1
|
Durairaj J, Follonier OM, Leuzinger K, Alexander LT, Wilhelm M, Pereira J, Hillenbrand CA, Weissbach FH, Schwede T, Hirsch HH. Structural implications of BK polyomavirus sequence variations in the major viral capsid protein Vp1 and large T-antigen: a computational study. mSphere 2024; 9:e0079923. [PMID: 38501831 PMCID: PMC11036806 DOI: 10.1128/msphere.00799-23] [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: 12/20/2023] [Accepted: 02/21/2024] [Indexed: 03/20/2024] Open
Abstract
BK polyomavirus (BKPyV) is a double-stranded DNA virus causing nephropathy, hemorrhagic cystitis, and urothelial cancer in transplant patients. The BKPyV-encoded capsid protein Vp1 and large T-antigen (LTag) are key targets of neutralizing antibodies and cytotoxic T-cells, respectively. Our single-center data suggested that variability in Vp1 and LTag may contribute to failing BKPyV-specific immune control and impact vaccine design. We, therefore, analyzed all available entries in GenBank (1516 VP1; 742 LTAG) and explored potential structural effects using computational approaches. BKPyV-genotype (gt)1 was found in 71.18% of entries, followed by BKPyV-gt4 (19.26%), BKPyV-gt2 (8.11%), and BKPyV-gt3 (1.45%), but rates differed according to country and specimen type. Vp1-mutations matched a serotype different than the assigned one or were serotype-independent in 43%, 18% affected more than one amino acid. Notable Vp1-mutations altered antibody-binding domains, interactions with sialic acid receptors, or were predicted to change conformation. LTag-sequences were more conserved, with only 16 mutations detectable in more than one entry and without significant effects on LTag-structure or interaction domains. However, LTag changes were predicted to affect HLA-class I presentation of immunodominant 9mers to cytotoxic T-cells. These global data strengthen single center observations and specifically our earlier findings revealing mutant 9mer epitopes conferring immune escape from HLA-I cytotoxic T cells. We conclude that variability of BKPyV-Vp1 and LTag may have important implications for diagnostic assays assessing BKPyV-specific immune control and for vaccine design. IMPORTANCE Type and rate of amino acid variations in BKPyV may provide important insights into BKPyV diversity in human populations and an important step toward defining determinants of BKPyV-specific immunity needed to protect vulnerable patients from BKPyV diseases. Our analysis of BKPyV sequences obtained from human specimens reveals an unexpectedly high genetic variability for this double-stranded DNA virus that strongly relies on host cell DNA replication machinery with its proof reading and error correction mechanisms. BKPyV variability and immune escape should be taken into account when designing further approaches to antivirals, monoclonal antibodies, and vaccines for patients at risk of BKPyV diseases.
Collapse
Affiliation(s)
- Janani Durairaj
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Océane M. Follonier
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
- Transplantation & Clinical Virology, Department of Biomedicine, Medical Faculty, University of Basel, Basel, Switzerland
| | - Karoline Leuzinger
- Transplantation & Clinical Virology, Department of Biomedicine, Medical Faculty, University of Basel, Basel, Switzerland
- Clinical Virology, Laboratory Medicine, Department Theragnostic, University Hospital Basel, Basel, Switzerland
| | - Leila T. Alexander
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Maud Wilhelm
- Transplantation & Clinical Virology, Department of Biomedicine, Medical Faculty, University of Basel, Basel, Switzerland
| | - Joana Pereira
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Caroline A. Hillenbrand
- Transplantation & Clinical Virology, Department of Biomedicine, Medical Faculty, University of Basel, Basel, Switzerland
| | - Fabian H. Weissbach
- Transplantation & Clinical Virology, Department of Biomedicine, Medical Faculty, University of Basel, Basel, Switzerland
| | - Torsten Schwede
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Hans H. Hirsch
- Transplantation & Clinical Virology, Department of Biomedicine, Medical Faculty, University of Basel, Basel, Switzerland
- Infectious Diseases & Hospital Epidemiology, Department Acute Medicine, University Hospital Basel, Basel, Switzerland
| |
Collapse
|
2
|
Rani JMS, Akkarshana P, Neelaveni V, Mohan S, Rekha PD, Rao RM, Muthulakshmi L. Evaluation of the inhibitory potential of bioactive compounds against SARS-CoV-2 by in silico approach. J Mol Model 2024; 30:60. [PMID: 38321299 DOI: 10.1007/s00894-024-05858-8] [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: 09/20/2023] [Accepted: 01/27/2024] [Indexed: 02/08/2024]
Abstract
CONTEXT The COVID-19 (coronavirus disease 19) pandemic brought on by the SARS-CoV-2 outbreak (severe acute respiratory syndrome coronavirus 2) has stimulated the exploration of various available chemical compounds that could be used to treat the infection. This has driven numerous researchers to investigate the antiviral potential of several bioactive compounds from medicinal plants due to their reduced adverse effects compared to chemicals. Some of the bioactive compounds used in folklore treatment strategies are reported as effective inhibitors against the proliferative and infective cycles of SARS-CoV-2. The secondary metabolites from plants are generally used to treat various diseases due to their intact medicinal properties. The present study analyzes the inhibitory potential of phytochemicals from medicinal plants like Sphaeranthus indicus, Lantana camara, and Nelumbo nucifera against SARS-CoV-2 by molecular docking. METHODS Ten druggable protein targets from SARS-CoV-2 are docked against the phytochemicals from the selected medicinal plants. The phytocompounds astragalin, isoquercetin, and 5-hydroxy-7-methoxy-6-c-glycosy flavone were found to have lower binding energy depicting their inhibitive potential compared with the reported inhibitors that are used in the treatment of SARS-CoV-2 infection. The phytocompounds found to have the least binding energy were selected for further analyses. To assess the compounds' potential as drugs, their ADMET characteristics were also examined. Sphaeranthus indicus, Lantana camara, and Nelumbo nucifera six possible compounds were separately screened for ADME and toxicity characteristics; then, the results were analyzed. To assess the impact of the phytocompound binding on the dynamics of SARS-CoV-2 ribonuclease protein NSP15, microsecond-level all atomistic molecular dynamics simulations were performed, and their dynamics were analyzed. Microsecond-level molecular dynamics simulations of both the ligands complexed with NSP15 revealed that the ligand induces allosteric effects on NSP15, which could lead to destabilization of NSP15 hexameric interface and loss of RNA binding. The low binding energy exhibited by the phytochemicals from Lantana camera, Sphaeranthus indicus, and Nelumbo nucifera against the protein targets of SARS-CoV-2 showed inhibitory potential by the selected molecules. Their predicted interference of the enzymes involved in the molecular mechanisms aiding the proliferation of SARS-CoV-2 indicated the inhibitive ability of the phytochemicals.
Collapse
Affiliation(s)
- J Mariya Sneha Rani
- Department of Biotechnology, Biomaterials and Product Development Laboratory, Kalasalingam Academy of Research and Education, Krishnankoil, 626126, India
| | - P Akkarshana
- Department of Biotechnology, Biomaterials and Product Development Laboratory, Kalasalingam Academy of Research and Education, Krishnankoil, 626126, India
| | - V Neelaveni
- Department of Biotechnology, Biomaterials and Product Development Laboratory, Kalasalingam Academy of Research and Education, Krishnankoil, 626126, India
| | - Shalini Mohan
- Department of Biotechnology, Biomaterials and Product Development Laboratory, Kalasalingam Academy of Research and Education, Krishnankoil, 626126, India
| | - P D Rekha
- Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangaluru, 575018, India
| | - Rajas M Rao
- Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangaluru, 575018, India.
| | - Lakshmanan Muthulakshmi
- Department of Biotechnology, Biomaterials and Product Development Laboratory, Kalasalingam Academy of Research and Education, Krishnankoil, 626126, India.
| |
Collapse
|
3
|
Mineeva-Sangwo O, Martí-Carreras J, Cleenders E, Kuypers D, Maes P, Andrei G, Naesens M, Snoeck R. Polyomavirus BK Genome Comparison Shows High Genetic Diversity in Kidney Transplant Recipients Three Months after Transplantation. Viruses 2022; 14:v14071533. [PMID: 35891513 PMCID: PMC9318200 DOI: 10.3390/v14071533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/05/2022] [Accepted: 07/12/2022] [Indexed: 11/16/2022] Open
Abstract
BK polyomavirus (BKPyV) is a human DNA virus generally divided into twelve subgroups based on the genetic diversity of Viral Protein 1 (VP1). BKPyV can cause polyomavirus-associated nephropathy (PVAN) after kidney transplantation. Detection of BKPyV DNA in blood (viremia) is a source of concern and increase in plasma viral load is associated with a higher risk of developing PVAN. In this work, we looked for possible associations of specific BKPyV genetic features with higher plasma viral load in kidney transplant patients. We analyzed BKPyV complete genome in three-month samples from kidney recipients who developed viremia during their follow-up period. BKPyV sequences were obtained by next-generation sequencing and were de novo assembled using the new BKAnaLite pipeline. Based on the data from 72 patients, we identified 24 viral groups with unique amino acid sequences: three in the VP1 subgroup IVc2, six in Ib1, ten in Ib2, one in Ia, and four in II. In none of the groups did the mean plasma viral load reach a statistically significant difference from the overall mean observed at three months after transplantation. Further investigation is needed to better understand the link between the newly described BKPyV genetic variants and pathogenicity in kidney transplant recipients.
Collapse
Affiliation(s)
- Olga Mineeva-Sangwo
- Laboratory of Virology and Chemotherapy, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, BE3000 Leuven, Belgium;
| | - Joan Martí-Carreras
- Zoonotic Infectious Diseases Unit, Laboratory of Clinical and Epidemiological Virology, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, BE3000 Leuven, Belgium; (J.M.-C.); (P.M.)
| | - Evert Cleenders
- Nephrology and Renal Transplantation Research Group, Department of Microbiology, Immunology and Transplantation, KU Leuven, BE3000 Leuven, Belgium; (E.C.); (D.K.); (M.N.)
| | - Dirk Kuypers
- Nephrology and Renal Transplantation Research Group, Department of Microbiology, Immunology and Transplantation, KU Leuven, BE3000 Leuven, Belgium; (E.C.); (D.K.); (M.N.)
- Department of Nephrology and Renal Transplantation, University Hospitals Leuven, BE3000 Leuven, Belgium
| | - Piet Maes
- Zoonotic Infectious Diseases Unit, Laboratory of Clinical and Epidemiological Virology, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, BE3000 Leuven, Belgium; (J.M.-C.); (P.M.)
| | - Graciela Andrei
- Laboratory of Virology and Chemotherapy, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, BE3000 Leuven, Belgium;
- Correspondence: (G.A.); (R.S.)
| | - Maarten Naesens
- Nephrology and Renal Transplantation Research Group, Department of Microbiology, Immunology and Transplantation, KU Leuven, BE3000 Leuven, Belgium; (E.C.); (D.K.); (M.N.)
- Department of Nephrology and Renal Transplantation, University Hospitals Leuven, BE3000 Leuven, Belgium
| | - Robert Snoeck
- Laboratory of Virology and Chemotherapy, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, BE3000 Leuven, Belgium;
- Correspondence: (G.A.); (R.S.)
| |
Collapse
|
4
|
Balloux F, Tan C, Swadling L, Richard D, Jenner C, Maini M, van Dorp L. The past, current and future epidemiological dynamic of SARS-CoV-2. OXFORD OPEN IMMUNOLOGY 2022; 3:iqac003. [PMID: 35872966 PMCID: PMC9278178 DOI: 10.1093/oxfimm/iqac003] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/11/2022] [Accepted: 06/15/2022] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2, the agent of the COVID-19 pandemic, emerged in late 2019 in China, and rapidly spread throughout the world to reach all continents. As the virus expanded in its novel human host, viral lineages diversified through the accumulation of around two mutations a month on average. Different viral lineages have replaced each other since the start of the pandemic, with the most successful Alpha, Delta and Omicron variants of concern (VoCs) sequentially sweeping through the world to reach high global prevalence. Neither Alpha nor Delta was characterized by strong immune escape, with their success coming mainly from their higher transmissibility. Omicron is far more prone to immune evasion and spread primarily due to its increased ability to (re-)infect hosts with prior immunity. As host immunity reaches high levels globally through vaccination and prior infection, the epidemic is expected to transition from a pandemic regime to an endemic one where seasonality and waning host immunization are anticipated to become the primary forces shaping future SARS-CoV-2 lineage dynamics. In this review, we consider a body of evidence on the origins, host tropism, epidemiology, genomic and immunogenetic evolution of SARS-CoV-2 including an assessment of other coronaviruses infecting humans. Considering what is known so far, we conclude by delineating scenarios for the future dynamic of SARS-CoV-2, ranging from the good-circulation of a fifth endemic 'common cold' coronavirus of potentially low virulence, the bad-a situation roughly comparable with seasonal flu, and the ugly-extensive diversification into serotypes with long-term high-level endemicity.
Collapse
Affiliation(s)
- François Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Cedric Tan
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 138672 Singapore, Singapore
| | - Leo Swadling
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Damien Richard
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Charlotte Jenner
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Mala Maini
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| |
Collapse
|
5
|
Gao R, Zu W, Liu Y, Li J, Li Z, Wen Y, Wang H, Yuan J, Cheng L, Zhang S, Zhang Y, Zhang S, Liu W, Lan X, Liu L, Li F, Zhang Z. Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis. Virulence 2021; 12:1209-1226. [PMID: 34030593 PMCID: PMC8158041 DOI: 10.1080/21505594.2021.1911477] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/28/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022] Open
Abstract
New SARS-CoV-2 mutants have been continuously indentified with enhanced transmission ever since its outbreak in early 2020. As an RNA virus, SARS-CoV-2 has a high mutation rate due to the low fidelity of RNA polymerase. To study the single nucleotide polymorphisms (SNPs) dynamics of SARS-CoV-2, 158 SNPs with high confidence were identified by deep meta-transcriptomic sequencing, and the most common SNP type was C > T. Analyses of intra-host population diversity revealed that intra-host quasispecies' composition varies with time during the early onset of symptoms, which implicates viral evolution during infection. Network analysis of co-occurring SNPs revealed the most abundant non-synonymous SNP 22,638 in the S glycoprotein RBD region and 28,144 in the ORF8 region. Furthermore, SARS-CoV-2 variations differ in an individual's respiratory tissue (nose, throat, BALF, or sputum), suggesting independent compartmentalization of SARS-CoV-2 populations in patients. The positive selection analysis of the SARS-CoV-2 genome uncovered the positive selected amino acid G251V on ORF3a. Alternative allele frequency spectrum (AAFS) of all variants revealed that ORF8 could bear alternate alleles with high frequency. Overall, the results show the quasispecies' profile of SARS-CoV-2 in the respiratory tract in the first two months after the outbreak.
Collapse
Affiliation(s)
- Rongsui Gao
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Wenhong Zu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Yang Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Junhua Li
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China
| | - Zeyao Li
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Yanling Wen
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Haiyan Wang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Jing Yuan
- Department of Infectious Diseases, Shenzhen Third People’s Hospital, National Clinical Research Center for Infectious Disease, Shenzhen, Guangdong Province, China
| | - Lin Cheng
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Shengyuan Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Yu Zhang
- National Supercomputing Center in Shenzhen (Shenzhen Cloud Computing Center), Shenzhen, China
| | - Shuye Zhang
- Shanghai Public Health Clinical Center, Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Weilong Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Xun Lan
- Department of Basic Medical Sciences at School of Medicine, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Lei Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Feng Li
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
- Shenzhen Research Center for Communicable Disease Diagnosis and Treatment of Chinese Academy of Medical Science, Shenzhen, Guangdong Province, China
- Guangdong Key Laboratory for Anti-infection Drug Quality Evaluation, Shenzhen, Guangdong Province, China
| |
Collapse
|
6
|
Moubarak M, Kasozi KI, Hetta HF, Shaheen HM, Rauf A, Al-kuraishy HM, Qusti S, Alshammari EM, Ayikobua ET, Ssempijja F, Afodun AM, Kenganzi R, Usman IM, Ochieng JJ, Osuwat LO, Matama K, Al-Gareeb AI, Kairania E, Musenero M, Welburn SC, Batiha GES. The Rise of SARS-CoV-2 Variants and the Role of Convalescent Plasma Therapy for Management of Infections. Life (Basel) 2021; 11:734. [PMID: 34440478 PMCID: PMC8399171 DOI: 10.3390/life11080734] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
Novel therapies for the treatment of COVID-19 are continuing to emerge as the SARS-Cov-2 pandemic progresses. PCR remains the standard benchmark for initial diagnosis of COVID-19 infection, while advances in immunological profiling are guiding clinical treatment. The SARS-Cov-2 virus has undergone multiple mutations since its emergence in 2019, resulting in changes in virulence that have impacted on disease severity globally. The emergence of more virulent variants of SARS-Cov-2 remains challenging for effective disease control during this pandemic. Major variants identified to date include B.1.1.7, B.1.351; P.1; B.1.617.2; B.1.427; P.2; P.3; B.1.525; and C.37. Globally, large unvaccinated populations increase the risk of more and more variants arising. With successive waves of COVID-19 emerging, strategies that mitigate against community transmission need to be implemented, including increased vaccination coverage. For treatment, convalescent plasma therapy, successfully deployed during recent Ebola outbreaks and for H1N1 influenza, can increase survival rates and improve host responses to viral challenge. Convalescent plasma is rich with cytokines (IL-1β, IL-2, IL-6, IL-17, and IL-8), CCL2, and TNFα, neutralizing antibodies, and clotting factors essential for the management of SARS-CoV-2 infection. Clinical trials can inform and guide treatment policy, leading to mainstream adoption of convalescent therapy. This review examines the limited number of clinical trials published, to date that have deployed this therapy and explores clinical trials in progress for the treatment of COVID-19.
Collapse
Affiliation(s)
- Mohamed Moubarak
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt; (M.M.); (H.M.S.)
| | - Keneth Iceland Kasozi
- Infection Medicine, Deanery of Biomedical Sciences, College of Medicine and Veterinary Medicine, The University of Edinburgh, 1 George Square, Edinburgh EH8 9JZ, UK
- School of Medicine, Kabale University, Kabale P.O. Box 317, Uganda
| | - Helal F. Hetta
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt;
| | - Hazem M. Shaheen
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt; (M.M.); (H.M.S.)
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Swabi 23561, Pakistan;
| | - Hayder M. Al-kuraishy
- Department of Clinical Pharmacology and Medicine, College of Medicine, Al-Mustansiriyia University, P.O. Box 14022 Baghdad, Iraq;
| | - Safaa Qusti
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Eida M. Alshammari
- Department of Chemistry, College of Sciences, University of Ha’il, Ha’il 2440, Saudi Arabia;
| | - Emmanuel Tiyo Ayikobua
- School of Health Sciences, Soroti University, Soroti P.O. Box 211, Uganda; (E.T.A.); (L.O.O.)
| | - Fred Ssempijja
- Department of Anatomy, Faculty of Biomedical Sciences, Kampala International University, Western Campus, Bushenyi P.O. Box 71, Uganda; (F.S.); (I.M.U.); (J.J.O.)
| | - Adam Moyosore Afodun
- Department of Anatomy and Cell Biology, Faculty of Health Sciences, Busitema University, Tororo P.O. Box 236, Uganda; (A.M.A.); (E.K.)
| | - Ritah Kenganzi
- Department of Medical Laboratory Sciences, School of Allied Health Sciences, Kampala International University Teaching Hospital, Bushenyi P.O. Box 71, Uganda;
| | - Ibe Michael Usman
- Department of Anatomy, Faculty of Biomedical Sciences, Kampala International University, Western Campus, Bushenyi P.O. Box 71, Uganda; (F.S.); (I.M.U.); (J.J.O.)
| | - Juma John Ochieng
- Department of Anatomy, Faculty of Biomedical Sciences, Kampala International University, Western Campus, Bushenyi P.O. Box 71, Uganda; (F.S.); (I.M.U.); (J.J.O.)
| | - Lawrence Obado Osuwat
- School of Health Sciences, Soroti University, Soroti P.O. Box 211, Uganda; (E.T.A.); (L.O.O.)
| | - Kevin Matama
- School of Pharmacy, Kampala International University, Western Campus, Bushenyi P.O. Box 71, Uganda;
| | - Ali I. Al-Gareeb
- Department of Pharmacology, Toxicology and Medicine, College of Medicine Al-Mustansiriya University, Baghdad P.O. Box 14022, Iraq;
| | - Emmanuel Kairania
- Department of Anatomy and Cell Biology, Faculty of Health Sciences, Busitema University, Tororo P.O. Box 236, Uganda; (A.M.A.); (E.K.)
| | - Monica Musenero
- Ministry of Science Technology and Innovations, Government of Uganda, Kampala P.O. Box 7466, Uganda;
| | - Susan Christina Welburn
- Infection Medicine, Deanery of Biomedical Sciences, College of Medicine and Veterinary Medicine, The University of Edinburgh, 1 George Square, Edinburgh EH8 9JZ, UK
- Zhejiang University-University of Edinburgh Joint Institute, Zhejiang University, International Campus, 718 East Haizhou Road, Haining 314400, China
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt; (M.M.); (H.M.S.)
| |
Collapse
|
7
|
J. Al-Awaida W, Jawabrah Al Hourani B, Swedan S, Nimer R, Alzoughool F, J. Al-Ameer H, E. Al Tamam S, Alashqar R, Al bawareed O, Gushchina Y, Samy Abousenna M, Ayyash AM, Sharab A, M. Alnaimat S, Imraish A, W. Akash M, R. Hadi N. Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. Genes (Basel) 2021; 12:1061. [PMID: 34356077 PMCID: PMC8306878 DOI: 10.3390/genes12071061] [Citation(s) in RCA: 3] [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: 05/17/2021] [Revised: 06/21/2021] [Accepted: 07/09/2021] [Indexed: 12/16/2022] Open
Abstract
The outbreak of coronavirus disease 2019 (COVID-19), by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has quickly developed into a worldwide pandemic. Mutations in the SARS-CoV-2 genome may affect various aspects of the disease including fatality ratio. In this study, 553,518 SARS-CoV-2 genome sequences isolated from patients from continents for the period 1 December 2020 to 15 March 2021 were comprehensively analyzed and a total of 82 mutations were identified concerning the reference sequence. In addition, associations between the mutations and the case fatality ratio (CFR), cases per million and deaths per million, were examined. The mutations having the highest frequencies among different continents were Spike_D614G and NSP12_P323L. Among the identified mutations, NSP2_T153M, NSP14_I42V and Spike_L18F mutations showed a positive correlation to CFR. While the NSP13_Y541C, NSP3_T73I and NSP3_Q180H mutations demonstrated a negative correlation to CFR. The Spike_D614G and NSP12_P323L mutations showed a positive correlation to deaths per million. The NSP3_T1198K, NS8_L84S and NSP12_A97V mutations showed a significant negative correlation to deaths per million. The NSP12_P323L and Spike_D614G mutations showed a positive correlation to the number of cases per million. In contrast, NS8_L84S and NSP12_A97V mutations showed a negative correlation to the number of cases per million. In addition, among the identified clades, none showed a significant correlation to CFR. The G, GR, GV, S clades showed a significant positive correlation to deaths per million. The GR and S clades showed a positive correlation to number of cases per million. The clades having the highest frequencies among continents were G, followed by GH and GR. These findings should be taken into consideration during epidemiological surveys of the virus and vaccine development.
Collapse
Affiliation(s)
- Wajdy J. Al-Awaida
- Department of Biology and Biotechnology, Faculty of Science, American University of Madaba, Madaba 11821, Jordan; (H.J.A.-A.); (S.E.A.T.); (R.A.); (A.S.)
| | | | - Samer Swedan
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan; (S.S.); (R.N.)
| | - Refat Nimer
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan; (S.S.); (R.N.)
| | - Foad Alzoughool
- Department of Medical Laboratory Sciences, The Hashemite University, Zarqa 13133, Jordan;
| | - Hamzeh J. Al-Ameer
- Department of Biology and Biotechnology, Faculty of Science, American University of Madaba, Madaba 11821, Jordan; (H.J.A.-A.); (S.E.A.T.); (R.A.); (A.S.)
| | - Sara E. Al Tamam
- Department of Biology and Biotechnology, Faculty of Science, American University of Madaba, Madaba 11821, Jordan; (H.J.A.-A.); (S.E.A.T.); (R.A.); (A.S.)
| | - Raghad Alashqar
- Department of Biology and Biotechnology, Faculty of Science, American University of Madaba, Madaba 11821, Jordan; (H.J.A.-A.); (S.E.A.T.); (R.A.); (A.S.)
| | - Omar Al bawareed
- Department of Normal Physiology, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, 117198 Moscow, Russia;
| | - Yulia Gushchina
- Department of General and Clinical Pharmacology, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, 117198 Moscow, Russia;
| | - Mohamed Samy Abousenna
- Central Laboratory for Evaluation of Veterinary Biologics, Agricultural Research Center, Cairo 11517, Egypt;
| | - Amani Marwan Ayyash
- Department of Pharmacy, Faculty of Heath Sciences, American University of Madaba, Madaba 11821, Jordan;
| | - Ahmad Sharab
- Department of Biology and Biotechnology, Faculty of Science, American University of Madaba, Madaba 11821, Jordan; (H.J.A.-A.); (S.E.A.T.); (R.A.); (A.S.)
| | - Sulaiman M. Alnaimat
- Biological Department, Faculty of Science, Al Hussein Bin Talal University, Ma’an P.O. Box 20, Jordan;
| | - Amer Imraish
- Department of Biology, Faculty of Science, The University of Jordan, Amman 11942, Jordan;
| | - Muhanad W. Akash
- Department of Horticulture and Crop Science, Faculty of Agriculture, The University of Jordan, Amman 11942, Jordan;
| | - Najah R. Hadi
- Department of Pharmacology and Therapeutics, Faculty of Medicine, University of Kufa, Najaf 540011, Iraq;
| |
Collapse
|
8
|
In Vivo Generation of BK and JC Polyomavirus Defective Viral Genomes in Human Urine Samples Associated with Higher Viral Loads. J Virol 2021; 95:JVI.00250-21. [PMID: 33827948 PMCID: PMC8316075 DOI: 10.1128/jvi.00250-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/25/2021] [Indexed: 12/22/2022] Open
Abstract
Defective viral genomes (DVGs) are parasitic viral sequences containing point mutations, deletions, or duplications that might interfere with replication. DVGs are often associated with viral passage at high multiplicities of infection in culture systems but have been increasingly reported in clinical specimens. To date however, only RNA viruses have been shown to contain DVGs in clinical specimens. Here, using direct deep sequencing with multiple library preparation strategies and confirmatory digital droplet PCR (ddPCR) of urine samples taken from immunosuppressed individuals, we show that clinical BK polyomavirus (BKPyV) and JC polyomavirus (JCPyV) strains contain widespread genomic rearrangements across multiple loci that likely interfere with viral replication. BKPyV DVGs were derived from BKPyV genotypes Ia, Ib-1, and Ic. The presence of DVGs was associated with specimens containing higher viral loads but never reached clonality, consistent with a model of parasitized replication. These DVGs persisted during clinical infection as evidenced in two separate pairs of samples containing BK virus collected from the same individual up to 302 days apart. In a separate individual, we observed the generation of DVGs after a 57.5-fold increase in viral load. In summary, by extending the presence of DVGs in clinical specimens to DNA viruses, we demonstrate the ubiquity of DVGs in clinical virology. IMPORTANCE Defective viral genomes (DVGs) can have a significant impact on the production of infectious virus particles. DVGs have only been identified in cultured viruses passaged at high multiplicities of infection and RNA viruses collected from clinical specimens; no DNA virus in the wild has been shown to contain DVGs. Here, we identified BK and JC polyomavirus DVGs in clinical urine specimens and demonstrated that these DVGs are more frequently identified in samples with higher viral loads. The strains containing DVGs had rearrangements throughout their genomes, with the majority affecting genes required for viral replication. Longitudinal analysis showed that these DVGs can persist during an infection but do not reach clonality within the chronically infected host. Our identification of polyomavirus DVGs suggests that these parasitic sequences exist across the many classes of viruses capable of causing human disease.
Collapse
|
9
|
Cagliani R, Mozzi A, Pontremoli C, Sironi M. Evolution and Origin of Human Viruses. Virology 2021. [DOI: 10.1002/9781119818526.ch8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
10
|
Rahimi A, Mirzazadeh A, Tavakolpour S. Genetics and genomics of SARS-CoV-2: A review of the literature with the special focus on genetic diversity and SARS-CoV-2 genome detection. Genomics 2021; 113:1221-1232. [PMID: 33007398 PMCID: PMC7525243 DOI: 10.1016/j.ygeno.2020.09.059] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/26/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023]
Abstract
The outbreak of 2019-novel coronavirus disease (COVID-19), caused by SARS-CoV-2, started in late 2019; in a short time, it has spread rapidly all over the world. Although some possible antiviral and anti-inflammatory medications are available, thousands of people are dying daily. Well-understanding of the SARS-CoV-2 genome is not only essential for the development of new treatments/vaccines, but it also can be used for improving the sensitivity and specificity of current approaches for virus detection. Accordingly, we reviewed the most critical findings related to the genetics of the SARS-CoV-2, with a specific focus on genetic diversity and reported mutations, molecular-based diagnosis assays, using interfering RNA technology for the treatment of patients, and genetic-related vaccination strategies. Additionally, considering the unanswered questions or uncertainties in these regards, different topics were discussed.
Collapse
Affiliation(s)
- Azadeh Rahimi
- Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Azin Mirzazadeh
- Department of Medical Genetics, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran,Joint Bioinformatics Graduate Program, University of Arkansas Little Rock and University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Soheil Tavakolpour
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, United States.
| |
Collapse
|
11
|
Burek Kamenaric M, Ivkovic V, Kovacevic Vojtusek I, Zunec R. The Role of HLA and KIR Immunogenetics in BK Virus Infection after Kidney Transplantation. Viruses 2020; 12:v12121417. [PMID: 33317205 PMCID: PMC7763146 DOI: 10.3390/v12121417] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022] Open
Abstract
BK virus (BKV) is a polyomavirus with high seroprevalence in the general population with an unremarkable clinical presentation in healthy people, but a potential for causing serious complications in immunosuppressed transplanted patients. Reactivation or primary infection in kidney allograft recipients may lead to allograft dysfunction and subsequent loss. Currently, there is no widely accepted specific treatment for BKV infection and reduction of immunosuppressive therapy is the mainstay therapy. Given this and the sequential appearance of viruria-viremia-nephropathy, screening and early detection are of utmost importance. There are numerous risk factors associated with BKV infection including genetic factors, among them human leukocyte antigens (HLA) and killer cell immunoglobulin-like receptors (KIR) alleles have been shown to be the strongest so far. Identification of patients at risk for BKV infection would be useful in prevention or early action to reduce morbidity and progression to frank nephropathy. Assessment of risk involving HLA ligands and KIR genotyping of recipients in the pre-transplant or early post-transplant period might be useful in clinical practice. This review summarizes current knowledge of the association between HLA, KIR and BKV infection and potential future directions of research, which might lead to optimal utilization of these genetic markers.
Collapse
Affiliation(s)
- Marija Burek Kamenaric
- Tissue Typing Center, Clinical Department of Transfusion Medicine and Transplantation Biology, University Hospital Center Zagreb, 10 000 Zagreb, Croatia;
| | - Vanja Ivkovic
- Department of Nephrology, Hypertension, Dialysis and Transplantation, University Hospital Center Zagreb, 10 000 Zagreb, Croatia; (V.I.); (I.K.V.)
- Department of Public Health, Faculty of Health Studies, University of Rijeka, 51 000 Rijeka, Croatia
| | - Ivana Kovacevic Vojtusek
- Department of Nephrology, Hypertension, Dialysis and Transplantation, University Hospital Center Zagreb, 10 000 Zagreb, Croatia; (V.I.); (I.K.V.)
| | - Renata Zunec
- Tissue Typing Center, Clinical Department of Transfusion Medicine and Transplantation Biology, University Hospital Center Zagreb, 10 000 Zagreb, Croatia;
- Correspondence:
| |
Collapse
|
12
|
van Dorp L, Richard D, Tan CCS, Shaw LP, Acman M, Balloux F. No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2. Nat Commun 2020; 11:5986. [PMID: 33239633 PMCID: PMC7688939 DOI: 10.1038/s41467-020-19818-2] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/30/2020] [Indexed: 02/07/2023] Open
Abstract
COVID-19 is caused by the coronavirus SARS-CoV-2, which jumped into the human population in late 2019 from a currently uncharacterised animal reservoir. Due to this recent association with humans, SARS-CoV-2 may not yet be fully adapted to its human host. This has led to speculations that SARS-CoV-2 may be evolving towards higher transmissibility. The most plausible mutations under putative natural selection are those which have emerged repeatedly and independently (homoplasies). Here, we formally test whether any homoplasies observed in SARS-CoV-2 to date are significantly associated with increased viral transmission. To do so, we develop a phylogenetic index to quantify the relative number of descendants in sister clades with and without a specific allele. We apply this index to a curated set of recurrent mutations identified within a dataset of 46,723 SARS-CoV-2 genomes isolated from patients worldwide. We do not identify a single recurrent mutation in this set convincingly associated with increased viral transmission. Instead, recurrent mutations currently in circulation appear to be evolutionary neutral and primarily induced by the human immune system via RNA editing, rather than being signatures of adaptation. At this stage we find no evidence for significantly more transmissible lineages of SARS-CoV-2 due to recurrent mutations.
Collapse
Affiliation(s)
- Lucy van Dorp
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
| | - Damien Richard
- Cirad, UMR PVBMT, F-97410 St Pierre, Réunion, France
- Université de la Réunion, UMR PVBMT, F-97490 St Denis, Réunion, France
| | - Cedric C S Tan
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Liam P Shaw
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Mislav Acman
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - François Balloux
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
| |
Collapse
|
13
|
van Dorp L, Acman M, Richard D, Shaw LP, Ford CE, Ormond L, Owen CJ, Pang J, Tan CCS, Boshier FAT, Ortiz AT, Balloux F. Emergence of genomic diversity and recurrent mutations in SARS-CoV-2. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 83:104351. [PMID: 32387564 PMCID: PMC7199730 DOI: 10.1016/j.meegid.2020.104351] [Citation(s) in RCA: 510] [Impact Index Per Article: 127.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 04/30/2020] [Accepted: 05/02/2020] [Indexed: 02/06/2023]
Abstract
SARS-CoV-2 is a SARS-like coronavirus of likely zoonotic origin first identified in December 2019 in Wuhan, the capital of China's Hubei province. The virus has since spread globally, resulting in the currently ongoing COVID-19 pandemic. The first whole genome sequence was published on January 5 2020, and thousands of genomes have been sequenced since this date. This resource allows unprecedented insights into the past demography of SARS-CoV-2 but also monitoring of how the virus is adapting to its novel human host, providing information to direct drug and vaccine design. We curated a dataset of 7666 public genome assemblies and analysed the emergence of genomic diversity over time. Our results are in line with previous estimates and point to all sequences sharing a common ancestor towards the end of 2019, supporting this as the period when SARS-CoV-2 jumped into its human host. Due to extensive transmission, the genetic diversity of the virus in several countries recapitulates a large fraction of its worldwide genetic diversity. We identify regions of the SARS-CoV-2 genome that have remained largely invariant to date, and others that have already accumulated diversity. By focusing on mutations which have emerged independently multiple times (homoplasies), we identify 198 filtered recurrent mutations in the SARS-CoV-2 genome. Nearly 80% of the recurrent mutations produced non-synonymous changes at the protein level, suggesting possible ongoing adaptation of SARS-CoV-2. Three sites in Orf1ab in the regions encoding Nsp6, Nsp11, Nsp13, and one in the Spike protein are characterised by a particularly large number of recurrent mutations (>15 events) which may signpost convergent evolution and are of particular interest in the context of adaptation of SARS-CoV-2 to the human host. We additionally provide an interactive user-friendly web-application to query the alignment of the 7666 SARS-CoV-2 genomes.
Collapse
Affiliation(s)
- Lucy van Dorp
- UCL Genetics Institute, University College London, London WC1E 6BT, UK.
| | - Mislav Acman
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Damien Richard
- Cirad, UMR PVBMT, F-97410, St Pierre, Réunion, France; Université de la Réunion, UMR PVBMT, F-97490, St Denis, Réunion, France
| | - Liam P Shaw
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Charlotte E Ford
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Louise Ormond
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | | | - Juanita Pang
- UCL Genetics Institute, University College London, London WC1E 6BT, UK; Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Cedric C S Tan
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | | | - Arturo Torres Ortiz
- UCL Genetics Institute, University College London, London WC1E 6BT, UK; Department of Infectious Disease, Imperial College, London W2 1NY, UK
| | - François Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK.
| |
Collapse
|
14
|
Daugavet MA, Shabelnikov SV, Podgornaya OI. Amino acid sequence associated with bacteriophage recombination site helps to reveal genes potentially acquired through horizontal gene transfer. BMC Bioinformatics 2020; 21:305. [PMID: 32703190 PMCID: PMC7379824 DOI: 10.1186/s12859-020-03599-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 12/04/2022] Open
Abstract
Background Horizontal gene transfer, i.e. the acquisition of genetic material from nonparent organism, is considered an important force driving species evolution. Many cases of horizontal gene transfer from prokaryotes to eukaryotes have been registered, but no transfer mechanism has been deciphered so far, although viruses were proposed as possible vectors in several studies. In agreement with this idea, in our previous study we discovered that in two eukaryotic proteins bacteriophage recombination site (AttP) was adjacent to the regions originating via horizontal gene transfer. In one of those cases AttP site was present inside the introns of cysteine-rich repeats. In the present study we aimed to apply computational tools for finding multiple horizontal gene transfer events in large genome databases. For that purpose we used a sequence of cysteine-rich repeats to identify genes potentially acquired through horizontal transfer. Results HMMER remote similarity search significantly detected 382 proteins containing cysteine-rich repeats. All of them, except 8 sequences, belong to eukaryotes. In 124 proteins the presence of conserved structural domains was predicted. In spite of the fact that cysteine-rich repeats are found almost exclusively in eukaryotic proteins, many predicted domains are most common for prokaryotes or bacteriophages. Ninety-eight proteins out of 124 contain typical prokaryotic domains. In those cases proteins were considered as potentially originating via horizontal transfer. In addition, HHblits search revealed that two domains of the same fungal protein, Glycoside hydrolase and Peptidase M15, have high similarity with proteins of two different prokaryotic species, hinting at independent horizontal gene transfer events. Conclusions Cysteine-rich repeats in eukaryotic proteins are usually accompanied by conserved domains typical for prokaryotes or bacteriophages. These proteins, containing both cysteine-rich repeats, and characteristic prokaryotic domains, might represent multiple independent horizontal gene transfer events from prokaryotes to eukaryotes. We believe that the presence of bacteriophage recombination site inside cysteine-rich repeat coding sequence may facilitate horizontal genes transfer. Thus computational approach, described in the present study, can help finding multiple sequences originated from horizontal transfer in eukaryotic genomes.
Collapse
Affiliation(s)
| | | | - Olga I Podgornaya
- Institute of Cytology, St. Petersburg, Russia, 194064.,School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia, 690090.,Department of Cytology and Histology, St. Pb State University, St. Petersburg, Russia, 199034
| |
Collapse
|
15
|
Kaszab E, Marton S, Dán Á, Farsang A, Bálint Á, Bányai K, Fehér E. Molecular epidemiology and phylodynamics of goose haemorrhagic polyomavirus. Transbound Emerg Dis 2020; 67:2602-2608. [PMID: 32374515 DOI: 10.1111/tbed.13608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/02/2020] [Accepted: 04/29/2020] [Indexed: 12/24/2022]
Abstract
Goose haemorrhagic polyomavirus (GHPV, or Anser anser polyomavirus 1) is a small dsDNA virus of the Polyomaviridae family. The virus infects the internal organs causing haemorrhagic nephritis and enteritis of geese that may be fatal for goslings. In this study, GHPV positivity was examined in goose and duck samples collected in Hungary between 2005 and 2019. In this period, 384 of the investigated 1,111 specimens were diagnosed as GHPV-positive by PCR assay. Twenty-two GHPV genomes were sequenced and subjected to phylogenetic and evolutionary analysis. Based on the sequence data, the mean evolutionary rates were estimated 6.57 × 10-6 -5.82 × 10-5 s/s/y for both GHPV complete genomes and individual genes, with negative selection acting on each gene. When GHPV VP1 sequences originating from wild birds were also included in the analyses, the nt and aa mutations inflated the substitution rate to 1.54 × 10-4 s/s/y that may imply adaptation of the virus to novel host species. Our data suggested the co-circulation of various GHPV strains in Hungarian goose farms; the source of these may be persistently infected domesticated or migratory wild birds. Detection and characterization of GHPV in wild birds and domestic waterfowls may help to elaborate new strategies for more effective disease control and prevention.
Collapse
Affiliation(s)
- Eszter Kaszab
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Szilvia Marton
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Ádám Dán
- University of Veterinary Medicine, Budapest, Hungary
| | | | - Ádám Bálint
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, Budapest, Hungary
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Enikő Fehér
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| |
Collapse
|
16
|
Blackard JT, Davies SM, Laskin BL. BK polyomavirus diversity-Why viral variation matters. Rev Med Virol 2020; 30:e2102. [PMID: 32128960 DOI: 10.1002/rmv.2102] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 02/06/2023]
Abstract
BK polyomavirus (BKPyV or BKV) is a non-enveloped, circular double-stranded DNA virus that may exceed 80% seroprevalence in adults. BKV infection typically occurs during childhood, and the majority of adults are latently infected. While BKV infection is rarely associated with clinical disease in most individuals, in immunosuppressed individuals, reactivation may cause kidney (BK-associated nephropathy) or bladder (hemorrhagic cystitis and ureteral stenosis) injury. No antiviral therapies have been approved for the treatment of BKV infection. Reducing immunosuppression is the most effective therapy, although this is not feasible in many patients. Thus, a robust understanding of viral pathogenesis and viral diversity remains important for the development of future therapeutic strategies. Studies of BKV diversity are quite sparse compared to other common viral infections; thus, much of our understanding of BVK variability and evolution relies heavily analogous studies of other viruses such as HIV or viral hepatitis. We provide a comprehensive review of BKV diversity at the population and individual level with careful consideration of how viral variability may impact viral replication, pathogenesis, tropism, and protein function. We also discuss a number of outstanding questions related to BK virus diversity that should be explored rigorously in future studies.
Collapse
Affiliation(s)
- Jason T Blackard
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Stella M Davies
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center and the Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Benjamin L Laskin
- Division of Nephrology, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| |
Collapse
|
17
|
Abstract
Viral quasispecies refers to a population structure that consists of extremely large numbers of variant genomes, termed mutant spectra, mutant swarms or mutant clouds. Fueled by high mutation rates, mutants arise continually, and they change in relative frequency as viral replication proceeds. The term quasispecies was adopted from a theory of the origin of life in which primitive replicons) consisted of mutant distributions, as found experimentally with present day RNA viruses. The theory provided a new definition of wild type, and a conceptual framework for the interpretation of the adaptive potential of RNA viruses that contrasted with classical studies based on consensus sequences. Standard clonal analyses and deep sequencing methodologies have confirmed the presence of myriads of mutant genomes in viral populations, and their participation in adaptive processes. The quasispecies concept applies to any biological entity, but its impact is more evident when the genome size is limited and the mutation rate is high. This is the case of the RNA viruses, ubiquitous in our biosphere, and that comprise many important pathogens. In virology, quasispecies are defined as complex distributions of closely related variant genomes subjected to genetic variation, competition and selection, and that may act as a unit of selection. Despite being an integral part of their replication, high mutation rates have an upper limit compatible with inheritable information. Crossing such a limit leads to RNA virus extinction, a transition that is the basis of an antiviral design termed lethal mutagenesis.
Collapse
Affiliation(s)
- Esteban Domingo
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Celia Perales
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, UAM, Madrid, Spain
| |
Collapse
|