1
|
Zheng SY, Zhang YP, Liu YX, Zhao W, Peng XL, Zheng YP, Fu YH, Yu JM, He JS. Tracking of Mutational Signature of SARS-CoV-2 Omicron on Distinct Continents and Little Difference was Found. Viruses 2023; 15:v15020321. [PMID: 36851535 PMCID: PMC9967123 DOI: 10.3390/v15020321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
The Omicron variant is currently ravaging the world, raising serious concern globally. Monitoring genomic variations and determining their influence on biological features are critical for tracing its ongoing transmission and facilitating effective measures. Based on large-scale sequences from different continents, this study found that: (i) The genetic diversity of Omicron is much lower than that of the Delta variant. Still, eight deletions (Del 1-8) and 1 insertion, as well as 130 SNPs, were detected on the Omicron genomes, with two deletions (Del 3 and 4) and 38 SNPs commonly detected on all continents and exhibiting high-occurring frequencies. (ii) Four groups of tightly linked SNPs (linkage I-IV) were detected, among which linkage I, containing 38 SNPs, with 6 located in the RBD, increased its occurring frequency remarkably over time. (iii) The third codons of the Omicron shouldered the most mutation pressures, while the second codons presented the least flexibility. (iv) Four major mutants with amino acid substitutions in the RBD were detected, and further structural analysis suggested that the substitutions did not alter the viral receptor binding ability greatly. It was inferred that though the Omicron genome harbored great changes in antigenicity and remarkable ability to evade immunity, it was immune-pressure selected. This study tracked mutational signatures of Omicron variant and the potential biological significance of the SNPs, and the linkages await further functional verification.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Jie-Mei Yu
- Correspondence: (J.-M.Y.); (J.-S.H.); Tel.: +86-10-51684358 (J.-M.Y.)
| | - Jin-Sheng He
- Correspondence: (J.-M.Y.); (J.-S.H.); Tel.: +86-10-51684358 (J.-M.Y.)
| |
Collapse
|
2
|
Nucleotide-based genetic networks: Methods and applications. J Biosci 2022. [PMID: 36226367 PMCID: PMC9554864 DOI: 10.1007/s12038-022-00290-7] [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] [Indexed: 11/21/2022]
Abstract
Genomic variations have been acclaimed as among the key players in understanding the biological mechanisms behind migration, evolution, and adaptation to extreme conditions. Due to stochastic evolutionary forces, the frequency of polymorphisms is affected by changes in the frequency of nearby polymorphisms in the same DNA sample, making them connected in terms of evolution. This article presents all the ingredients to understand the cumulative effects and complex behaviors of genetic variations in the human mitochondrial genome by analyzing co-occurrence networks of nucleotides, and shows key results obtained from such analyses. The article emphasizes recent investigations of these co-occurrence networks, describing the role of interactions between nucleotides in fundamental processes of human migration and viral evolution. The corresponding co-mutation-based genetic networks revealed genetic signatures of human adaptation in extreme environments. This article provides the methods of constructing such networks in detail, along with their graph-theoretical properties, and applications of the genomic networks in understanding the role of nucleotide co-evolution in evolution of the whole genome.
Collapse
|
3
|
Alam ASMRU, Islam OK, Hasan MS, Islam MR, Mahmud S, Al‐Emran HM, Jahid IK, Crandall KA, Hossain MA. Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. J Med Virol 2022; 94:1035-1049. [PMID: 34676891 PMCID: PMC8661685 DOI: 10.1002/jmv.27416] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 10/15/2021] [Accepted: 10/20/2021] [Indexed: 01/18/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into eight fundamental clades with four of these clades (G, GH, GR, and GV) globally prevalent in 2020. To explain plausible epistatic effects of the signature co-occurring mutations of these circulating clades on viral replication and transmission fitness, we proposed a hypothetical model using in silico approach. Molecular docking and dynamics analyses showed the higher infectiousness of a spike mutant through more favorable binding of G614 with the elastase-2. RdRp mutation p.P323L significantly increased genome-wide mutations (p < 0.0001), allowing for more flexible RdRp (mutated)-NSP8 interaction that may accelerate replication. Superior RNA stability and structural variation at NSP3:C241T might impact protein, RNA interactions, or both. Another silent 5'-UTR:C241T mutation might affect translational efficiency and viral packaging. These four G-clade-featured co-occurring mutations might increase viral replication. Sentinel GH-clade ORF3a:p.Q57H variants constricted the ion-channel through intertransmembrane-domain interaction of cysteine(C81)-histidine(H57). The GR-clade N:p.RG203-204KR would stabilize RNA interaction by a more flexible and hypo-phosphorylated SR-rich region. GV-clade viruses seemingly gained the evolutionary advantage of the confounding factors; nevertheless, N:p.A220V might modulate RNA binding with no phenotypic effect. Our hypothetical model needs further retrospective and prospective studies to understand detailed molecular events and their relationship to the fitness of SARS-CoV-2.
Collapse
Affiliation(s)
| | - Ovinu Kibria Islam
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - Md. Shazid Hasan
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - Mir Raihanul Islam
- Division of Poverty, Health, and NutritionInternational Food Policy Research InstituteBangladesh
| | - Shafi Mahmud
- Department Genetic Engineering and BiotechnologyUniversity of RajshahiRajshahiBangladesh
| | - Hassan M. Al‐Emran
- Department of Biomedical EngineeringJashore University of Science and TechnologyJashoreBangladesh
| | - Iqbal Kabir Jahid
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - Keith A. Crandall
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, Milken Institute School of Public HealthThe George Washington UniversityWashington DCUSA
| | - M. Anwar Hossain
- Office of the Vice ChancellorJashore University of Science and TechnologyJashoreBangladesh
- Department of MicrobiologyUniversity of DhakaDhakaBangladesh
| |
Collapse
|
4
|
Kiseleva I, Isakova-Sivak I, Stukova M, Erofeeva M, Donina S, Larionova N, Krutikova E, Bazhenova E, Stepanova E, Vasilyev K, Matyushenko V, Krylova M, Galatonova J, Ershov A, Lioznov D, Sparrow EG, Torelli G, Rudenko L. A Phase 1 Randomized Placebo-Controlled Study to Assess the Safety, Immunogenicity and Genetic Stability of a New Potential Pandemic H7N9 Live Attenuated Influenza Vaccine in Healthy Adults. Vaccines (Basel) 2020; 8:vaccines8020296. [PMID: 32532097 PMCID: PMC7350028 DOI: 10.3390/vaccines8020296] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/30/2020] [Accepted: 06/09/2020] [Indexed: 01/06/2023] Open
Abstract
This study describes a double-blind randomized placebo-controlled phase I clinical trial in healthy adults of a new potential pandemic H7N9 live attenuated influenza vaccine (LAIV) based on the human influenza virus of Yangtze River Delta hemagglutinin lineage (ClinicalTrials.gov Identifier: NCT03739229). Two doses of H7N9 LAIV or placebo were administered intranasally to 30 and 10 subjects, respectively. The vaccine was well-tolerated and not associated with increased rates of adverse events or with any serious adverse events. Vaccine virus was detected in nasal swabs during the 6 days after vaccination or revaccination. A lower frequency of shedding was observed after the second vaccination. Twenty-five clinical viral isolates obtained after the first and second doses of vaccine retained the temperature-sensitive and cold-adapted phenotypic characteristics of LAIV. There was no confirmed transmission of the vaccine strain from vaccinees to placebo recipients. After the two H7N9 LAIV doses, an immune response was observed in 96.6% of subjects in at least one of the assays conducted.
Collapse
Affiliation(s)
- Irina Kiseleva
- Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (I.I.-S.); (S.D.); (N.L.); (E.K.); (E.B.); (E.S.); (V.M.); (L.R.)
- Correspondence: ; Tel.: +7-(812)-2346-860
| | - Irina Isakova-Sivak
- Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (I.I.-S.); (S.D.); (N.L.); (E.K.); (E.B.); (E.S.); (V.M.); (L.R.)
| | - Marina Stukova
- Smorodintsev Research Institute of Influenza, Ministry of Health of the Russian Federation, 197376 St Petersburg, Russia; (M.S.); (M.E.); (K.V.); (D.L.)
| | - Marianna Erofeeva
- Smorodintsev Research Institute of Influenza, Ministry of Health of the Russian Federation, 197376 St Petersburg, Russia; (M.S.); (M.E.); (K.V.); (D.L.)
| | - Svetlana Donina
- Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (I.I.-S.); (S.D.); (N.L.); (E.K.); (E.B.); (E.S.); (V.M.); (L.R.)
| | - Natalie Larionova
- Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (I.I.-S.); (S.D.); (N.L.); (E.K.); (E.B.); (E.S.); (V.M.); (L.R.)
| | - Elena Krutikova
- Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (I.I.-S.); (S.D.); (N.L.); (E.K.); (E.B.); (E.S.); (V.M.); (L.R.)
| | - Ekaterina Bazhenova
- Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (I.I.-S.); (S.D.); (N.L.); (E.K.); (E.B.); (E.S.); (V.M.); (L.R.)
| | - Ekaterina Stepanova
- Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (I.I.-S.); (S.D.); (N.L.); (E.K.); (E.B.); (E.S.); (V.M.); (L.R.)
| | - Kirill Vasilyev
- Smorodintsev Research Institute of Influenza, Ministry of Health of the Russian Federation, 197376 St Petersburg, Russia; (M.S.); (M.E.); (K.V.); (D.L.)
| | - Victoria Matyushenko
- Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (I.I.-S.); (S.D.); (N.L.); (E.K.); (E.B.); (E.S.); (V.M.); (L.R.)
| | - Marina Krylova
- The Federal State Unitary Enterprise “Scientific and Production Association for Immunological Preparations “Microgen”, Ministry of Health of Russian Federation, 127473 Moscow, Russia; (M.K.); (J.G.); (A.E.)
| | - Julia Galatonova
- The Federal State Unitary Enterprise “Scientific and Production Association for Immunological Preparations “Microgen”, Ministry of Health of Russian Federation, 127473 Moscow, Russia; (M.K.); (J.G.); (A.E.)
| | - Aleksey Ershov
- The Federal State Unitary Enterprise “Scientific and Production Association for Immunological Preparations “Microgen”, Ministry of Health of Russian Federation, 127473 Moscow, Russia; (M.K.); (J.G.); (A.E.)
| | - Dmitry Lioznov
- Smorodintsev Research Institute of Influenza, Ministry of Health of the Russian Federation, 197376 St Petersburg, Russia; (M.S.); (M.E.); (K.V.); (D.L.)
| | | | - Guido Torelli
- World Health Organization, 1211 Geneva, Switzerland; (E.G.S.); (G.T.)
| | - Larisa Rudenko
- Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (I.I.-S.); (S.D.); (N.L.); (E.K.); (E.B.); (E.S.); (V.M.); (L.R.)
| |
Collapse
|
5
|
|
6
|
Cueno ME, Shiotsu H, Nakano K, Sugiyama E, Kikuta M, Usui R, Oya R, Imai K. Structural significance of residues 158-160 in the H3N2 hemagglutnin globular head: A computational study with implications in viral evolution and infection. J Mol Graph Model 2019; 89:33-40. [PMID: 30849718 DOI: 10.1016/j.jmgm.2019.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 01/28/2019] [Accepted: 02/18/2019] [Indexed: 01/14/2023]
Abstract
Influenza A H3N2 has been linked to annual outbreaks within the human population attributable to continuous structural changes. H3N2 HA contains well identified antigenic sites and receptor-binding sites (RBS) that are possibly correlated to viral evolution and infection. However, the structural significance of amino acid residues associated with both viral evolution and infection were not fully demonstrated. Throughout this study, we generated and analyzed H3N2 HA models that represented the clade 3C.2 population (comprised of clades 3C.2, 3C.2a, and 3C.21 from the transitioning 2014-2018 H3N2 strains) and 3C.3a (from the 2016 H3N2 strain). Model quality estimation, structural analyses and superimposition, and network analytics of H3N2 HA1 evolution were performed. We found that the structural properties of residues 158-160 could influence the overall HA backbone. More specifically, amino acid substitutions at residues 159-160 affected the amino acid orientation at residue 158, thereby, causing the overall HA backbone structure to vary. Our results were consistent with 1968-2018 HA1 evolution. Taken together, we propose that our results would highlight the structural significance of residues 158-160 in HA1 for both antigenic drift and RBS.
Collapse
Affiliation(s)
- Marni E Cueno
- Department of Microbiology, Nihon University School of Dentistry, Tokyo, 101-8310, Japan; Immersion Physics Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, 178-0063, Japan; Immersion Biology Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, 178-0063, Japan.
| | - Hayato Shiotsu
- Immersion Physics Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, 178-0063, Japan
| | - Karin Nakano
- Immersion Physics Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, 178-0063, Japan
| | - Emiko Sugiyama
- Immersion Biology Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, 178-0063, Japan
| | - Mari Kikuta
- Immersion Biology Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, 178-0063, Japan
| | - Rikuya Usui
- Immersion Physics Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, 178-0063, Japan
| | - Riku Oya
- Immersion Physics Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, 178-0063, Japan
| | - Kenichi Imai
- Department of Microbiology, Nihon University School of Dentistry, Tokyo, 101-8310, Japan
| |
Collapse
|
7
|
Schönbach C, Verma C, Wee LJK, Bond PJ, Ranganathan S. 2016 update on APBioNet's annual international conference on bioinformatics (InCoB). BMC Genomics 2016; 17:1036. [PMID: 28155656 PMCID: PMC5259860 DOI: 10.1186/s12864-016-3362-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
InCoB became since its inception in 2002 one of the largest annual bioinformatics conferences in the Asia-Pacific region with attendance ranging between 150 and 250 delegates depending on the venue location. InCoB 2016 in Singapore was attended by almost 220 delegates. This year, sessions on structural bioinformatics, sequence and sequencing, and next-generation sequencing fielded the highest number of oral presentation. Forty-four out 96 oral presentations were associated with an accepted manuscript in supplemental issues of BMC Bioinformatics, BMC Genomics, BMC Medical Genomics or BMC Systems Biology. Articles with a genomics focus are reviewed in this editorial. Next year's InCoB will be held in Shenzen, China from September 20 to 22, 2017.
Collapse
Affiliation(s)
- Christian Schönbach
- International Research Center for Medical Sciences, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, 860-0811 Japan
| | - Chandra Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A∗STAR), Singapore, 138671 Singapore
| | - Lawrence Jin Kiat Wee
- Institute for Infocomm Research, Agency for Science, Technology and Research (A*STAR), Singapore, 138632 Singapore
| | - Peter John Bond
- Bioinformatics Institute, Agency for Science, Technology and Research (A∗STAR), Singapore, 138671 Singapore
| | - Shoba Ranganathan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109 Australia
| |
Collapse
|