other viral proteins are understudied. To fill in this knowledge gap, a few recent studies have identified nonstructural protein 6 (nsp6) as a major contributor to SARS-CoV-2 replication through the formation of replication organelles, antagonism of interferon type I (IFN-I) responses, and NLRP3 inflammasome activation (a major factor of severe disease in COVID-19 patients). Here, we review the most recent progress on the multiple roles of nsp6 in modulating SARS-CoV-2 replication and pathogenesis.
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Affiliation(s)
- Cody Bills
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, USA; World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, USA; Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, USA; Sealy Institute for Drug Discovery, University of Texas Medical Branch, Galveston, Texas, USA.
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27
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Ren W, Zhang Y, Rao J, Wang Z, Lan J, Liu K, Zhang X, Hu X, Yang C, Zhong G, Zhang R, Wang X, Shan C, Ding Q. Evolution of Immune Evasion and Host Range Expansion by the SARS-CoV-2 B.1.1.529 (Omicron) Variant. mBio 2023; 14:e0041623. [PMID: 37010428 PMCID: PMC10127688 DOI: 10.1128/mbio.00416-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/07/2023] [Indexed: 04/04/2023] Open
Abstract
Recently, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant B.1.1.529 (Omicron) has rapidly become the dominant strain, with an unprecedented number of mutations within its spike gene. However, it remains unknown whether these variants have alterations in their entry efficiency, host tropism, and sensitivity to neutralizing antibodies and entry inhibitors. In this study, we found that Omicron spike has evolved to escape neutralization by three-dose inactivated-vaccine-elicited immunity but remains sensitive to an angiotensin-converting enzyme 2 (ACE2) decoy receptor. Moreover, Omicron spike could use human ACE2 with a slightly increased efficiency while gaining a significantly increased binding affinity for a mouse ACE2 ortholog, which exhibits limited binding with wild-type (WT) spike. Furthermore, Omicron could infect wild-type C57BL/6 mice and cause histopathological changes in the lungs. Collectively, our results reveal that evasion of neutralization by vaccine-elicited antibodies and enhanced human and mouse ACE2 receptor engagement may contribute to the expanded host range and rapid spread of the Omicron variant. IMPORTANCE The recently emerged SARS-CoV-2 Omicron variant with numerous mutations in the spike protein has rapidly become the dominant strain, thereby raising concerns about the effectiveness of vaccines. Here, we found that the Omicron variant exhibits a reduced sensitivity to serum neutralizing activity induced by a three-dose inactivated vaccine but remains sensitive to entry inhibitors or an ACE2-Ig decoy receptor. Compared with the ancestor strain isolated in early 2020, the spike protein of Omicron utilizes the human ACE2 receptor with enhanced efficiency while gaining the ability to utilize mouse ACE2 for cell entry. Moreover, Omicron could infect wild-type mice and cause pathological changes in the lungs. These results reveal that antibody evasion, enhanced human ACE2 utilization, and an expanded host range may contribute to its rapid spread.
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Affiliation(s)
- Wenlin Ren
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Yu Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Juhong Rao
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ziyi Wang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Jun Lan
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Kunpeng Liu
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xuekai Zhang
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xue Hu
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Chen Yang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Guocai Zhong
- Shenzhen Bay Laboratory, Shenzhen, China
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Rong Zhang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Biosafety Level 3 Laboratory, Fudan University, Shanghai, China
| | - Xinquan Wang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Chao Shan
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Qiang Ding
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
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28
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Carabelli AM, Peacock TP, Thorne LG, Harvey WT, Hughes J, Peacock SJ, Barclay WS, de Silva TI, Towers GJ, Robertson DL. SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nat Rev Microbiol 2023; 21:162-177. [PMID: 36653446 PMCID: PMC9847462 DOI: 10.1038/s41579-022-00841-7] [Citation(s) in RCA: 279] [Impact Index Per Article: 279.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2022] [Indexed: 01/19/2023]
Abstract
In late 2020, after circulating for almost a year in the human population, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exhibited a major step change in its adaptation to humans. These highly mutated forms of SARS-CoV-2 had enhanced rates of transmission relative to previous variants and were termed 'variants of concern' (VOCs). Designated Alpha, Beta, Gamma, Delta and Omicron, the VOCs emerged independently from one another, and in turn each rapidly became dominant, regionally or globally, outcompeting previous variants. The success of each VOC relative to the previously dominant variant was enabled by altered intrinsic functional properties of the virus and, to various degrees, changes to virus antigenicity conferring the ability to evade a primed immune response. The increased virus fitness associated with VOCs is the result of a complex interplay of virus biology in the context of changing human immunity due to both vaccination and prior infection. In this Review, we summarize the literature on the relative transmissibility and antigenicity of SARS-CoV-2 variants, the role of mutations at the furin spike cleavage site and of non-spike proteins, the potential importance of recombination to virus success, and SARS-CoV-2 evolution in the context of T cells, innate immunity and population immunity. SARS-CoV-2 shows a complicated relationship among virus antigenicity, transmission and virulence, which has unpredictable implications for the future trajectory and disease burden of COVID-19.
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Affiliation(s)
| | - Thomas P Peacock
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - Lucy G Thorne
- Division of Infection and Immunity, University College London, London, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - Wendy S Barclay
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
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29
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Chaguza C, Hahn AM, Petrone ME, Zhou S, Ferguson D, Breban MI, Pham K, Peña-Hernández MA, Castaldi C, Hill V, Schulz W, Swanstrom RI, Roberts SC, Grubaugh ND. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. Cell Rep Med 2023; 4:100943. [PMID: 36791724 PMCID: PMC9906997 DOI: 10.1016/j.xcrm.2023.100943] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/12/2022] [Accepted: 01/20/2023] [Indexed: 01/28/2023]
Abstract
The chronic infection hypothesis for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant emergence is increasingly gaining credence following the appearance of Omicron. Here, we investigate intrahost evolution and genetic diversity of lineage B.1.517 during a SARS-CoV-2 chronic infection lasting for 471 days (and still ongoing) with consistently recovered infectious virus and high viral genome copies. During the infection, we find an accelerated virus evolutionary rate translating to 35 nucleotide substitutions per year, approximately 2-fold higher than the global SARS-CoV-2 evolutionary rate. This intrahost evolution results in the emergence and persistence of at least three genetically distinct genotypes, suggesting the establishment of spatially structured viral populations continually reseeding different genotypes into the nasopharynx. Finally, we track the temporal dynamics of genetic diversity to identify advantageous mutations and highlight hallmark changes for chronic infection. Our findings demonstrate that untreated chronic infections accelerate SARS-CoV-2 evolution, providing an opportunity for the emergence of genetically divergent variants.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Shuntai Zhou
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David Ferguson
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kien Pham
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mario A Peña-Hernández
- Department of Biological and Biomedical Sciences, Yale School of Medicine, New Haven, CT, USA
| | | | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Wade Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Ronald I Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott C Roberts
- Infectious Disease, Yale School of Medicine, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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30
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Hanifa M, Salman M, Fatima M, Mukhtar N, Almajhdi FN, Zaman N, Suleman M, Ali SS, Waheed Y, Khan A. Mutational analysis of the spike protein of SARS-COV-2 isolates revealed atomistic features responsible for higher binding and infectivity. Front Cell Dev Biol 2023; 10:940863. [PMID: 36733340 PMCID: PMC9888553 DOI: 10.3389/fcell.2022.940863] [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: 05/10/2022] [Accepted: 12/30/2022] [Indexed: 01/18/2023] Open
Abstract
Introduction: The perpetual appearance of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV-2), and its new variants devastated the public health and social fabric around the world. Understanding the genomic patterns and connecting them to phenotypic attributes is of great interest to devise a treatment strategy to control this pandemic. Materials and Methods: In this regard, computational methods to understand the evolution, dynamics and mutational spectrum of SARS-CoV-2 and its new variants are significantly important. Thus, herein, we used computational methods to screen the genomes of SARS-CoV-2 isolated from Pakistan and connect them to the phenotypic attributes of spike protein; we used stability-function correlation methods, protein-protein docking, and molecular dynamics simulation. Results: Using the Global initiative on sharing all influenza data (GISAID) a total of 21 unique mutations were identified, among which five were reported as stabilizing while 16 were destabilizing revealed through mCSM, DynaMut 2.0, and I-Mutant servers. Protein-protein docking with Angiotensin-converting enzyme 2 (ACE2) and monoclonal antibody (4A8) revealed that mutation G446V in the receptor-binding domain; R102S and G181V in the N-terminal domain (NTD) significantly affected the binding and thus increased the infectivity. The interaction pattern also revealed significant variations in the hydrogen bonding, salt bridges and non-bonded contact networks. The structural-dynamic features of these mutations revealed the global dynamic trend and the finding energy calculation further established that the G446V mutation increases the binding affinity towards ACE2 while R102S and G181V help in evading the host immune response. The other mutations reported supplement these processes indirectly. The binding free energy results revealed that wild type-RBD has a TBE of -60.55 kcal/mol while G446V-RBD reported a TBE of -73.49 kcal/mol. On the other hand, wild type-NTD reported -67.77 kcal/mol of TBE, R102S-NTD reported -51.25 kcal/mol of TBE while G181V-NTD reported a TBE of -63.68 kcal/mol. Conclusions: In conclusion, the current findings revealed basis for higher infectivity and immune evasion associated with the aforementioned mutations and structure-based drug discovery against such variants.
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Affiliation(s)
- Muhammad Hanifa
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh, Khyber Pakhtunkhwa, Pakistan
| | | | | | - Naila Mukhtar
- Department of Botany, University of Okara, Punjab, Pakistan
| | - Fahad N. Almajhdi
- COVID-19 Virus Research Chair, Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Nasib Zaman
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Suleman
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh, Khyber Pakhtunkhwa, Pakistan
| | - Syed Shujait Ali
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh, Khyber Pakhtunkhwa, Pakistan
| | - Yasir Waheed
- Office of Research, Innovation and Commercialization, Shaheed Zulfiqar Ali Bhutto Medical University (SZABMU), Islamabad, Pakistan,Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon,*Correspondence: Yasir Waheed, ; Abbas Khan,
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Yasir Waheed, ; Abbas Khan,
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31
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Deletions across the SARS-CoV-2 Genome: Molecular Mechanisms and Putative Functional Consequences of Deletions in Accessory Genes. Microorganisms 2023; 11:microorganisms11010229. [PMID: 36677521 PMCID: PMC9862619 DOI: 10.3390/microorganisms11010229] [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: 12/21/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
The analysis of deletions may reveal evolutionary trends and provide new insight into the surprising variability and rapidly spreading capability that SARS-CoV-2 has shown since its emergence. To understand the factors governing genomic stability, it is important to define the molecular mechanisms of deletions in the viral genome. In this work, we performed a statistical analysis of deletions. Specifically, we analyzed correlations between deletions in the SARS-CoV-2 genome and repetitive elements and documented a significant association of deletions with runs of identical (poly-) nucleotides and direct repeats. Our analyses of deletions in the accessory genes of SARS-CoV-2 suggested that there may be a hypervariability in ORF7A and ORF8 that is not associated with repetitive elements. Such recurrent search in a "sequence space" of accessory genes (that might be driven by natural selection) did not yet cause increased viability of the SARS-CoV-2 variants. However, deletions in the accessory genes may ultimately produce new variants that are more successful compared to the viral strains with the conventional architecture of the SARS-CoV-2 accessory genes.
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32
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Stanevich OV, Alekseeva EI, Sergeeva M, Fadeev AV, Komissarova KS, Ivanova AA, Simakova TS, Vasilyev KA, Shurygina AP, Stukova MA, Safina KR, Nabieva ER, Garushyants SK, Klink GV, Bakin EA, Zabutova JV, Kholodnaia AN, Lukina OV, Skorokhod IA, Ryabchikova VV, Medvedeva NV, Lioznov DA, Danilenko DM, Chudakov DM, Komissarov AB, Bazykin GA. SARS-CoV-2 escape from cytotoxic T cells during long-term COVID-19. Nat Commun 2023; 14:149. [PMID: 36627290 PMCID: PMC9831376 DOI: 10.1038/s41467-022-34033-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 10/11/2022] [Indexed: 01/11/2023] Open
Abstract
Evolution of SARS-CoV-2 in immunocompromised hosts may result in novel variants with changed properties. While escape from humoral immunity certainly contributes to intra-host evolution, escape from cellular immunity is poorly understood. Here, we report a case of long-term COVID-19 in an immunocompromised patient with non-Hodgkin's lymphoma who received treatment with rituximab and lacked neutralizing antibodies. Over the 318 days of the disease, the SARS-CoV-2 genome gained a total of 40 changes, 34 of which were present by the end of the study period. Among the acquired mutations, 12 reduced or prevented the binding of known immunogenic SARS-CoV-2 HLA class I antigens. By experimentally assessing the effect of a subset of the escape mutations, we show that they resulted in a loss of as much as ~1% of effector CD8 T cell response. Our results indicate that CD8 T cell escape represents a major underappreciated contributor to SARS-CoV-2 evolution in humans.
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Affiliation(s)
| | | | - Maria Sergeeva
- Smorodintsev Research Institute of Influenza, Saint-Petersburg, Russia
| | - Artem V Fadeev
- Smorodintsev Research Institute of Influenza, Saint-Petersburg, Russia
| | | | - Anna A Ivanova
- Smorodintsev Research Institute of Influenza, Saint-Petersburg, Russia
| | | | - Kirill A Vasilyev
- Smorodintsev Research Institute of Influenza, Saint-Petersburg, Russia
| | | | - Marina A Stukova
- Smorodintsev Research Institute of Influenza, Saint-Petersburg, Russia
| | - Ksenia R Safina
- Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia
| | - Elena R Nabieva
- A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Sofya K Garushyants
- A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Galya V Klink
- A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Evgeny A Bakin
- First Pavlov State Medical University, Saint-Petersburg, Russia.,Bioinformatics Institute, Saint Petersburg, Russia
| | | | - Anastasia N Kholodnaia
- First Pavlov State Medical University, Saint-Petersburg, Russia.,City Hospital 31, Saint-Petersburg, Russia
| | - Olga V Lukina
- First Pavlov State Medical University, Saint-Petersburg, Russia
| | | | | | | | - Dmitry A Lioznov
- Smorodintsev Research Institute of Influenza, Saint-Petersburg, Russia.,First Pavlov State Medical University, Saint-Petersburg, Russia
| | - Daria M Danilenko
- Smorodintsev Research Institute of Influenza, Saint-Petersburg, Russia
| | - Dmitriy M Chudakov
- Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Georgii A Bazykin
- Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia. .,A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.
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Zambrana Montaño R, Culasso ACA, Fernández F, Marquez N, Debat H, Salmerón M, Zamora AM, Ruíz de Huidobro G, Costas D, Alabarse G, Charre MA, Fridman AD, Mamani C, Vaca F, Maza Diaz C, Raskovsky V, Lavaque E, Lesser V, Cajal P, Agüero F, Calvente C, Torres C, Viegas M. Evolution of SARS-CoV-2 during the first year of the COVID-19 pandemic in Northwestern Argentina. Virus Res 2023; 323:198936. [PMID: 36181975 PMCID: PMC9599208 DOI: 10.1016/j.virusres.2022.198936] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/10/2022] [Accepted: 09/24/2022] [Indexed: 01/25/2023]
Abstract
Studies about the evolution of SARS-CoV-2 lineages in different backgrounds such as naive populations are still scarce, especially from South America. This work aimed to study the introduction and diversification pattern of SARS-CoV-2 during the first year of the COVID-19 pandemic in the Northwestern Argentina (NWA) region and to analyze the evolutionary dynamics of the main lineages found. In this study, we analyzed a total of 260 SARS-CoV-2 whole-genome sequences from Argentina, belonging to the Provinces of Jujuy, Salta, and Tucumán, from March 31st, 2020, to May 22nd, 2021, which covered the full first wave and the early second wave of the COVID-19 pandemic in Argentina. In the first wave, eight lineages were identified: B.1.499 (76.9%), followed by N.5 (10.2%), B.1.1.274 (3.7%), B.1.1.348 (3.7%), B.1 (2.8%), B.1.600 (0.9%), B.1.1.33 (0.9%) and N.3 (0.9%). During the early second wave, the first-wave lineages were displaced by the introduction of variants of concern (VOC) (Alpha, Gamma), or variants of interest (VOI) (Lambda, Zeta, Epsilon) and other lineages with more limited distribution. Phylodynamic analyses of the B.1.499 and N.5, the two most prevalent lineages in the NWA, revealed that the rate of evolution of lineage N.5 (7.9 × 10-4 substitutions per site per year, s/s/y) was a ∼40% faster than that of lineage B.1.499 (5.6 × 10-4 s/s/y), although both are in the same order of magnitude than other non-VOC lineages. No mutations associated with a biological characteristic of importance were observed as signatures markers of the phylogenetic groups established in Northwestern Argentina, however, single sequences in non-VOC lineages did present mutations of biological importance or associated with VOCs as sporadic events, showing that many of these mutations could emerge from circulation in the general population. This study contributed to the knowledge about the evolution of SARS-CoV-2 in a pre-vaccination and without post-exposure immunization period.
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Affiliation(s)
- Romina Zambrana Montaño
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Andrés Carlos Alberto Culasso
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Franco Fernández
- Centro de Investigaciones Agropecuarias, Instituto de Patología Vegetal, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba, Argentina
| | - Nathalie Marquez
- Centro de Investigaciones Agropecuarias, Instituto de Patología Vegetal, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba, Argentina
| | - Humberto Debat
- Centro de Investigaciones Agropecuarias, Instituto de Patología Vegetal, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba, Argentina
| | - Mariana Salmerón
- Laboratorio de Salud Pública, San Miguel de Tucumán, Tucumán, Argentina
| | - Ana María Zamora
- Laboratorio de Salud Pública, San Miguel de Tucumán, Tucumán, Argentina
| | | | - Dardo Costas
- Laboratorio de Salud Pública, San Miguel de Tucumán, Tucumán, Argentina
| | - Graciela Alabarse
- Laboratorio de Salud Pública, San Miguel de Tucumán, Tucumán, Argentina
| | | | - Ariel David Fridman
- Laboratorio Central de Salud Pública, San Salvador de Jujuy, Jujuy, Argentina
| | - Claudia Mamani
- Laboratorio Central de Salud Pública, San Salvador de Jujuy, Jujuy, Argentina
| | - Fabiana Vaca
- Laboratorio Central de Salud Pública, San Salvador de Jujuy, Jujuy, Argentina
| | - Claudia Maza Diaz
- Laboratorio Central de Salud Pública, San Salvador de Jujuy, Jujuy, Argentina
| | - Viviana Raskovsky
- Laboratorio de Virus Respiratorios y Neurovirosis, Hospital Señor del Milagro, Salta capital, Salta, Argentina
| | - Esteban Lavaque
- Laboratorio de Virus Respiratorios y Neurovirosis, Hospital Señor del Milagro, Salta capital, Salta, Argentina
| | - Veronica Lesser
- Laboratorio de Virus Respiratorios y Neurovirosis, Hospital Señor del Milagro, Salta capital, Salta, Argentina
| | - Pamela Cajal
- Laboratorio de Virus Respiratorios y Neurovirosis, Hospital Señor del Milagro, Salta capital, Salta, Argentina
| | - Fernanda Agüero
- Laboratorio de Virus Respiratorios y Neurovirosis, Hospital Señor del Milagro, Salta capital, Salta, Argentina
| | - Cintia Calvente
- Laboratorio de Virus Respiratorios y Neurovirosis, Hospital Señor del Milagro, Salta capital, Salta, Argentina
| | - Carolina Torres
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Mariana Viegas
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, CABA, Gallo 1330, 2do piso, C1425EFD, Argentina.
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Lustig G, Ganga Y, Rodel H, Tegally H, Jackson L, Cele S, Khan K, Jule Z, Reedoy K, Karim F, Bernstein M, Moosa MYS, Archary D, de Oliveira T, Lessells R, Abdool Karim SS, Sigal A. SARS-CoV-2 evolves increased infection elicited cell death and fusion in an immunosuppressed individual. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.11.23.22282673. [PMID: 36451879 PMCID: PMC9709797 DOI: 10.1101/2022.11.23.22282673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The milder clinical manifestations of Omicron infection relative to pre-Omicron SARS CoV-2 raises the possibility that extensive evolution results in reduced pathogenicity. To test this hypothesis, we quantified induction of cell fusion and cell death in SARS CoV-2 evolved from ancestral virus during long-term infection. Both cell fusion and death were reduced in Omicron BA.1 infection relative to ancestral virus. Evolved virus was isolated at different times during a 6-month infection in an immunosuppressed individual with advanced HIV disease. The virus isolated 16 days post-reported symptom onset induced fusogenicity and cell death at levels similar to BA.1. However, fusogenicity was increased in virus isolated at 6 months post-symptoms to levels intermediate between BA.1 and ancestral SARS-CoV-2. Similarly, infected cell death showed a graded increase from earlier to later isolates. These results may indicate that, at least by the cellular measures used here, evolution in long-term infection does not necessarily attenuate the virus.
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Affiliation(s)
- Gila Lustig
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Yashica Ganga
- Africa Health Research Institute, Durban, South Africa
| | - Hylton Rodel
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | | | - Sandile Cele
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Khadija Khan
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Zesuliwe Jule
- Africa Health Research Institute, Durban, South Africa
| | - Kajal Reedoy
- Africa Health Research Institute, Durban, South Africa
| | - Farina Karim
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Mahomed-Yunus S Moosa
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Derseree Archary
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Department of Global Health, University of Washington, Seattle, USA
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Alex Sigal
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
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35
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Dingemans J, van der Veer BMJW, Gorgels KMF, Hackert V, den Heijer CDJ, Hoebe CJPA, Savelkoul PHM, van Alphen LB. Investigating SARS-CoV-2 breakthrough infections per variant and vaccine type. Front Microbiol 2022; 13:1027271. [PMID: 36504818 PMCID: PMC9729533 DOI: 10.3389/fmicb.2022.1027271] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/02/2022] [Indexed: 11/27/2022] Open
Abstract
Breakthrough SARS-CoV-2 infections have been reported in fully vaccinated individuals, in spite of the high efficacy of the currently available vaccines, proven in trials and real-world studies. Several variants of concern (VOC) have been proffered to be associated with breakthrough infections following immunization. In this study, we investigated 378 breakthrough infections recorded between January and July 2021 and compared the distribution of SARS-CoV-2 genotypes identified in 225 fully vaccinated individuals to the frequency of circulating community lineages in the region of South Limburg (The Netherlands) in a week-by-week comparison. Although the proportion of breakthrough infections was relatively low and stable when the Alpha variant was predominant, the rapid emergence of the Delta variant lead to a strong increase in breakthrough infections, with a higher relative proportion of individuals vaccinated with Vaxzevria or Jcovden being infected compared to those immunized with mRNA-based vaccines. A significant difference in median age was observed when comparing fully vaccinated individuals with severe symptoms (83 years) to asymptomatic cases (46.5 years) or individuals with mild-to-moderate symptoms (42 years). There was no association between SARS-CoV-2 genotype or vaccine type and disease symptoms. Furthermore, the majority of adaptive mutations were concentrated in the N-terminal domain of the Spike protein, highlighting its role in immune evasion. Interestingly, symptomatic individuals harbored significantly higher SARS-CoV-2 loads than asymptomatic vaccinated individuals and breakthrough infections caused by the Delta variant were associated with increased viral loads compared to those caused by the Alpha variant. In addition, we investigated the role of the Omicron variant in causing breakthrough infections by analyzing 135 samples that were randomly selected for genomic surveillance during the transition period from Delta to Omicron. We found that the proportion of Omicron vs. Delta infections was significantly higher in individuals who received a booster vaccine compared to both unvaccinated and fully vaccinated individuals. Altogether, these results indicate that the emergence of the Delta variant and in particular Omicron has lowered the efficiency of particular vaccine types to prevent SARS-CoV-2 infections and that, although rare, the elderly are particularly at risk of becoming severely infected as the consequence of a breakthrough infection.
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Affiliation(s)
- Jozef Dingemans
- Department of Medical Microbiology, Infectious diseases and Infection prevention, Care and Public Health Research Institute (CAPHRI), Faculty of Health, Medicine and Life Sciences, Maastricht University Medical Center (MUMC+), Maastricht, Netherlands,*Correspondence: Jozef Dingemans, ; Brian M. J. W. van der Veer,
| | - Brian M. J. W. van der Veer
- Department of Medical Microbiology, Infectious diseases and Infection prevention, Care and Public Health Research Institute (CAPHRI), Faculty of Health, Medicine and Life Sciences, Maastricht University Medical Center (MUMC+), Maastricht, Netherlands,*Correspondence: Jozef Dingemans, ; Brian M. J. W. van der Veer,
| | - Koen M. F. Gorgels
- Department of Sexual Health, Infectious Diseases and Environmental Health, South Limburg Public Health Service, Heerlen, Netherlands
| | - Volker Hackert
- Department of Sexual Health, Infectious Diseases and Environmental Health, South Limburg Public Health Service, Heerlen, Netherlands,Department of Social Medicine, Care and Public Health Research Institute (CAPHRI), Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, Netherlands
| | - Casper D. J. den Heijer
- Department of Sexual Health, Infectious Diseases and Environmental Health, South Limburg Public Health Service, Heerlen, Netherlands,Department of Social Medicine, Care and Public Health Research Institute (CAPHRI), Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, Netherlands
| | - Christian J. P. A Hoebe
- Department of Medical Microbiology, Infectious diseases and Infection prevention, Care and Public Health Research Institute (CAPHRI), Faculty of Health, Medicine and Life Sciences, Maastricht University Medical Center (MUMC+), Maastricht, Netherlands,Department of Sexual Health, Infectious Diseases and Environmental Health, South Limburg Public Health Service, Heerlen, Netherlands,Department of Social Medicine, Care and Public Health Research Institute (CAPHRI), Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, Netherlands
| | - Paul H. M. Savelkoul
- Department of Medical Microbiology, Infectious diseases and Infection prevention, Care and Public Health Research Institute (CAPHRI), Faculty of Health, Medicine and Life Sciences, Maastricht University Medical Center (MUMC+), Maastricht, Netherlands
| | - Lieke B. van Alphen
- Department of Medical Microbiology, Infectious diseases and Infection prevention, Care and Public Health Research Institute (CAPHRI), Faculty of Health, Medicine and Life Sciences, Maastricht University Medical Center (MUMC+), Maastricht, Netherlands
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Subgenomic RNAs and Their Encoded Proteins Contribute to the Rapid Duplication of SARS-CoV-2 and COVID-19 Progression. Biomolecules 2022; 12:biom12111680. [DOI: 10.3390/biom12111680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/30/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is currently widespread throughout the world, accompanied by a rising number of people infected and breakthrough infection of variants, which make the virus highly transmissible and replicable. A comprehensive understanding of the molecular virological events and induced immunological features during SARS-CoV-2 replication can provide reliable targets for vaccine and drug development. Among the potential targets, subgenomic RNAs and their encoded proteins involved in the life cycle of SARS-CoV-2 are extremely important in viral duplication and pathogenesis. Subgenomic RNAs employ a range of coping strategies to evade immune surveillance from replication to translation, which allows RNAs to synthesize quickly, encode structural proteins efficiently and complete the entire process of virus replication and assembly successfully. This review focuses on the characteristics and functions of SARS-CoV-2 subgenomic RNAs and their encoded proteins and explores in depth the role of subgenomic RNAs in the replication and infection of host cells to provide important clues to the mechanism of COVID-19 pathogenesis.
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37
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Yu HG, Sizemore G, Martinez I, Perrotta P. Inhibition of SARS-CoV-2 Viral Channel Activity Using FDA-Approved Channel Modulators Independent of Variants. Biomolecules 2022; 12:1673. [PMID: 36421688 PMCID: PMC9687591 DOI: 10.3390/biom12111673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/29/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND SARS-CoV-2 has undergone mutations, yielding clinically relevant variants. HYPOTHESIS We hypothesized that in SARS-CoV-2, two highly conserved Orf3a and E channels directly related to the virus replication were a target for the detection and inhibition of the viral replication, independent of the variant, using FDA-approved ion channel modulators. METHODS A combination of a fluorescence potassium ion assay with channel modulators was developed to detect SARS-CoV-2 Orf3a/E channel activity. Two FDA-approved drugs, amantadine (an antiviral) and amitriptyline (an antidepressant), which are ion channel blockers, were tested as to whether they inhibited Orf3a/E channel activity in isolated virus variants and in nasal swab samples from COVID-19 patients. The variants were confirmed by PCR sequencing. RESULTS In isolated SARS-CoV-2 Alpha, Beta, and Delta variants, the channel activity of Orf3a/E was detected and inhibited by emodin and gliclazide (IC50 = 0.42 mM). In the Delta swab samples, amitriptyline and amantadine inhibited the channel activity of viral proteins, with IC50 values of 0.73 mM and 1.11 mM, respectively. In the Omicron swab samples, amitriptyline inhibited the channel activity, with an IC50 of 0.76 mM. CONCLUSIONS We developed an efficient method to screen FDA-approved ion channel modulators that could be repurposed to detect and inhibit SARS-CoV-2 viral replication, independent of variants.
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Affiliation(s)
- Han-Gang Yu
- Department of Physiology and Pharmacology, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
| | - Gina Sizemore
- Clinical Medicine Resources, EZCARE Walk-in Medical Center, Moorefield, WV 26836, USA
| | - Ivan Martinez
- Department of Microbiology, Immunology, & Cell Biology, Cancer Institute, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
| | - Peter Perrotta
- Anatomy & Laboratory Medicine, Department of Pathology, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
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38
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Singh R, Kumar A, Rane JS, Khan R, Tripathi G, Ajay AK, Prakash A, Ray S. Arylcoumarin perturbs SARS-CoV-2 pathogenesis by targeting the S-protein/ACE2 interaction. Sci Rep 2022; 12:17038. [PMID: 36220880 PMCID: PMC9552724 DOI: 10.1038/s41598-022-20759-7] [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: 09/06/2021] [Accepted: 09/19/2022] [Indexed: 12/29/2022] Open
Abstract
The vaccination drive against COVID-19 worldwide was quite successful. However, the second wave of infections was even more disastrous. There was a rapid increase in reinfections and human deaths due to the appearance of new SARS-CoV-2 variants. The viral genome mutations in the variants were acquired while passing through different human hosts that could escape antibodies in convalescent or vaccinated individuals. The treatment was based on oxygen supplements and supportive protocols due to the lack of a specific drug. In this study, we identified three lead inhibitors of arylated coumarin derivatives 4,6,8-tri(naphthalen-2-yl)-2H-chromen-2-one (NF1), 8-(4-hydroxyphenyl)-4,6-di(naphthalen-2-yl)-2H-chromen-2-one (NF12) and 8-(4-hydroxyphenyl)-3,6-di(naphthalen-2-yl)-2H-chromen-2-one (NF-13) that showed higher binding affinity towards the junction of SARS-CoV-2 spike glycoprotein (S-protein) and human angiotensin-converting enzyme 2 (ACE2) receptor. Using molecular docking analysis, we identified the putative binding sites of these potent inhibitors. Notably, molecular dynamics (MD) simulation and MM-PBSA studies confirmed that these inhibitors have the potential ability to bind Spike-protein/ACE2 protein complex with minimal energy. Further, the two major concerns are an adaptive mutation of spike proteins- N501Y and D614G which displayed strong affinity towards NF-13 in docking analysis. Additionally, in vitro and in vivo studies are required to confirm the above findings and develop the inhibitors as potential drugs against SARS-CoV-2.
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Affiliation(s)
- Ruhar Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Abhijeet Kumar
- Department of Chemistry, Mahatma Gandhi Central University, Motihari, 845401, India
| | - Jitendra Subhash Rane
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Rajni Khan
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Hajipur, 844102, India
| | - Garima Tripathi
- Department of Chemistry, T.N.B. College, Bhagalpur, Tilka Manjhi Bhagalpur University, Bhagalpur, 812007, India
| | - Amrendra K Ajay
- Renal Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurgaon, 122413, India.
| | - Shashikant Ray
- Department of Biotechnology, Mahatma Gandhi Central University, Motihari, 845401, India.
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39
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Gao Y, Wang T, Li J, Wei Y, Qi H. Toehold-controlled ligation and transcription for accurate COVID-19 genotyping. Anal Biochem 2022; 654:114803. [PMID: 35843299 PMCID: PMC9283128 DOI: 10.1016/j.ab.2022.114803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/21/2022] [Accepted: 06/30/2022] [Indexed: 11/01/2022]
Abstract
The global pandemic of coronavirus disease 2019 (COVID-19) has significant impact on the entire human society. However, in the face of continually emerging more contagious SARS-CoV-2 variant, the risk to bog down into more severe crisis is around us anytime. Here, we introduce an isothermal, ultrasensitive method for identifying important SNV mutations of SARS-CoV-2. It is based on combined specificity of toehold-assisted linear probe ligation and in vitro transcription signal enlargement, TLT. A ready-to-use panel of TLT assay is developed including detection of 80 crucial SARS-CoV-2 SNVs, by which people could response to the next coming contagious virus variant more rapidly. These advanced point-of-care features make TLT one good approach for large scale population testing of special SARS-CoV-2 variants of interesting.
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Affiliation(s)
- Yanmin Gao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300350, China; Zhejiang Shaoxing Research Institute of Tianjin University, Zhejiang, 312369, China
| | - Taoxue Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300350, China; Zhejiang Shaoxing Research Institute of Tianjin University, Zhejiang, 312369, China
| | - Jiaojiao Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300350, China; Zhejiang Shaoxing Research Institute of Tianjin University, Zhejiang, 312369, China
| | - Yanan Wei
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300350, China; Zhejiang Shaoxing Research Institute of Tianjin University, Zhejiang, 312369, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300350, China; Zhejiang Shaoxing Research Institute of Tianjin University, Zhejiang, 312369, China.
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Lubinski B, Frazier LE, Phan MVT, Bugembe DL, Cunningham JL, Tang T, Daniel S, Cotten M, Jaimes JA, Whittaker GR. Spike Protein Cleavage-Activation in the Context of the SARS-CoV-2 P681R Mutation: an Analysis from Its First Appearance in Lineage A.23.1 Identified in Uganda. Microbiol Spectr 2022; 10:e0151422. [PMID: 35766497 PMCID: PMC9430374 DOI: 10.1128/spectrum.01514-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/06/2022] [Indexed: 11/20/2022] Open
Abstract
Based on its predicted ability to affect transmissibility and pathogenesis, surveillance studies have highlighted the role of a specific mutation (P681R) in the S1/S2 furin cleavage site of the SARS-CoV-2 spike protein. Here we analyzed A.23.1, first identified in Uganda, as a P681R-containing virus several months prior to the emergence of B.1.617.2 (Delta variant). We performed assays using peptides mimicking the S1/S2 from A.23.1 and B.1.617 and observed significantly increased cleavability with furin compared to both an original B lineage (Wuhan-Hu1) and B.1.1.7 (Alpha variant). We also performed cell-cell fusion and functional infectivity assays using pseudotyped particles and observed an increase in activity for A.23.1 compared to an original B lineage spike. However, these changes in activity were not reproduced in the B lineage spike bearing only the P681R substitution. Our findings suggest that while A.23.1 has increased furin-mediated cleavage linked to the P681R substitution, this substitution needs to occur on the background of other spike protein changes to enable its functional consequences. IMPORTANCE During the course of the SARS-CoV-2 pandemic, viral variants have emerged that often contain notable mutations in the spike gene. Mutations that encode changes in the spike S1/S2 (furin) activation site have been considered especially impactful. The S1/S2 change from proline to arginine at position 681 (P681R) first emerged in the A.23.1 variant in Uganda, and subsequently occurred in the more widely transmitted Delta variant. We show that the A.23.1 spike is more readily activated by the host cell protease furin, but that this is not reproduced in an original SARS-CoV-2 spike containing the P681R mutation. Changes to the S1/S2 (furin) activation site play a role in SARS-CoV-2 infection and spread, but successful viruses combine these mutations with other less well identified changes, occurring as part of natural selection.
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Affiliation(s)
- Bailey Lubinski
- Graduate Program in Biological & Biomedical Sciences, Cornell University, Ithaca, New York, USA
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Laura E. Frazier
- Graduate Program in Biological & Biomedical Sciences, Cornell University, Ithaca, New York, USA
| | - My V. T. Phan
- MRC/UVRI and London School of Hygiene and Tropical Medicine – Uganda Research Unit, Entebbe, Uganda
| | - Daniel L. Bugembe
- MRC/UVRI and London School of Hygiene and Tropical Medicine – Uganda Research Unit, Entebbe, Uganda
| | - Jessie L. Cunningham
- Graduate Program in Biological & Biomedical Sciences, Cornell University, Ithaca, New York, USA
| | - Tiffany Tang
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA
| | - Susan Daniel
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA
| | - Matthew Cotten
- MRC/UVRI and London School of Hygiene and Tropical Medicine – Uganda Research Unit, Entebbe, Uganda
- MRC Centre of Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Javier A. Jaimes
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Gary R. Whittaker
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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41
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Al Khalaf R, Bernasconi A, Pinoli P, Ceri S. Analysis of co-occurring and mutually exclusive amino acid changes and detection of convergent and divergent evolution events in SARS-CoV-2. Comput Struct Biotechnol J 2022; 20:4238-4250. [PMID: 35945925 PMCID: PMC9352683 DOI: 10.1016/j.csbj.2022.07.051] [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: 05/18/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 11/28/2022] Open
Abstract
The inflation of SARS-CoV-2 lineages with a high number of accumulated mutations (such as the recent case of Omicron) has risen concerns about the evolutionary capacity of this virus. Here, we propose a computational study to examine non-synonymous mutations gathered within genomes of SARS-CoV-2 from the beginning of the pandemic until February 2022. We provide both qualitative and quantitative descriptions of such corpus, focusing on statistically significant co-occurring and mutually exclusive mutations within single genomes. Then, we examine in depth the distributions of mutations over defined lineages and compare those of frequently co-occurring mutation pairs. Based on this comparison, we study mutations' convergence/divergence on the phylogenetic tree. As a result, we identify 1,818 co-occurring pairs of non-synonymous mutations showing at least one event of convergent evolution and 6,625 co-occurring pairs with at least one event of divergent evolution. Notable examples of both types are shown by means of a tree-based representation of lineages, visually capturing mutations' behaviors. Our method confirms several well-known cases; moreover, the provided evidence suggests that our workflow can explain aspects of the future mutational evolution of SARS-CoV-2.
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Affiliation(s)
- Ruba Al Khalaf
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy
| | - Anna Bernasconi
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy
| | - Pietro Pinoli
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy
| | - Stefano Ceri
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy
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Feng Y, Zhao X, Chen Z, Nie K, Yin Z, Xia Y, Wang J, Niu P, A R, Li L, Wang D, Tan W, Ma X, Wang S, Wang H, Gao GF, Chen C, Xu W. Genomic Surveillance for SARS-CoV-2 Variants of Concern from Imported COVID-19 Cases - the Mainland of China, 2021. China CDC Wkly 2022; 4:680-684. [PMID: 36059791 PMCID: PMC9433767 DOI: 10.46234/ccdcw2022.144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/03/2022] [Indexed: 11/06/2022] Open
Abstract
Introduction After the epidemic in Wuhan City was brought under control in 2020, local outbreaks of coronavirus disease 2019 (COVID-19) in the mainland of China were mainly due to imported COVID-19 cases. The ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to generate new variants. Some have been designated as variants of concern (VOCs) by the World Health Organization (WHO). To better assess the role of imported SARS-CoV-2 surveillance and the prevalence of VOCs in 2021, the genomic surveillance data of SARS-CoV-2 from imported COVID-19 cases of 2021 in the mainland of China were analyzed. Methods The analyses included the number of sequence submissions, time of sequence deposition, and time of detection of the VOCs in order to determine the timeliness and sensitivity of the surveillance. The proportions of VOCs were analyzed and compared with data from the Global Initiative of Sharing All Influenza Data (GISAID). Results A total of 3,355 sequences of imported cases were submitted from 29 provincial-level administrative divisions, with differences in the number of sequence submissions and median time of sequence deposition. A total of 2,388 sequences with more than 90% genomic coverage were used for lineage analysis. The epidemic trend from Alpha to Delta to Omicron in imported cases was consistent with that in the GISAID. In addition, VOCs from imported cases were usually identified after WHO designation and before causing local outbreaks. Conclusions The global distribution of SARS-CoV-2 VOCs changed rapidly in 2021. Robust genomic surveillance of the imported SARS-CoV-2 in the mainland of China is of great significance.
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Affiliation(s)
- Yenan Feng
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,National Health Commission Key Laboratory for Medical Virology and Viral Diseases, Beijing, China
| | - Xiang Zhao
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,National Health Commission Key Laboratory for Medical Virology and Viral Diseases, Beijing, China
| | - Zhixiao Chen
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kai Nie
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,National Health Commission Key Laboratory for Medical Virology and Viral Diseases, Beijing, China
| | - Zeyuan Yin
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ying Xia
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ji Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,National Health Commission Key Laboratory for Medical Virology and Viral Diseases, Beijing, China
| | - Peihua Niu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,National Health Commission Key Laboratory for Medical Virology and Viral Diseases, Beijing, China
| | - Ruhan A
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lili Li
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wenjie Tan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xuejun Ma
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,National Health Commission Key Laboratory for Medical Virology and Viral Diseases, Beijing, China
| | - Shiwen Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,National Health Commission Key Laboratory for Medical Virology and Viral Diseases, Beijing, China
| | - Huanyu Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - George F. Gao
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,National Health Commission Key Laboratory for Medical Virology and Viral Diseases, Beijing, China
| | - Cao Chen
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,National Health Commission Key Laboratory for Medical Virology and Viral Diseases, Beijing, China,Cao Chen,
| | - Wenbo Xu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,National Health Commission Key Laboratory for Medical Virology and Viral Diseases, Beijing, China,Wenbo Xu,
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Tang X, Yu W, Shen L, Qi J, Hu T. Conjugation with 8-arm PEG and CRM197 enhances the immunogenicity of SARS-CoV-2 ORF8 protein. Int Immunopharmacol 2022; 109:108922. [PMID: 35687905 PMCID: PMC9168007 DOI: 10.1016/j.intimp.2022.108922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/01/2022] [Accepted: 06/01/2022] [Indexed: 11/06/2022]
Abstract
Safe and effective vaccines are urgently needed to combat the COVID-19 pandemic. However, the SARS-CoV-2 variants raise concerns about the effectiveness of vaccines. As a SARS-CoV-2 antigen target, ORF8 strongly inhibits the IFN-β and NF-κB-responsive promoter, and can be potentially used for the development of SARS-CoV-2 vaccine. However, it is necessary to improve the immunogenicity of ORF8 by adjuvants or delivery systems. CRM197 was a carrier protein with the ability to activate T helper cells for antigens. Eight-arm PEG could conjugate multiple antigen molecules in one entity with inherent adjuvant effect. In the present study, ORF8 was conjugated with CRM197 and 8-arm PEG, respectively. The cellular and humoral immune responses to the conjugates (ORF8-CRM and ORF8-PEG) were evaluated in the BALB/c mice. As compared with ORF8-CRM and ORF8 administrated with aluminum adjuvant (ORF8/AL), ORF8-PEG induced a higher ORF8-specific IgG titer (2.6 × 104), higher levels of cytokines (IFN-γ, TNF-α, IFN-β, and IL-5), stronger splenocyte proliferation. Thus, conjugation with 8-arm PEG was an effective method to improve the immune response to ORF8. Moreover, ORF8-PEG did not lead to apparent toxicity to the cardiac, liver and renal functions. ORF8-PEG was expected to act as an effective vaccine to provide the immune protection against SARS-CoV-2.
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Espeseth AS, Yuan M, Citron M, Reiserova L, Morrow G, Wilson A, Horton M, Rukhman M, Kinek K, Hou F, Li SL, Li F, Choi Y, Heidecker G, Luo B, Wu G, Zhang L, Strable E, DeStefano J, Secore S, Mukhopadhyay TK, Richardson DD, Sayeed E, Welch LS, Bett AJ, Feinberg MB, Gupta SB, Cooper CL, Parks CL. Preclinical immunogenicity and efficacy of a candidate COVID-19 vaccine based on a vesicular stomatitis virus-SARS-CoV-2 chimera. EBioMedicine 2022; 82:104203. [PMID: 35915046 PMCID: PMC9338221 DOI: 10.1016/j.ebiom.2022.104203] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 07/22/2022] [Accepted: 07/22/2022] [Indexed: 12/17/2022] Open
Abstract
Background To investigate a vaccine technology with potential to protect against coronavirus disease 2019 (COVID-19) and reduce transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with a single vaccine dose, we developed a SARS-CoV-2 candidate vaccine using the live vesicular stomatitis virus (VSV) chimeric virus approach previously used to develop a licensed Ebola virus vaccine. Methods We generated a replication-competent chimeric VSV-SARS-CoV-2 vaccine candidate by replacing the VSV glycoprotein (G) gene with coding sequence for the SARS-CoV-2 Spike glycoprotein (S). Immunogenicity of the lead vaccine candidate (VSV∆G-SARS-CoV-2) was evaluated in cotton rats and golden Syrian hamsters, and protection from SARS-CoV-2 infection also was assessed in hamsters. Findings VSV∆G-SARS-CoV-2 delivered with a single intramuscular (IM) injection was immunogenic in cotton rats and hamsters and protected hamsters from weight loss following SARS-CoV-2 challenge. When mucosal vaccination was evaluated, cotton rats did not respond to the vaccine, whereas mucosal administration of VSV∆G-SARS-CoV-2 was found to be more immunogenic than IM injection in hamsters and induced immunity that significantly reduced SARS-CoV-2 challenge virus loads in both lung and nasal tissues. Interpretation VSV∆G-SARS-CoV-2 delivered by IM injection or mucosal administration was immunogenic in golden Syrian hamsters, and both vaccination methods effectively protected the lung from SARS-CoV-2 infection. Hamsters vaccinated by mucosal application of VSV∆G-SARS-CoV-2 also developed immunity that controlled SARS-CoV-2 replication in nasal tissue. Funding The study was funded by Merck Sharp & Dohme, Corp., a subsidiary of Merck & Co., Inc., Rahway, NJ, USA, and The International AIDS Vaccine Initiative, Inc. (IAVI), New York, USA. Parts of this research was supported by the Biomedical Advanced Research and Development Authority (BARDA) and the Defense Threat Reduction Agency (DTRA) of the US Department of Defense.
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Affiliation(s)
| | - Maoli Yuan
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | | | - Lucia Reiserova
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | - Gavin Morrow
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | - Aaron Wilson
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | | | - Mark Rukhman
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | | | - Fuxiang Hou
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | - Shui L Li
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | | | - Yesle Choi
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | | | - Bin Luo
- Merck & Co., Inc., Rahway, New Jersey, USA
| | - Guoxin Wu
- Merck & Co., Inc., Rahway, New Jersey, USA
| | - Lan Zhang
- Merck & Co., Inc., Rahway, New Jersey, USA
| | | | - Joanne DeStefano
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | | | | | | | - Eddy Sayeed
- The International AIDS Vaccine Initiative, Inc. (IAVI), New York, USA
| | - Lisa S Welch
- The International AIDS Vaccine Initiative, Inc. (IAVI), New York, USA; Currently at Clover Biopharmaceuticals, Boston, Massachusetts, USA
| | | | - Mark B Feinberg
- The International AIDS Vaccine Initiative, Inc. (IAVI), New York, USA
| | - Swati B Gupta
- The International AIDS Vaccine Initiative, Inc. (IAVI), New York, USA
| | - Christopher L Cooper
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA
| | - Christopher L Parks
- The International AIDS Vaccine Initiative, Inc. (IAVI), Vaccine Design and Development Laboratory, New York, USA.
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Neutralizing antibody activity against 21 SARS-CoV-2 variants in older adults vaccinated with BNT162b2. Nat Microbiol 2022; 7:1180-1188. [PMID: 35836002 PMCID: PMC9352594 DOI: 10.1038/s41564-022-01163-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/24/2022] [Indexed: 11/16/2022]
Abstract
SARS-CoV-2 variants may threaten the effectiveness of vaccines and antivirals to mitigate serious COVID-19 disease. This is of most concern in clinically vulnerable groups such as older adults. We analysed 72 sera samples from 37 individuals, aged 70–89 years, vaccinated with two doses of BNT162b2 (Pfizer–BioNTech) 3 weeks apart, for neutralizing antibody responses to wildtype SARS-CoV-2. Between 3 and 20 weeks after the second vaccine dose, neutralizing antibody titres fell 4.9-fold to a median titre of 21.3 (neutralization dose 80%), with 21.6% of individuals having no detectable neutralizing antibodies at the later time point. Next, we examined neutralization of 21 distinct SARS-CoV-2 variant spike proteins with these sera, and confirmed substantial antigenic escape, especially for the Omicron (B.1.1.529, BA.1/BA.2), Beta (B.1.351), Delta (B.1.617.2), Theta (P.3), C.1.2 and B.1.638 spike variants. By combining pseudotype neutralization with specific receptor-binding domain (RBD) enzyme-linked immunosorbent assays, we showed that changes to position 484 in the spike RBD were mainly responsible for SARS-CoV-2 neutralizing antibody escape. Nineteen sera from the same individuals boosted with a third dose of BNT162b2 contained higher neutralizing antibody titres, providing cross-protection against Omicron BA.1 and BA.2. Despite SARS-CoV-2 immunity waning over time in older adults, booster vaccines can elicit broad neutralizing antibodies against a large number of SARS-CoV-2 variants in this clinically vulnerable cohort. Analysis of the neutralizing antibody activity from sera of vaccinated individuals aged between 70 and 89 reveals a reduction of antibody titres against SARS-CoV-2 wildtype and antigenic escape of various variants of concern that links to specific mutations within the RBD. A booster vaccination helps increasing neutralizing antibody titres against the Omicron BA.1 and BA.2 variants in older adults.
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Chaguza C, Hahn AM, Petrone ME, Zhou S, Ferguson D, Breban MI, Pham K, Peña-Hernández MA, Castaldi C, Hill V, Schulz W, Swanstrom RI, Roberts SC, Grubaugh ND. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.06.29.22276868. [PMID: 35794895 PMCID: PMC9258298 DOI: 10.1101/2022.06.29.22276868] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The chronic infection hypothesis for novel SARS-CoV-2 variant emergence is increasingly gaining credence following the appearance of Omicron. Here we investigate intrahost evolution and genetic diversity of lineage B.1.517 during a SARS-CoV-2 chronic infection lasting for 471 days (and still ongoing) with consistently recovered infectious virus and high viral loads. During the infection, we found an accelerated virus evolutionary rate translating to 35 nucleotide substitutions per year, approximately two-fold higher than the global SARS-CoV-2 evolutionary rate. This intrahost evolution led to the emergence and persistence of at least three genetically distinct genotypes suggesting the establishment of spatially structured viral populations continually reseeding different genotypes into the nasopharynx. Finally, using unique molecular indexes for accurate intrahost viral sequencing, we tracked the temporal dynamics of genetic diversity to identify advantageous mutations and highlight hallmark changes for chronic infection. Our findings demonstrate that untreated chronic infections accelerate SARS-CoV-2 evolution, ultimately providing opportunity for the emergence of genetically divergent and potentially highly transmissible variants as seen with Delta and Omicron.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Anne M. Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Shuntai Zhou
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David Ferguson
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kien Pham
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mario A. Peña-Hernández
- Department of Biological and Biomedical Sciences, Yale School of Medicine, New Haven, Connecticut, USA
| | | | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | - Wade Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Ronald I. Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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Wilkinson SAJ, Richter A, Casey A, Osman H, Mirza JD, Stockton J, Quick J, Ratcliffe L, Sparks N, Cumley N, Poplawski R, Nicholls SN, Kele B, Harris K, Peacock TP, Loman NJ. Recurrent SARS-CoV-2 mutations in immunodeficient patients. Virus Evol 2022; 8:veac050. [PMID: 35996593 PMCID: PMC9384748 DOI: 10.1093/ve/veac050] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/11/2022] [Accepted: 08/08/2022] [Indexed: 01/19/2023] Open
Abstract
Long-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in immunodeficient patients are an important source of variation for the virus but are understudied. Many case studies have been published which describe one or a small number of long-term infected individuals but no study has combined these sequences into a cohesive dataset. This work aims to rectify this and study the genomics of this patient group through a combination of literature searches as well as identifying new case series directly from the COVID-19 Genomics UK (COG-UK) dataset. The spike gene receptor-binding domain and N-terminal domain (NTD) were identified as mutation hotspots. Numerous mutations associated with variants of concern were observed to emerge recurrently. Additionally a mutation in the envelope gene, T30I was determined to be the second most frequent recurrently occurring mutation arising in persistent infections. A high proportion of recurrent mutations in immunodeficient individuals are associated with ACE2 affinity, immune escape, or viral packaging optimisation. There is an apparent selective pressure for mutations that aid cell-cell transmission within the host or persistence which are often different from mutations that aid inter-host transmission, although the fact that multiple recurrent de novo mutations are considered defining for variants of concern strongly indicates that this potential source of novel variants should not be discounted.
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Affiliation(s)
- S A J Wilkinson
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Alex Richter
- Institute of Immunology and Immunotherapy (III), College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Anna Casey
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Husam Osman
- Queen Elizabeth Hospital, University Hospitals Birmingham, Birmingham B15 2TH, UK
| | - Jeremy D Mirza
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Joanne Stockton
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Josh Quick
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Liz Ratcliffe
- Queen Elizabeth Hospital, University Hospitals Birmingham, Birmingham B15 2TH, UK
| | - Natalie Sparks
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Nicola Cumley
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Radoslaw Poplawski
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Samuel N Nicholls
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Beatrix Kele
- Virology Department, Royal London Hospital, Barts Health NHS Trust, London, EC1A 7BE, UK
| | - Kathryn Harris
- Virology Department, Royal London Hospital, Barts Health NHS Trust, London, EC1A 7BE, UK
- Department of Infectious Disease, Imperial College London, London, Westminster W2 1PG, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, Westminster W2 1PG, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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Ham RE, Smothers AR, Che R, Sell KJ, Peng CA, Dean D. Identifying SARS-CoV-2 Variants of Concern through Saliva-Based RT-qPCR by Targeting Recurrent Mutation Sites. Microbiol Spectr 2022; 10:e0079722. [PMID: 35546574 PMCID: PMC9241879 DOI: 10.1128/spectrum.00797-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/14/2022] [Indexed: 11/20/2022] Open
Abstract
SARS-CoV-2 variants of concern (VOCs) continue to pose a public health threat which necessitates a real-time monitoring strategy to complement whole genome sequencing. Thus, we investigated the efficacy of competitive probe RT-qPCR assays for six mutation sites identified in SARS-CoV-2 VOCs and, after validating the assays with synthetic RNA, performed these assays on positive saliva samples. When compared with whole genome sequence results, the SΔ69-70 and ORF1aΔ3675-3677 assays demonstrated 93.60 and 68.00% accuracy, respectively. The SNP assays (K417T, E484K, E484Q, L452R) demonstrated 99.20, 96.40, 99.60, and 96.80% accuracies, respectively. Lastly, we screened 345 positive saliva samples from 7 to 22 December 2021 using Omicron-specific mutation assays and were able to quickly identify rapid spread of Omicron in Upstate South Carolina. Our workflow demonstrates a novel approach for low-cost, real-time population screening of VOCs. IMPORTANCE SARS-CoV-2 variants of concern and their many sublineages can be characterized by mutations present within their genetic sequences. These mutations can provide selective advantages such as increased transmissibility and antibody evasion, which influences public health recommendations such as mask mandates, quarantine requirements, and treatment regimens. Our RT-qPCR workflow allows for strain identification of SARS-CoV-2 positive saliva samples by targeting common mutation sites shared between variants of concern and detecting single nucleotides present at the targeted location. This differential diagnostic system can quickly and effectively identify a wide array of SARS-CoV-2 strains, which can provide more informed public health surveillance strategies in the future.
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Affiliation(s)
- Rachel E. Ham
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, South Carolina, USA
| | - Austin R. Smothers
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, South Carolina, USA
- Department of Bioengineering, Clemson University, Clemson, South Carolina, USA
| | - Rui Che
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, South Carolina, USA
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Keegan J. Sell
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, South Carolina, USA
| | - Congyue Annie Peng
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, South Carolina, USA
| | - Delphine Dean
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, South Carolina, USA
- Department of Bioengineering, Clemson University, Clemson, South Carolina, USA
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Khan A, Khan SA, Zia K, Altowyan MS, Barakat A, Ul-Haq Z. Deciphering the Impact of Mutations on the Binding Efficacy of SARS-CoV-2 Omicron and Delta Variants With Human ACE2 Receptor. Front Chem 2022; 10:892093. [PMID: 35755247 PMCID: PMC9213841 DOI: 10.3389/fchem.2022.892093] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/28/2022] [Indexed: 12/26/2022] Open
Abstract
The pandemic of COVID-19, caused by SARS-CoV-2, has globally affected the human health and economy. Since the emergence of the novel coronavirus SARS-CoV-2, the life-threatening virus continues to mutate and evolve. Irrespective of acquired natural immunity and vaccine-induced immunity, the emerging multiple variants are growing exponentially, crossing the territorial barriers of the modern world. The rapid emergence of SARS-CoV-2 multiple variants challenges global researchers regarding the efficacy of available vaccines and variant transmissibility. SARS-CoV-2 surface-anchored S-protein recognizes and interacts with the host-cell ACE2, facilitating viral adherence and entrance into the cell. Understanding the interfacial interactions between the spike protein of SARS-CoV-2 variants and human ACE2 receptor is important for the design and development of antiviral therapeutics against SARS-CoV-2 emerging variants. Despite extensive research, the crucial determinants related to the molecular interactions between the spike protein of SARS-CoV-2 variants and host receptors are poorly understood. Thus, in this study, we explore the comparative interfacial binding pattern of SARS-CoV-2 spike RBD of wild type, Delta, and Omicron with the human ACE2 receptor to determine the crucial determinants at the atomistic level, using MD simulation and MM/GBSA energy calculations. Based on our findings, the substitution of Q493R, G496S, Q498R, and Y505H induced internal conformational changes in Omicron spike RBD, which leads to higher binding affinity than Delta spike RBD with the human ACE2 receptor, eventually contributing to higher transmission and infectivity. Taken together, these results could be used for the structure-based design of effective antiviral therapeutics against SARS-CoV-2 variants.
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Affiliation(s)
- Alamgir Khan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Salman Ali Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Komal Zia
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Mezna Saleh Altowyan
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Assem Barakat
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia.,Department of Chemistry, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Zaheer Ul-Haq
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.,Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
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50
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Brinkac L, Diepold S, Mitchell S, Sarnese S, Kolakowski LF, Nelson WM, Jennings K. SARS-CoV-2 Delta variant isolates from vaccinated individuals. BMC Genomics 2022; 23:417. [PMID: 35658876 PMCID: PMC9166184 DOI: 10.1186/s12864-022-08652-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 05/18/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The SARS-CoV-2 Delta variant was first identified in the U.S. in March 2021 and has rapidly become the predominant lineage across the U.S. due to increased transmissibility, immune evasion and vaccine breakthrough. The aim of this study was to better understand the genetic diversity and the potential impact of mutations observed in SARS-CoV-2 viruses circulating in the U.S. in vaccinated individuals. RESULTS Whole genome sequencing was performed on thirty-four SARS-CoV-2 positive samples using the Oxford Nanopore MinION. Evolutionary genomic analysis revealed two novel mutations, ORF1b:V2354F and a premature stop codon, ORF7a:Q94*, identified in a cluster of SARS-CoV-2 Delta isolates collected from vaccinated individuals in Colorado. The ORF1b:V2354F mutation, corresponding to NSP15:V303F, may induce a conformational change and result in a disruption to a flanking beta-sheet structure. The premature stop codon, ORF7a:Q94*, truncates the transmembrane protein and cytosolic tail used to mediate protein transport. This may affect protein localization to the ER-Golgi. In addition to these novel mutations, the cluster of vaccinated isolates contain an additional mutation in the spike protein, at position 112, compared to the Delta variant defining mutations. This mutation, S112L, exists in isolates previously obtained in the U.S. The S112L mutation substitutes a bulky hydrophobic side chain for a polar side chain, which results in a non-conservative substitution within the protein that may affect antibody-binding affinity. Additionally, the vaccinated cluster of isolates contains non-synonymous mutations within ORF8 and NSPs which further distinguish this cluster from the respective ancestral Delta variant. CONCLUSIONS These results show there is an emerging sub-lineage of the ancestral Delta variant circulating in the U.S. As mutations emerge in constellations, those with a potentially beneficial advantage to the virus may continue to circulate while others will cease.
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