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Rout M, Dahiya SS, Subramaniam S, Acharya R, Samanta R, Biswal JK, Mohapatra JK, Singh RP. Complete coding region sequence analyses and antigenic characterization of emerging lineage G-IX of foot- and-mouth disease virus serotype Asia1. Vet Q 2024; 44:1-10. [PMID: 38903046 PMCID: PMC11195457 DOI: 10.1080/01652176.2024.2367215] [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: 01/12/2024] [Accepted: 06/06/2024] [Indexed: 06/22/2024] Open
Abstract
Foot-and-mouth disease Virus (FMDV) serotype Asia1 is prevalent in the Indian subcontinent, with only G-III and G-VIII reported in India until 2020. However, in 2019, a novel genetic group within serotype Asia1, designated as G-IX, emerged in Bangladesh, followed by its detection in India in 2020. This report presents analyses of the complete coding region sequences of the G-IX lineage isolates. The length of the open reading frame (ORF) of the two G-IX isolates was 6990 nucleotides without any deletion or insertion. The G-IX isolates showed the highest sequence similarity with an isolate of G-III at the ORF, L, P2, and P3 regions, and with an isolate of G-VIII at the P1 region. Phylogenetic analysis based on the capsid region (P1) supports the hypothesis that G-VIII and G-IX originated from a common ancestor, as speculated earlier. Further, VP1 region-based phylogenetic analyses revealed the re-emergence of G-VIII after a gap of 3 years. One isolate of G-VIII collected during 2023 revealed a codon insertion in the G-H loop of VP1. The vaccine matching studies support the suitability of the currently used Indian vaccine strain IND63/1972 to contain outbreaks due to viruses belonging to G-IX.
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Affiliation(s)
- Manoranjan Rout
- International Centre for Foot and Mouth Disease, ICAR-National Institute on Foot and Mouth Disease, Bhubaneswar, India
| | - Shyam Singh Dahiya
- International Centre for Foot and Mouth Disease, ICAR-National Institute on Foot and Mouth Disease, Bhubaneswar, India
| | - Saravanan Subramaniam
- International Centre for Foot and Mouth Disease, ICAR-National Institute on Foot and Mouth Disease, Bhubaneswar, India
| | - Ramakant Acharya
- International Centre for Foot and Mouth Disease, ICAR-National Institute on Foot and Mouth Disease, Bhubaneswar, India
| | - Reshama Samanta
- International Centre for Foot and Mouth Disease, ICAR-National Institute on Foot and Mouth Disease, Bhubaneswar, India
| | - Jitendra Kumar Biswal
- International Centre for Foot and Mouth Disease, ICAR-National Institute on Foot and Mouth Disease, Bhubaneswar, India
| | - Jajati Keshari Mohapatra
- International Centre for Foot and Mouth Disease, ICAR-National Institute on Foot and Mouth Disease, Bhubaneswar, India
| | - Rabindra Prasad Singh
- International Centre for Foot and Mouth Disease, ICAR-National Institute on Foot and Mouth Disease, Bhubaneswar, India
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2
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Kojom Foko LP, Hawadak J, Eboumbou Moukoko CE, Das A, Singh V. Genetic analysis of the circumsporozoite gene in Plasmodium falciparum isolates from Cameroon: Implications for efficacy and deployment of RTS,S/AS01 vaccine. Gene 2024; 927:148744. [PMID: 38964492 DOI: 10.1016/j.gene.2024.148744] [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: 03/12/2024] [Revised: 06/26/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Current understanding of genetic polymorphisms and natural selection in Plasmodium falciparum circumsporozoite (PfCSP), the leading malaria vaccine, is crucial for the development of next-generation vaccines, and such data is lacking in Africa. Blood samples were collected among Plasmodium-infected individuals living in four Cameroonian areas (Douala, Maroua, Mayo-Oulo, Pette). DNA samples were amplified using nested PCR protocols, sequenced, and BLASTed. Single nucleotide polymorphisms (SNPs) were analysed in each PfCSP region, and their impact on PfCSP function/structure was predicted in silico. The N-terminal region showed a limited polymorphism with four haplotypes, and three novel SNPs (N68Y, R87W, K93E) were found. Thirty-five haplotypes were identified in the central region, with several variants (e.g., NVNP and KANP). The C-terminal region was also highly diverse, with 25 haplotypes and eight novel SNPs (N290D, N308I, S312G, K317A, V344I, D356E, E357L, D359Y). Most polymorphic codon sites were mainly observed in the Th2R subregion in isolates from Douala and Pette. The codon site 321 was under episodic positive selection. One novel (E357L) and three known (K322I, G349D, D359Y) SNPs show an impact on function/structure. This study showed extensive genetic diversity with geographical patterns and evidence of the selection of Cameroonian PfCSP central and C-terminal regions.
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Affiliation(s)
| | - Joseph Hawadak
- Parasite & Host Biology Group, National Institute of Malaria Research, New-Delhi, India
| | - Carole Else Eboumbou Moukoko
- Department of Biological Sciences, Faculty of Medicine and Pharmaceutical Sciences, The University of Douala, Cameroon; Malaria Research Unit, Centre Pasteur Cameroon, Yaoundé, Cameroon; Laboratory of Parasitology, Mycology and Virology, Postgraduate Training Unit for Health Sciences, Postgraduate School for Pure and Applied Sciences, The University of Douala, Cameroon
| | - Aparup Das
- Division of Vector Borne Diseases, National Institute of Research in Tribal Health, Madhya Pradesh, India
| | - Vineeta Singh
- Parasite & Host Biology Group, National Institute of Malaria Research, New-Delhi, India; Academy of Scientific and Innovative Research, Ghaziabad, India.
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3
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Fandilolu P, Kumar C, Palia D, Idicula-Thomas S. Investigating role of positively selected genes and mutation sites of ERG11 in drug resistance of Candida albicans. Arch Microbiol 2024; 206:437. [PMID: 39422772 DOI: 10.1007/s00203-024-04159-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Accepted: 10/04/2024] [Indexed: 10/19/2024]
Abstract
The steep increase in acquired drug resistance in Candida isolates has posed a great challenge in the clinical management of candidiasis globally. Information of genes and codon sites that are positively selected during evolution can provide insights into the mechanisms driving antifungal resistance in Candida. This study aimed to create a manually curated list of genes of Candida spp. reported to be associated with antifungal resistance in literature, and further investigate the structure-function implications of positively selected genes and mutation sites. Sequence analysis of antifungal drug resistance associated gene sequences from various species and strains of Candida revealed that ERG11 and MRR1 of C. albicans were positively selected during evolution. Four sites in ERG11 and two sites in MRR1 of C. albicans were positively selected and associated with drug resistance. These four sites (132, 405, 450, and 464) of ERG11 are predictive markers for azole resistance and have evolved over time. A well-characterized crystal structure of sterol-14-α-demethylase (CYP51) encoded by ERG11 is available in PDB. Therefore, the stability of CYP51 in complex with fluconazole was evaluated using MD simulations and molecular docking studies for two mutations (Y132F and Y132H) reported to be associated with azole resistance in literature. These mutations induced high flexibility in functional motifs of CYP51. It was also observed that residues such as I304, G308, and I379 of CYP51 play a critical role in fluconazole binding affinity. The insights gained from this study can further guide drug design strategies addressing antimicrobial resistance.
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Affiliation(s)
- Prayagraj Fandilolu
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive and Child Health, Mumbai, Maharashtra, 400012, India
| | - Chandan Kumar
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive and Child Health, Mumbai, Maharashtra, 400012, India
| | - Dushyant Palia
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive and Child Health, Mumbai, Maharashtra, 400012, India
| | - Susan Idicula-Thomas
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive and Child Health, Mumbai, Maharashtra, 400012, India.
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4
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Tu F, Qiao Y, Zhao W, Wu T. Comparative selective pressure analysis on mitochondrial protein-coding genes in flying squirrels (Pteromyini) and tree squirrels (Sciurini). Mitochondrial DNA A DNA Mapp Seq Anal 2024:1-9. [PMID: 39417543 DOI: 10.1080/24701394.2024.2416179] [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: 02/29/2024] [Accepted: 10/07/2024] [Indexed: 10/19/2024]
Abstract
Different animal groups with varying locomotion modes may have unique energy requirements. Mitochondria produce adenosine triphosphate (ATP) and reactive oxygen species via oxidative phosphorylation to support organisms energy requirements. The tribes Pteromyini (flying squirrels) and Sciurini (tree squirrels), two closely related taxa within the family Sciuridae, exhibit distinct locomotion modes, energy requirements, and likely face different selective pressures on mitochondrial protein-coding genes (PCGs). We analysed 13 mitochondrial genome sequences from species belonging to the tribe Pteromyini and 117 from species belonging to the tribe Sciurini. Phylogenetic analysis revealed Pteromyini and Sciurini formed a sister relationship within the family Sciuridae. Among the 13 PCGs, ATP8 exhibited the highest dN/dS values, while COX1 showed the lowest. The background selection ratio (ω2) values for six genes (ND1, ND2, ND4, ATP6, ND5, and COX3) in Pteromyini were lower than the foreground selection ratio (ω0) values observed in Sciurini. A RELAX analysis revealed that CYTB, ND4, ATP6, and COX3 genes experienced intensified in selection strength. BUSTED analysis identified stronger signatures of diversifying selection in CYTB and ATP6, highlighting amino acid changes. MEME identified episodic diversifying selection at specific sites among eight PCGs. These findings revealed distinct selective pressures on PCGs in flying and tree squirrels.
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Affiliation(s)
- Feiyun Tu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Yaqin Qiao
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Wenjing Zhao
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Tong Wu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
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5
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Zehr JD, Kosakovsky Pond SL, Shank SD, McQueary H, Grenier JK, Whittaker GR, Stanhope MJ, Goodman LB. Positive selection, genetic recombination, and intra-host evolution in novel equine coronavirus genomes and other members of the Embecovirus subgenus. Microbiol Spectr 2024:e0086724. [PMID: 39373506 DOI: 10.1128/spectrum.00867-24] [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: 05/09/2024] [Accepted: 08/24/2024] [Indexed: 10/08/2024] Open
Abstract
There are several examples of coronaviruses in the Betacoronavirus subgenus Embecovirus that have jumped from an animal to the human host. Studying how evolutionary factors shape coronaviruses in non-human hosts may provide insight into the coronavirus host-switching potential. Equids, such as horses and donkeys, are susceptible to equine coronaviruses (ECoVs). With increased testing prevalence, several ECoV genome sequences have become available for molecular evolutionary analyses, especially those from the United States of America (USA). To date, no analyses have been performed to characterize evolution within coding regions of the ECoV genome. Here, we obtain and describe four new ECoV genome sequences from infected equines from across the USA presenting clinical symptoms of ECoV, and infer ECoV-specific and Embecovirus-wide patterns of molecular evolution. Within two of the four data sets analyzed, we find evidence of intra-host evolution within the nucleocapsid (N) gene, suggestive of quasispecies development. We also identify 12 putative genetic recombination events within the ECoV genome, 11 of which fall in ORF1ab. Finally, we infer and compare sites subject to positive selection on the ancestral branch of each major Embecovirus member clade. Specifically, for the two currently identified human coronavirus (HCoV) embecoviruses that have spilled from animals to humans (HCoV-OC43 and HCoV-HKU1), we find that there are 42 and 2 such sites, respectively, perhaps reflective of the more complex ancestral evolutionary history of HCoV-OC43, which involves several different animal hosts.IMPORTANCEThe Betacoronavirus subgenus Embecovirus contains coronaviruses that not only pose a health threat to animals and humans, but also have jumped from animal to human host. Equids, such as horses and donkeys are susceptible to equine coronavirus (ECoV) infections. No studies have systematically examined evolutionary patterns within ECoV genomes. Our study addresses this gap and provides insight into intra-host ECoV evolution from infected horses. Further, we identify and report natural selection pattern differences between two embecoviruses that have jumped from animals to humans [human coronavirus OC43 and HKU1 (HCoV-OC43 and HCoV-HKU1, respectively)], and hypothesize that the differences observed may be due to the different animal host(s) that each virus circulated in prior to its jump into humans. Finally, we contribute four novel, high-quality ECoV genomes to the scientific community.
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Affiliation(s)
- Jordan D Zehr
- Department of Biology, Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, USA
- James A. Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Sergei L Kosakovsky Pond
- Department of Biology, Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Stephen D Shank
- Department of Biology, Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Holly McQueary
- James A. Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Jennifer K Grenier
- Cornell Institute of Biotechnology, Transcriptional Regulation and Expression Facility, Ithaca, New York, USA
| | - Gary R Whittaker
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Michael J Stanhope
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Laura B Goodman
- James A. Baker Institute for Animal Health, 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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Kwak JS, León-Tapia MÁ, Diblasi C, Manousi D, Grønvold L, Sandvik GK, Saitou M. Functional and regulatory diversification of Period genes responsible for circadian rhythm in vertebrates. G3 (BETHESDA, MD.) 2024; 14:jkae162. [PMID: 39028850 PMCID: PMC11457068 DOI: 10.1093/g3journal/jkae162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/08/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024]
Abstract
The Period genes (Per) play essential roles in modulating the molecular circadian clock timing in a broad range of species, which regulates the physiological and cellular rhythms through the transcription-translation feedback loop. While the Period gene paralogs are widely observed among vertebrates, the evolutionary history and the functional diversification of Per genes across vertebrates are not well known. In this study, we comprehensively investigated the evolution of Per genes at the copy number and sequence levels, including de novo binding motif discovery by comparative genomics. We also determined the lineage-specific transcriptome landscape across tissues and developmental stages and phenotypic effects in public RNA-seq data sets of model species. We observed multiple lineage-specific gain and loss events Per genes, though no simple association was observed between ecological factors and Per gene numbers in each species. Among salmonid fish species, the per3 gene has been lost in the majority, whereas those retaining the per3 gene exhibit not a signature of relaxed selective constraint but rather a signature of intensified selection. We also determined the signature of adaptive diversification of the CRY-binding region in Per1 and Per3, which modulates the circadian rhythm. We also discovered putative regulatory sequences, which are lineage-specific, suggesting that these cis-regulatory elements may have evolved rapidly and divergently across different lineages. Collectively, our findings revealed the evolution of Per genes and their fine-tuned contribution to the plastic and precise regulation of circadian rhythms in various vertebrate taxa.
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Affiliation(s)
- Jun Soung Kwak
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - M Ángel León-Tapia
- Colección Nacional de Mamíferos, Pabellón Nacional de la Biodiversidad, Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Mexico City 04510, Mexico
| | - Celian Diblasi
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Domniki Manousi
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Lars Grønvold
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Guro Katrine Sandvik
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Marie Saitou
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, 1433 Ås, Norway
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7
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Limaye S, Lohar T, Dube H, Ramasamy S, Kale M, Kulkarni-Kale U, Kuchipudi SV. Rapid evolution leads to extensive genetic diversification of cattle flu Influenza D virus. Commun Biol 2024; 7:1276. [PMID: 39375524 PMCID: PMC11458855 DOI: 10.1038/s42003-024-06954-4] [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: 03/15/2024] [Accepted: 09/24/2024] [Indexed: 10/09/2024] Open
Abstract
Influenza D virus (IDV), the cattle flu virus, is a novel multi-host RNA virus, circulating silently worldwide, with widespread seropositivity among US cattle, reaching up to 80% in some areas raising a potential threat of cattle-to-human transmission. Currently, five genetic lineages of IDV have been described, but their evolutionary dynamics have not been studied. Although IDV was first identified in 2011, our comprehensive analysis of all known IDV genomes suggests that the earliest ancestors of IDV likely to have evolved towards the end of the 20th century and D/OK lineage appears to have emerged in 2005. We confirmed a significantly higher substitution rate in IDV than in Influenza C virus, which is consistent with their global distribution and multi-host tropism. We identified multiple sub-populations within the D/OK lineage, highlighting extensive diversification and dissemination. Other findings are evidence for potential reassortment among IDV strains in the USA and transboundary circulation of IDV in Europe with introductions into Danish cattle, some of which potentially originated from France. IDV, an emerging virus with a higher rate of evolution and uncontrolled circulation, could facilitate its adaptation to humans. Our findings underscore the importance of targeted surveillance for IDV in humans and at-risk animal populations.
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Affiliation(s)
- Sanket Limaye
- Bioinformatics Centre, Savitribai Phule Pune University (Formerly University of Pune), Pune, 411007, India
| | - Tejas Lohar
- Department of Statistics, Savitribai Phule Pune University (Formerly University of Pune), Pune, 411007, India
| | - Harita Dube
- Department of Statistics, Savitribai Phule Pune University (Formerly University of Pune), Pune, 411007, India
| | - Santhamani Ramasamy
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, 15261, USA
| | - Mohan Kale
- Department of Statistics, Savitribai Phule Pune University (Formerly University of Pune), Pune, 411007, India
| | - Urmila Kulkarni-Kale
- Bioinformatics Centre, Savitribai Phule Pune University (Formerly University of Pune), Pune, 411007, India.
- Department of Natural Sciences and Environmental Health, University of South Eastern Norway, Bo, Norway.
- CIS-Citadel Precision Medicine LLC, Hyderabad, India.
| | - Suresh V Kuchipudi
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, 15261, USA.
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
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8
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Macedo MA, Melgarejo TA, Vasquez-Mayorga M, Cespedes M, Rojas MR, Turini TA, Batuman O, Wintermantel WM, Gilbertson RL. Squash vein yellowing virus from California emerged in the Middle East via intragenic and intergeneric recombination events in the hypervariable potyvirus P1 and ipomovirus P1a genes. J Gen Virol 2024; 105. [PMID: 39418084 DOI: 10.1099/jgv.0.002033] [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: 10/19/2024] Open
Abstract
We present the complete sequence of the genomic RNA of an isolate of squash vein yellowing virus (Ipomovirus cucurbitavenaflavi) from California (SqVYV-CA) and show it is a recombinant virus with a highly divergent 5' UTR and proximal P1a gene. The evolution of SqVYV-CA involved an intrageneric event between unknown potyviruses, related to isolates of papaya ringspot virus (Potyvirus papayanuli) from the Old World, and an intergeneric event between this recombinant potyvirus (minor parent) and an isolate of SqVYV from Israel (SqVYV-IL) (major parent). These events occurred in mixed infections and in the potyvirus P1 and ipomovirus P1a recombination hotspots and resulted in SqVYV-CA having a potyvirus 5' UTR and chimeric P1-P1a gene/protein and the remainder of the genome from SqVYV-IL. The SqVYV-CA chimeric P1-P1a gene is under positive selection, and the protein is intrinsically disordered and may localize to the nucleus via nuclear localization signals in the P1 part. The C-terminal SqVYV-IL P1a part also diverged but retained the conserved serine protease motif. Furthermore, substantial divergence in SqVYV isolates from the Middle East was associated with genetic drift and a long evolutionary history in this region. The finding that the host range and symptomatology in cucurbits of SqVYV-CA is similar to those of SqVYV from Florida and SqVYV-IL, indicated that the recombinant part of the genome had no obvious effect on the virus-host interaction. A divergent part of the P1 sequence of the SqVYV-CA P1-P1a gene was used to develop a primer pair and RT-PCR test for specific detection of SqVYV-CA. This test was used to detect spread of SqVYV-CA to a new production area of California in 2021 and 2022. Together, these results demonstrate (i) a high level of genetic diversity exists among isolates of SqVYV and involved intra- and intergeneric recombination and genetic drift (mutation), (ii) evidence that SqVYV originated in the Middle East and that there were independent introductions into the New World and (iii) the remarkable genetic flexibility of the 5' proximal genes of these viruses.
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Affiliation(s)
- M A Macedo
- Federal Institution of Brasília, Brasília, Federal District, Brazil
| | - T A Melgarejo
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - M Vasquez-Mayorga
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - M Cespedes
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - M R Rojas
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - T A Turini
- University of California Agriculture and Natural Resources, Fresno, CA, USA
| | - O Batuman
- Department of Plant Pathology, Southwest Florida Research and Education Center, University of Florida, Immokalee, Florida, USA
| | - W M Wintermantel
- United States Department of Agriculture, Agricultural Research Service, Salinas, CA, USA
| | - R L Gilbertson
- Department of Plant Pathology, University of California, Davis, CA, USA
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9
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Hosseini SM, Ullah F, Ahmad MZ, Pasandideh M, Liang A, Hua G, Yang L. Adaptive evolution and functional significance of the PPARGC1A gene across diverse animal species. Ecol Evol 2024; 14:e11238. [PMID: 39364034 PMCID: PMC11449627 DOI: 10.1002/ece3.11238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 10/05/2024] Open
Abstract
Codon-based analyses of the PPARGC1A gene across 38 vertebrate species were deployed to elucidate patterns of evolutionary change. Employing maximum likelihood assessments through MEGA, we scrutinized 447 codon positions addressing the entire coding region, excluding positions mired by gaps or missing data. Distinct codons manifested variance in selection pressures, particularly codons 4, 11, 66, and 123, which exhibited positive dN-dS values suggestive of positive selection. Codon 137 displayed the most pronounced dN-dS value, signifying intensified selective advantage. Meanwhile, codons 30 and 90 portrayed near-neutral scores, indicative of purifying selection. Complementary computational methods (IFEL, REL, FUBAR, and SLAC) confirmed positive selection at specific codon sites, with varying degrees of corroboration. The integration of mixed-effect modeling (MEME) identified episodic diversifying selection, pinpointing codons that underwent selection episodes in certain lineages. Refined codon model selection lent insight into substitution rates, revealing nuanced degrees of evolutionary conservation among different codons. Supporting these genetic insights, the phylogenetic analysis highlighted relationships among the PPARGC1A sequences and domain analysis confirmed conserved features across species, while protein-protein interaction networks suggested a complex web of functional interdependencies. These findings advance our understanding of the PPARGC1A gene's evolutionary trajectory and underscore the gene's potential adaptive significance within diverse vertebrate lineages.
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Affiliation(s)
- Seyed Mahdi Hosseini
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR)College of Animal Science and Technology, Huazhong Agricultural UniversityWuhanChina
| | - Farman Ullah
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR)College of Animal Science and Technology, Huazhong Agricultural UniversityWuhanChina
| | - Muhammad Zulfiqar Ahmad
- Department of Plant Breeding and Genetics, Faculty of AgricultureGomal UniversityDera Ismail KhanPakistan
| | - Majid Pasandideh
- Department of Animal Science, Faculty of AgricultureShahrekord UniversityShahrekordIran
| | - Aixin Liang
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR)College of Animal Science and Technology, Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Guohua Hua
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR)College of Animal Science and Technology, Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Liguo Yang
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR)College of Animal Science and Technology, Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
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10
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Telizhenko V, Kosiol C, McGowen MR, Gol'din P. Relaxed selection in evolution of genes regulating limb development gives clue to variation in forelimb morphology of cetaceans and other mammals. Proc Biol Sci 2024; 291:20241106. [PMID: 39378996 DOI: 10.1098/rspb.2024.1106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/29/2024] [Accepted: 09/02/2024] [Indexed: 10/10/2024] Open
Abstract
Cetaceans have evolved unique limb structures, such as flippers, due to genetic changes during their transition to aquatic life. However, the full understanding of the genetic and evolutionary mechanisms behind these changes is still developing. By examining 25 limb-related protein-coding genes across various mammalian species, we compared genetic changes between aquatic mammals, like whales, and other mammals with unique limb structures such as bats, rodents and elephants. Our findings revealed significant modifications in limb-related genes, including variations in the Hox, GDF5 and Evx genes. Notably, a relaxed selection in several key genes was observed, suggesting a lifting of developmental constraints, which might have facilitated the emergence of morphological innovations in cetacean limb morphology. We also uncovered non-synonymous changes, insertions and deletions in these genes, particularly in the polyalanine tract of HOXD13, which are distinctive to cetaceans or convergent with other aquatic mammals. These genetic variations correlated with the diverse and specialized limb structures observed in cetaceans, indicating a complex interplay of relaxed selection and specific mutations in mammalian limb evolution.
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Affiliation(s)
| | - Carolin Kosiol
- University of St Andrews , St Andrews, Fife KY16 9TF, UK
| | - Michael R McGowen
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History , Washington, DC 20560, USA
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11
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Yao Z, Ramachandran S, Huang S, Kim E, Jami-Alahmadi Y, Kaushal P, Bouhaddou M, Wohlschlegel JA, Li MM. Interaction of chikungunya virus glycoproteins with macrophage factors controls virion production. EMBO J 2024; 43:4625-4655. [PMID: 39261662 PMCID: PMC11480453 DOI: 10.1038/s44318-024-00193-3] [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: 09/22/2023] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 09/13/2024] Open
Abstract
Despite their role as innate sentinels, macrophages can serve as cellular reservoirs of chikungunya virus (CHIKV), a highly-pathogenic arthropod-borne alphavirus that has caused large outbreaks among human populations. Here, with the use of viral chimeras and evolutionary selection analysis, we define CHIKV glycoproteins E1 and E2 as critical for virion production in THP-1 derived human macrophages. Through proteomic analysis and functional validation, we further identify signal peptidase complex subunit 3 (SPCS3) and eukaryotic translation initiation factor 3 subunit K (eIF3k) as E1-binding host proteins with anti-CHIKV activities. We find that E1 residue V220, which has undergone positive selection, is indispensable for CHIKV production in macrophages, as its mutation attenuates E1 interaction with the host restriction factors SPCS3 and eIF3k. Finally, we show that the antiviral activity of eIF3k is translation-independent, and that CHIKV infection promotes eIF3k translocation from the nucleus to the cytoplasm, where it associates with SPCS3. These functions of CHIKV glycoproteins late in the viral life cycle provide a new example of an intracellular evolutionary arms race with host restriction factors, as well as potential targets for therapeutic intervention.
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Affiliation(s)
- Zhenlan Yao
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sangeetha Ramachandran
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Serina Huang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Erin Kim
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Prashant Kaushal
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Mehdi Bouhaddou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Melody Mh Li
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA.
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12
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Ramirez-Medina E, Velazquez-Salinas L, Valladares A, Meyers A, Burton L, Silva E, Clark J, Borca MV, Gladue DP. Evaluation of the Deletion of African Swine Fever Virus E111R Gene from the Georgia Isolate in Virus Replication and Virulence in Domestic Pigs. Viruses 2024; 16:1502. [PMID: 39339977 PMCID: PMC11437470 DOI: 10.3390/v16091502] [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: 08/17/2024] [Revised: 09/11/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024] Open
Abstract
African swine fever virus (ASFV) is the causative agent of an often lethal disease in domestic pigs, African swine fever (ASF). ASF is currently a pandemic disease challenging pig production in Eurasia. While the ASFV genome encodes for over 160 proteins, the function of most of them are still not characterized. Among those ASF genes with unknown functions is the E111R gene. It has been recently reported that the deletion of the E111R gene from the genome of the virulent Chinese field isolate SY18 strain produced a reduction of virus virulence when pigs were inoculated at relatively low doses. Conversely, we report here that deletion of the ASFV gene E111R in the Georgia 2010 isolate does not alter the virulence of the parental virus in experimentally inoculated pigs. A recombinant virus lacking the E111R gene, ASFV-G-∆E111R was intramuscularly (IM) inoculated in domestic pigs at a dose of 102 HAD50 of ASFV-G-∆E111R and compared with animals that received a similar dose of virulent ASFV-G. Both, animals inoculated with either the recombinant ASFV-G-∆E111R or the parental virus developed a fatal form of the disease and were euthanized around the 6th-7th day post-inoculation (dpi).
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Affiliation(s)
- Elizabeth Ramirez-Medina
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center (PIADC), P.O. Box 848, Greenport, NY 11944, USA; (L.V.-S.); (A.V.); (A.M.); (L.B.); (E.S.); (J.C.)
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA
| | - Lauro Velazquez-Salinas
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center (PIADC), P.O. Box 848, Greenport, NY 11944, USA; (L.V.-S.); (A.V.); (A.M.); (L.B.); (E.S.); (J.C.)
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA
| | - Alyssa Valladares
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center (PIADC), P.O. Box 848, Greenport, NY 11944, USA; (L.V.-S.); (A.V.); (A.M.); (L.B.); (E.S.); (J.C.)
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA
| | - Amanda Meyers
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center (PIADC), P.O. Box 848, Greenport, NY 11944, USA; (L.V.-S.); (A.V.); (A.M.); (L.B.); (E.S.); (J.C.)
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA
| | - Leeanna Burton
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center (PIADC), P.O. Box 848, Greenport, NY 11944, USA; (L.V.-S.); (A.V.); (A.M.); (L.B.); (E.S.); (J.C.)
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA
| | - Ediane Silva
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center (PIADC), P.O. Box 848, Greenport, NY 11944, USA; (L.V.-S.); (A.V.); (A.M.); (L.B.); (E.S.); (J.C.)
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA
| | - Jason Clark
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center (PIADC), P.O. Box 848, Greenport, NY 11944, USA; (L.V.-S.); (A.V.); (A.M.); (L.B.); (E.S.); (J.C.)
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA
| | - Manuel V. Borca
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center (PIADC), P.O. Box 848, Greenport, NY 11944, USA; (L.V.-S.); (A.V.); (A.M.); (L.B.); (E.S.); (J.C.)
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA
| | - Douglas P. Gladue
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center (PIADC), P.O. Box 848, Greenport, NY 11944, USA; (L.V.-S.); (A.V.); (A.M.); (L.B.); (E.S.); (J.C.)
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13
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Domanska-Blicharz K, Lisowska A, Opolska J, Ruszkowski JJ, Gogulski M, Pomorska-Mól M. Whole genome characteristics of hedgehog coronaviruses from Poland and analysis of the evolution of the Spike protein for its interspecies transmission potential. BMC Vet Res 2024; 20:424. [PMID: 39304831 PMCID: PMC11415979 DOI: 10.1186/s12917-024-04277-4] [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: 05/21/2024] [Accepted: 09/11/2024] [Indexed: 09/22/2024] Open
Abstract
BACKGROUND The hedgehogs have been recently identified as possible reservoir of Middle East respiratory syndrome coronavirus like (MERS-CoV-like). These viruses were classified as a distinct Betacoronavirus erinacei (BCoV-Eri) species within the MerBCoV-Eriirus subgenus. As coronaviruses are known for their ability to jump between different hosts, including humans, this can pose a particular threat to people in direct contact with hedgehogs, such as those working at animal asylums. Our previous studies have shown the presence of BCoV-Eri strains in animals collected in the wildlife rehabilitation centre. This study aimed to investigate the presence of CoV in subsequent hedgehogs collected from the urban area of Poland and their molecular characteristics. RESULTS Monitoring for the presence of coronavirus infection in hedgehogs revealed five positive individuals. The presence of BCoV-Eri was found in a total of 20% of animals tested. Our analyses revealed no correlation between CoVs positivity and animal health conditions but a higher probability of such infection in juveniles and females. The whole genome of two Polish Hedgehog coronavirus 1 strains were sequenced and compared with available counterparts from European and Asian countries. Phylogenetic analysis showed that both CoV strains formed common cluster with other similar MerBCoV-Eriirus, but they were also found to be genetically variable and most changes in the S protein were identified. Our analysis revealed that some S protein sites of the Hedgehog coronavirus 1 strains evolved under positive selection pressure and of five such sites, three are in the S1 region while the other two in the S2 region of the Spike. CONCLUSIONS BCoV-Eri is to some extent prevalent in wildlife asylums in Poland. Given that the S protein of BCoVs-Eri is highly variable and that some sites of this protein evolve under positive selection pressure, these strains could potentially acquire a favourable feature for cross-species transmission. Consequently, the threat to humans working in such asylums is particularly high. Adequate biosecurity safeguards, but also human awareness of such risks, are therefore essential.
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Affiliation(s)
- Katarzyna Domanska-Blicharz
- Department of Poultry Diseases, National Veterinary Research Institute, al. Partyzantów 57, Puławy, 24-100, Poland.
| | - Anna Lisowska
- Department of Poultry Diseases, National Veterinary Research Institute, al. Partyzantów 57, Puławy, 24-100, Poland
| | - Justyna Opolska
- Department of Poultry Diseases, National Veterinary Research Institute, al. Partyzantów 57, Puławy, 24-100, Poland
| | - Jakub J Ruszkowski
- Department of Animal Anatomy, University of Life Sciences in Poznań, ul. Wojska Polskiego 71C, Poznań, 60-625, Poland
- University Centre for Veterinary Medicine, University of Life Sciences in Poznań, Szydłowska 43, Poznań, 60-656, Poland
| | - Maciej Gogulski
- Department of Animal Anatomy, University of Life Sciences in Poznań, ul. Wojska Polskiego 71C, Poznań, 60-625, Poland
- University Centre for Veterinary Medicine, University of Life Sciences in Poznań, Szydłowska 43, Poznań, 60-656, Poland
| | - Małgorzata Pomorska-Mól
- Department of Preclinical Sciences and Infectious Diseases, University of Life Sciences in Poznań, ul. Wołyńska 35, Poznań, 60-637, Poland
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14
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Grzech D, Smit SJ, Alam RM, Boccia M, Nakamura Y, Hong B, Barbole R, Heinicke S, Kunert M, Seibt W, Grabe V, Caputi L, Lichman BR, O'Connor SE, Aharoni A, Sonawane PD. Incorporation of nitrogen in antinutritional Solanum alkaloid biosynthesis. Nat Chem Biol 2024:10.1038/s41589-024-01735-w. [PMID: 39271954 DOI: 10.1038/s41589-024-01735-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 08/19/2024] [Indexed: 09/15/2024]
Abstract
Steroidal glycoalkaloids (SGAs) are specialized metabolites produced by hundreds of Solanum species including food crops, such as tomato, potato and eggplant. Unlike true alkaloids, nitrogen is introduced at a late stage of SGA biosynthesis through an unknown transamination reaction. Here, we reveal the mechanism by which GLYCOALKALOID METABOLISM12 (GAME12) directs the biosynthesis of nitrogen-containing steroidal alkaloid aglycone in Solanum. We report that GAME12, a neofunctionalized γ-aminobutyric acid (GABA) transaminase, undergoes changes in both active site specificity and subcellular localization to switch from its renown and generic activity in core metabolism to function in a specialized metabolic pathway. Moreover, overexpression of GAME12 alone in engineered S. nigrum leaves is sufficient for de novo production of nitrogen-containing SGAs. Our results highlight how hijacking a core metabolism GABA shunt enzyme is crucial in numerous Solanum species for incorporating a nitrogen to a steroidal-specialized metabolite backbone and form defensive alkaloids.
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Affiliation(s)
- Dagny Grzech
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Samuel J Smit
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Ryan M Alam
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Marianna Boccia
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Yoko Nakamura
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Benke Hong
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Ranjit Barbole
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sarah Heinicke
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Maritta Kunert
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Wibke Seibt
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Veit Grabe
- Microscopic Imaging Service Group, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Lorenzo Caputi
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany.
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
| | - Prashant D Sonawane
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany.
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15
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Pyke AT, Wilson DJ, Michie A, Mackenzie JS, Imrie A, Cameron J, Doggett SL, Haniotis J, Herrero LJ, Caly L, Lynch SE, Mee PT, Madzokere ET, Ramirez AL, Paramitha D, Hobson-Peters J, Smith DW, Weir R, Sullivan M, Druce J, Melville L, Robson J, Gibb R, van den Hurk AF, Duchene S. Independent repeated mutations within the alphaviruses Ross River virus and Barmah Forest virus indicates convergent evolution and past positive selection in ancestral populations despite ongoing purifying selection. Virus Evol 2024; 10:veae080. [PMID: 39411152 PMCID: PMC11477980 DOI: 10.1093/ve/veae080] [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: 05/30/2024] [Revised: 07/25/2024] [Accepted: 09/12/2024] [Indexed: 10/19/2024] Open
Abstract
Ross River virus (RRV) and Barmah Forest virus (BFV) are arthritogenic arthropod-borne viruses (arboviruses) that exhibit generalist host associations and share distributions in Australia and Papua New Guinea (PNG). Using stochastic mapping and discrete-trait phylogenetic analyses, we profiled the independent evolution of RRV and BFV signature mutations. Analysis of 186 RRV and 88 BFV genomes demonstrated their viral evolution trajectories have involved repeated selection of mutations, particularly in the nonstructural protein 1 (nsP1) and envelope 3 (E3) genes suggesting convergent evolution. Convergent mutations in the nsP1 genes of RRV (residues 248 and 441) and BFV (residues 297 and 447) may be involved with catalytic enzyme mechanisms and host membrane interactions during viral RNA replication and capping. Convergent E3 mutations (RRV site 59 and BFV site 57) may be associated with enzymatic furin activity and cleavage of E3 from protein precursors assisting viral maturation and infectivity. Given their requirement to replicate in disparate insect and vertebrate hosts, convergent evolution in RRV and BFV may represent a dynamic link between their requirement to selectively 'fine-tune' intracellular host interactions and viral replicative enzymatic processes. Despite evidence of evolutionary convergence, selection pressure analyses did not reveal any RRV or BFV amino acid sites under strong positive selection and only weak positive selection for nonstructural protein sites. These findings may indicate that their alphavirus ancestors were subject to positive selection events which predisposed ongoing pervasive convergent evolution, and this largely supports continued purifying selection in RRV and BFV populations during their replication in mosquito and vertebrate hosts.
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Affiliation(s)
- Alyssa T Pyke
- Public Health Virology Laboratory, Public and Environmental Health Reference Laboratories, Department of Health, Queensland Government, P.O. Box 594, Archerfield, Coopers Plains, Queensland, Australia
| | - Daniel J Wilson
- Big Data Institute, Oxford Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford OX3 7LF, United Kingdom
- Department for Continuing Education, University of Oxford, 1 Wellington Square, Oxford OX1 2JA, United Kingdom
| | - Alice Michie
- School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Perth, Western Australia 6009, Australia
| | - John S Mackenzie
- Faculty of Health Sciences, Curtin University, G.P.O. Box U1987, Bentley, Western Australia 6845, Australia
| | - Allison Imrie
- School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Perth, Western Australia 6009, Australia
| | - Jane Cameron
- Public Health Virology Laboratory, Public and Environmental Health Reference Laboratories, Department of Health, Queensland Government, P.O. Box 594, Archerfield, Coopers Plains, Queensland, Australia
| | - Stephen L Doggett
- NSW Health Pathology, Westmead Hospital, 166-174 Hawkesbury Road Westmead, Sydney, New South Wales 2145, Australia
| | - John Haniotis
- NSW Health Pathology, Westmead Hospital, 166-174 Hawkesbury Road Westmead, Sydney, New South Wales 2145, Australia
| | - Lara J Herrero
- Gold Coast Campus, Institute for Glycomics, Griffith University, 1 Parklands Drive, Southport, Queensland 4215, Australia
| | - Leon Caly
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
| | - Stacey E Lynch
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia
| | - Peter T Mee
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia
| | - Eugene T Madzokere
- Gold Coast Campus, Institute for Glycomics, Griffith University, 1 Parklands Drive, Southport, Queensland 4215, Australia
| | - Ana L Ramirez
- College of Public Health, Medical and Veterinary Sciences, James Cook University, P.O. Box 6811, Cairns, Queensland 4870, Australia
- Australian Institute of Tropical Health and Medicine, James Cook University, P.O. Box 6811, Cairns, Queensland 4870, Australia
- The Jackson Laboratory, 10 Discovery Drive Connecticut, Farmington, CT 06032, United States of America
| | - Devina Paramitha
- School of Chemistry and Molecular Biosciences, The University of Queensland, Bdg 68 Cooper Road, St. Lucia, Queensland 4072, Australia
| | - Jody Hobson-Peters
- School of Chemistry and Molecular Biosciences, The University of Queensland, Bdg 68 Cooper Road, St. Lucia, Queensland 4072, Australia
| | - David W Smith
- NSW Health Pathology, Westmead Hospital, 166-174 Hawkesbury Road Westmead, Sydney, New South Wales 2145, Australia
- School of Medicine, University of Western Australia, 35 Stirling Highway, Perth, Western Australia 6009, Australia
| | - Richard Weir
- Department of Primary Industries and Fisheries, Berrimah Veterinary Laboratory, P.O. Box 3000, Darwin, Northern Territory 0801, Australia
| | - Mitchell Sullivan
- Public and Environmental Health Reference Laboratories, Department of Health, Queensland Government, P.O Box 594 Archerfield, Coopers Plains, Queensland 4108, Australia
| | - Julian Druce
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
| | - Lorna Melville
- Department of Primary Industries and Fisheries, Berrimah Veterinary Laboratory, P.O. Box 3000, Darwin, Northern Territory 0801, Australia
| | - Jennifer Robson
- Department of Microbiology and Molecular Pathology, Sullivan Nicolaides Pathology, P.O. Box 2014 Fortitude Valley, Brisbane, Queensland 4006, Australia
| | - Robert Gibb
- Serology, Pathology Queensland Central Laboratory, Royal Brisbane and Women’s Hospital, 40 Butterfield Street Herston, Brisbane, Queensland 4029, Australia
| | - Andrew F van den Hurk
- Public Health Virology Laboratory, Public and Environmental Health Reference Laboratories, Department of Health, Queensland Government, P.O. Box 594, Archerfield, Coopers Plains, Queensland, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
- Evolutionary Dynamics of Infectious Diseases, Department of Computational Biology, Institut Pasteur, 28 Rue du Dr Roux, Paris 75015, France
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16
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Sang S, Chen P, Li C, Zhang A, Wang Y, Liu Q. The classification, origin, and evolutionary dynamics of severe fever with thrombocytopenia syndrome virus circulating in East Asia. Virus Evol 2024; 10:veae072. [PMID: 39310090 PMCID: PMC11416872 DOI: 10.1093/ve/veae072] [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: 06/13/2024] [Revised: 08/01/2024] [Accepted: 09/06/2024] [Indexed: 09/25/2024] Open
Abstract
The classification of severe fever with thrombocytopenia syndrome virus (SFTSV) lacked consistency due to limited virus sequences used across previous studies, and the origin and transmission dynamics of the SFTSV remains not fully understood. In this study, we analyzed the diversity and phylodynamics of SFTSV using the most comprehensive and largest dataset publicly available for a better understanding of SFTSV classification and transmission. A total of 1267 L segments, 1289 M segments, and 1438 S segments collected from China, South Korea, and Japan were included in this study. Maximum likelihood trees were reconstructed to classify the lineages. Discrete phylogeographic analysis was conducted to infer the phylodynamics of SFTSV. We found that the L, M, and S segments were highly conserved, with mean pairwise nucleotide distances of 2.80, 3.36, and 3.35% and could be separated into 16, 13, and 15 lineages, respectively. The evolutionary rate for L, M, and the S segment was 0.61 × 10-4 (95% HPD: 0.48-0.73 × 10-4), 1.31 × 10-4 (95% HPD: 0.77-1.77 × 10-4) and 1.27 × 10-4 (95% HPD: 0.65-1.85 × 10-4) subs/site/year. The SFTSV most likely originated from South Korea around the year of 1617.6 (95% HPD: 1513.1-1724.3), 1700.4 (95% HPD: 1493.7-1814.0), and 1790.1 (95% HPD: 1605.4-1887.2) for L, M, and S segments, respectively. Hubei Province in China played a critical role in the geographical expansion of the SFTSV. The effective population size of SFTSV peaked around 2010 to 2013. We also identified several codons under positive selection in the RdRp, Gn-Gc, and NS genes. By leveraging the largest dataset of SFTSV, our analysis could provide new insights into the evolution and dispersal of SFTSV, which may be beneficial for the control and prevention of severe fever with thrombocytopenia syndrome.
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Affiliation(s)
- Shaowei Sang
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, No. 107 Wenhua Road, Lixia District, Jinan 250012, People’s Republic of China
- Clinical Research Center of Shandong University, No. 107 Wenhua Road, Lixia District, Jinan 250012, People’s Republic of China
| | - Peng Chen
- Department of Healthcare-associated Infection Management, School and Hospital of Stomatology, Shandong University, No. 44-1 Wenhua Road, Lixia District, Jinan 250012, People’s Republic of China
| | - Chuanxi Li
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, No. 107 Wenhua Road, Lixia District, Jinan 250012, People’s Republic of China
| | - Anran Zhang
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, No. 107 Wenhua Road, Lixia District, Jinan 250012, People’s Republic of China
| | - Yiguan Wang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, No. 300 Fenglin Road, Xuhui District, Shanghai 200032, People’s Republic of China
| | - Qiyong Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Vector Surveillance and Management, No. 55 Changbai Road, Changping District, Beijing 102206, People’s Republic of China
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17
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Babin CH, Leiva FP, Verberk WCEP, Rees BB. Evolution of Key Oxygen-Sensing Genes Is Associated with Hypoxia Tolerance in Fishes. Genome Biol Evol 2024; 16:evae183. [PMID: 39165136 PMCID: PMC11370800 DOI: 10.1093/gbe/evae183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 08/05/2024] [Accepted: 08/14/2024] [Indexed: 08/22/2024] Open
Abstract
Low dissolved oxygen (hypoxia) is recognized as a major threat to aquatic ecosystems worldwide. Because oxygen is paramount for the energy metabolism of animals, understanding the functional and genetic drivers of whole-animal hypoxia tolerance is critical to predicting the impacts of aquatic hypoxia. In this study, we investigate the molecular evolution of key genes involved in the detection of and response to hypoxia in ray-finned fishes: the prolyl hydroxylase domain (PHD)-hypoxia-inducible factor (HIF) oxygen-sensing system, also known as the EGLN (egg-laying nine)-HIF oxygen-sensing system. We searched fish genomes for HIFA and EGLN genes, discovered new paralogs from both gene families, and analyzed protein-coding sites under positive selection. The physicochemical properties of these positively selected amino acid sites were summarized using linear discriminants for each gene. We employed phylogenetic generalized least squares to assess the relationship between these linear discriminants for each HIFA and EGLN and hypoxia tolerance as reflected by the critical oxygen tension (Pcrit) of the corresponding species. Our results demonstrate that Pcrit in ray-finned fishes correlates with the physicochemical variation of positively selected sites in specific HIFA and EGLN genes. For HIF2A, two linear discriminants captured more than 90% of the physicochemical variation of these sites and explained between 20% and 39% of the variation in Pcrit. Thus, variation in HIF2A among fishes may contribute to their capacity to cope with aquatic hypoxia, similar to its proposed role in conferring tolerance to high-altitude hypoxia in certain lineages of terrestrial vertebrates.
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Affiliation(s)
- Courtney H Babin
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA
| | - Félix P Leiva
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven 27570, Germany
| | - Wilco C E P Verberk
- Department of Animal Ecology and Physiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Bernard B Rees
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA
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18
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Forni D, Mozzi A, Sironi M, Cagliani R. Positive Selection Drives the Evolution of the Structural Maintenance of Chromosomes (SMC) Complexes. Genes (Basel) 2024; 15:1159. [PMID: 39336750 PMCID: PMC11431564 DOI: 10.3390/genes15091159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 08/20/2024] [Accepted: 08/30/2024] [Indexed: 09/30/2024] Open
Abstract
Structural Maintenance of Chromosomes (SMC) complexes are an evolutionary conserved protein family. In most eukaryotes, three SMC complexes have been characterized, as follows: cohesin, condensin, and SMC5/6 complexes. These complexes are involved in a plethora of functions, and defects in SMC genes can lead to an increased risk of chromosomal abnormalities, infertility, and cancer. To investigate the evolution of SMC complex genes in mammals, we analyzed their selective patterns in an extended phylogeny. Signals of positive selection were identified for condensin NCAPG, for two SMC5/6 complex genes (SMC5 and NSMCE4A), and for all cohesin genes with almost exclusive meiotic expression (RAD21L1, REC8, SMC1B, and STAG3). For the latter, evolutionary rates correlate with expression during female meiosis, and most positively selected sites fall in intrinsically disordered regions (IDRs). Our results support growing evidence that IDRs are fast evolving, and that they most likely contribute to adaptation through modulation of phase separation. We suggest that the natural selection signals identified in SMC complexes may be the result of different selective pressures: a host-pathogen arms race in the condensin and SMC5/6 complexes, and an intragenomic conflict for meiotic cohesin genes that is similar to that described for centromeres and telomeres.
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Affiliation(s)
| | | | | | - Rachele Cagliani
- Computational Biology Unit, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy; (D.F.); (A.M.); (M.S.)
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19
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Thuy DTN, Sasaki M, Orba Y, Thammahakin P, Maezono K, Kobayashi S, Kariwa H. Molecular evolution of Hokkaido virus, a genotype of Orthohantavirus puumalaense, among Myodes rodents. Virology 2024; 597:110168. [PMID: 38991257 DOI: 10.1016/j.virol.2024.110168] [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: 05/02/2024] [Revised: 06/24/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024]
Abstract
Viruses in the genus Orthohantavirus within the family Hantaviridae cause human hantavirus infections and represent a threat to public health. Hokkaido virus (HOKV), a genotype of Orthohantavirus puumalaense (Puumala virus; PUUV), was first identified in Tobetsu, Hokkaido, Japan. Although it is genetically related to the prototype of PUUV, the evolutionary pathway of HOKV is unclear. We conducted a field survey in a forest in Tobetsu in 2022 and captured 44 rodents. Complete coding genome sequences of HOKVs were obtained from five viral-RNA-positive rodents (four Myodes rufocanus bedfordiae and one Apodemus speciosus). Phylogenetic analysis revealed a close relationship between the phylogenies and geographical origins of M. rufocanus-related orthohantaviruses. Comparison of the phylogenetic trees of the S segments of orthohantaviruses and the cytochrome b genes of Myodes species suggested that Myodes-related orthohantaviruses evolved in Myodes rodent species as a result of genetic isolation and host switching.
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Affiliation(s)
- Duong Thi Ngoc Thuy
- Laboratory of Public Health, Department of Preventive Veterinary Medicine, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan; Department of Microbiology and Immunology, Tay Nguyen Institute of Hygiene and Epidemiology, Buon Ma Thuot, Viet Nam
| | - Michihito Sasaki
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Passawat Thammahakin
- Laboratory of Public Health, Department of Preventive Veterinary Medicine, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Keisuke Maezono
- Laboratory of Public Health, Department of Preventive Veterinary Medicine, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan; Veterinary Research Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Shintaro Kobayashi
- Laboratory of Public Health, Department of Preventive Veterinary Medicine, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan; Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan; Veterinary Research Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hiroaki Kariwa
- Laboratory of Public Health, Department of Preventive Veterinary Medicine, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan; Veterinary Research Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
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20
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Bhat S, Kattoor JJ, Sircar S, VinodhKumar OR, Thomas P, Ghosh S, Malik YS. Detection and Molecular Characterization of Porcine Teschoviruses in India: Identification of New Genotypes. Indian J Microbiol 2024; 64:963-972. [PMID: 39282184 PMCID: PMC11399526 DOI: 10.1007/s12088-023-01173-7] [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: 08/17/2023] [Accepted: 11/30/2023] [Indexed: 09/18/2024] Open
Abstract
Porcine Teschoviruses (PTVs) are ubiquitous enteric viral pathogens that infect pigs and wild boars worldwide. PTVs have been responsible for causing the severe clinical disease (Teschen disease) to asymptomatic infections. However, to date, limited information is available on large-scale epidemiological data and molecular characterization of PTVs in several countries. In this study, we report epidemiological data on PTVs based on screening of 534 porcine fecal samples from different states of India and a RT-PCR based detection of PTVs shows a percent positivity of 8.24% (44/534). The PTV prevalence varied among different regions of the country with the highest detection rates observed in the state of Karnataka (38.1%). Phylogenetic analysis based on VP1 gene reveals the presence of PTV genotype 6 and 13 along with some unassigned novel genotypes which did not cluster with any of the established PTV genotypes (PTV 1-PTV 13). Indian PTV 6 strains are genetically closest to the Spanish strains (85.7-94.4%) whereas PTV 13 and novel genotype strains were found to be more similar to the Chinese strains (88.1-99.1%). Using recombination detection software, no Indian PTVs found to be recombinant on VP1 gene and selection pressure analysis revealed the purifying selection in the several sites of the VP1 gene of PTVs. The Bayesian analysis of Indian PTVs shows 1.16 × 10-4 substitution/site/year as the mean evolutionary rate. Further, isolation of the novel PTV strains from India and more detailed investigation much needed to know the evolutionary history of PTV strains circulating in porcine populations in India.
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Affiliation(s)
- Sudipta Bhat
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, 243 122 India
| | - Jobin Jose Kattoor
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, 243 122 India
- Animal Disease Diagnostic Laboratory, Purdue University, West Lafayette, IN 47907 USA
| | - Shubhankar Sircar
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, 243 122 India
- Department of Animal Sciences, Washington State University, Pullman, WA 99164 USA
| | - O R VinodhKumar
- Division of Epidemiology, ICAR-Indian Veterinary Research Institute, Bareilly, 243 122 India
| | - Prasad Thomas
- Division of Bacteriology and Mycology, ICAR-Indian Veterinary Research Institute, Bareilly, 243 122 India
| | - Souvik Ghosh
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, P.O. 334, Basseterre, Saint Kitts and Nevis
| | - Yashpal Singh Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, 243 122 India
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, 141001 India
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21
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Philomenadin FS, Mohammed S, Jayagandan S, Ramamurthy N, Ratchagadasse VR, Chandrasekaran V, Dhodapkar R. Characterizing human respiratory syncytial virus among children admitted with acute respiratory tract infections from 2019 to 2022. J Med Virol 2024; 96:e29896. [PMID: 39206836 DOI: 10.1002/jmv.29896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 08/08/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
Respiratory syncytial virus is a major causative agent of lower respiratory tract infection in children, especially infants with substantial morbidity and mortality implications. The virus undergoes continuous evolution documented by accumulation of mutations in the glycoprotein gene necessitating vigilant surveillance to provide essential data to epidemiologists and researchers involved in development of vaccines. This study was aimed to perform molecular characterization of respiratory syncytial virus (RSV) among children ≤ 5 years admitted in hospital. In the current study we observed RSV-A (2019 (n = 95) and 2021 (n = 61) seasons) and RSV-B (2022 season (n = 68)). Phylogenetic analysis revealed all RSV-A strains (n = 47) to be GA.2.3.5 and RSV-B (n = 22) were classified as GB.5.0.5a. Selection pressure analysis identified one positive (P274L/V) and one negative site (P230T) in RSV-A, while in RSV-B there was only one negatively selected site (S295). This study spanning over three seasons contributes to RSV evolutionary dynamics in India emphasizing the importance of on-going surveillance to inform effective public health strategies and vaccine development efforts.
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Affiliation(s)
| | - Shameema Mohammed
- Regional Virus Research and Diagnostic Laboratory (RVRDL), Department of Microbiology, JIPMER, Pondicherry, India
| | - Sangitha Jayagandan
- Regional Virus Research and Diagnostic Laboratory (RVRDL), Department of Microbiology, JIPMER, Pondicherry, India
| | - Narayan Ramamurthy
- Regional Virus Research and Diagnostic Laboratory (RVRDL), Department of Microbiology, JIPMER, Pondicherry, India
| | - Vimal Raj Ratchagadasse
- Regional Virus Research and Diagnostic Laboratory (RVRDL), Department of Microbiology, JIPMER, Pondicherry, India
| | | | - Rahul Dhodapkar
- Regional Virus Research and Diagnostic Laboratory (RVRDL), Department of Microbiology, JIPMER, Pondicherry, India
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22
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Khan N, Kakakhel S, Malik A, Nigar K, Akhtar S, Khan AA, Khan A. Genetic substructure and host-specific natural selection trend across vaccine-candidate ORF-2 capsid protein of hepatitis-E virus. J Viral Hepat 2024; 31:524-534. [PMID: 38804127 DOI: 10.1111/jvh.13959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/03/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024]
Abstract
Hepatitis E virus is a primary cause of acute hepatitis worldwide. The present study attempts to assess the genetic variability and evolutionary divergence among HEV genotypes. A vaccine promising capsid-protein coding ORF-2 gene sequences of HEV was evaluated using phylogenetics, model-based population genetic methods and principal component analysis. The analyses unveiled nine distinct clusters as subpopulations for six HEV genotypes. HEV-3 genotype samples stratified into four different subgroups, while HEV-4 stratified into three additional subclusters. Rabbit-infectious HEV-3ra samples constitute a distinct cluster. Pairwise analysis identified marked genetic distinction of HEV-4c and HEV-4i subgenotypes compared to other genotypes. Numerous admixed, inter and intragenotype recombinant strains were detected. The MEME method identified several ORF-2 codon sites under positive selection. Some selection signatures lead to amino acid substitutions within ORF-2, resulting in altered physicochemical features. Moreover, a pattern of host-specific adaptive signatures was identified among HEV genotypes. The analyses conclusively depict that recombination and episodic positive selection events have shaped the observed genetic diversity among different HEV genotypes. The significant genetic diversity and stratification of HEV-3 and HEV-4 genotypes into subgroups, as identified in the current study, are noteworthy and may have implications for the efficacy of anti-HEV vaccines.
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Affiliation(s)
- Nasir Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Sehrish Kakakhel
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Abdul Malik
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Kiran Nigar
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Suhail Akhtar
- Department of Biochemistry, A.T. Still University of Health Sciences, Kirksville, Missouri, USA
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
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23
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Ding X, Ge S, Chen J, Qi L, Wei J, Zhang H, Hao C, Zhao Q. Differences between phytophagous and predatory species in Pentatomidae based on the mitochondrial genome. Ecol Evol 2024; 14:e70320. [PMID: 39310734 PMCID: PMC11416871 DOI: 10.1002/ece3.70320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 08/31/2024] [Accepted: 09/04/2024] [Indexed: 09/25/2024] Open
Abstract
Pentatomidae includes many species of significant economic value as plant pests and biological control agents. The feeding habits of Pentatomidae are closely related to their energy metabolism and ecological adaptations. In this study, we sequenced the mitochondrial genomes of 12 Asopinae species using the next-generation sequencing to explore the effect of dietary changes on mitochondrial genome evolution. Notably, all sequences were double-stranded circular DNA molecules containing 37 genes and one control region. We then compared and analyzed the mitochondrial genome characteristics of phytophagous and predatory bugs. Notably, no significant difference was observed in the length of the mitochondrial genomes between the predatory and phytophagous bugs. However, the AT content was higher in the mitochondrial genomes of phytophagous bugs than that of predatory bugs. Moreover, phytophagous bugs prefer codon usage patterns ending in A/T compared with predatory bugs. The evolution rate of predatory bugs was lower than that of phytophagous bugs. The phylogenetic relationships across phytophagous bugs' lineages were largely consistent at depth nodes based on different datasets and tree-reconstructing methods, and strongly supported the monophyly of predatory bugs. Additionally, the estimated divergence times indicated that Pentatomidae explosively radiated in the Early Cretaceous. Subsequently, the subfamily Asopinae and the genus Menida diverged in the Late Cretaceous. Our research results provide data supporting for the evolutionary patterns and classification of Pentatomidae.
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Affiliation(s)
- Xiaofei Ding
- College of Plant ProtectionShanxi Agricultural UniversityTaiguShanxiChina
| | - Siyuan Ge
- College of Plant ProtectionShanxi Agricultural UniversityTaiguShanxiChina
| | - Jing Chen
- College of Plant ProtectionShanxi Agricultural UniversityTaiguShanxiChina
| | - Long Qi
- College of Plant ProtectionShanxi Agricultural UniversityTaiguShanxiChina
| | - Jiufeng Wei
- College of Plant ProtectionShanxi Agricultural UniversityTaiguShanxiChina
| | - Hufang Zhang
- Department of BiologyXinzhou Teachers UniversityXinzhouShanxiChina
| | - Chi Hao
- College of Plant ProtectionShanxi Agricultural UniversityTaiguShanxiChina
| | - Qing Zhao
- College of Plant ProtectionShanxi Agricultural UniversityTaiguShanxiChina
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24
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Li J, Zhan Z, Li Y, Sun Y, Zhou T, Xu K. Chromosome-level genome assembly of a deep-sea Venus flytrap sea anemone sheds light upon adaptations to an extremely oligotrophic environment. Mol Ecol 2024:e17504. [PMID: 39166453 DOI: 10.1111/mec.17504] [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: 01/12/2024] [Revised: 06/29/2024] [Accepted: 08/09/2024] [Indexed: 08/23/2024]
Abstract
The Venus flytrap sea anemone Actinoscyphia liui inhabits the nutrient-limited deep ocean in the tropical western Pacific. Compared with most other sea anemones, it has undergone a distinct modification of body shape similar to that of the botanic flytrap. However, the molecular mechanism by which such a peculiar sea anemone adapts to a deep-sea oligotrophic environment is unknown. Here, we report the chromosomal-level genome of A. liui constructed from PacBio and Hi-C data. The assembled genome is 522 Mb in size and exhibits a continuous scaffold N50 of 58.4 Mb. Different from most other sea anemones, which typically possess 14-18 chromosomes per haplotype, A. liui has only 11. The reduced number of chromosomes is associated with chromosome fusion, which likely represents an adaptive strategy to economize energy in oligotrophic deep-sea environments. Comparative analysis with other deep-sea sea anemones revealed adaptive evolution in genes related to cellular autophagy (TMBIM6, SESN1, SCOCB and RPTOR) and mitochondrial energy metabolism (MDH1B and KAD2), which may aid in A. liui coping with severe food scarcity. Meanwhile, the genome has undergone at least two rounds of expansion in gene families associated with fast synaptic transmission, facilitating rapid responses to water currents and prey. Positive selection was detected on putative phosphorylation sites of muscle contraction-related proteins, possibly further improving feeding efficiency. Overall, the present study provides insights into the molecular adaptation to deep-sea oligotrophic environments and sheds light upon potential effects of a novel morphology on the evolution of Cnidaria.
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Affiliation(s)
- Junyuan Li
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- College of Agriculture and Bioengineering, Taizhou Vocational College of Science and Technology, Taizhou, China
| | - Zifeng Zhan
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Yang Li
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Yanan Sun
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Tong Zhou
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Kuidong Xu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
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25
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Gladue DP, Gomez-Lucas L, Largo E, Ramirez-Medina E, Torralba J, Queralt-Martín M, Alcaraz A, Velazquez-Salinas L, Nieva JL, Borca MV. Viroporin-like activity of the hairpin transmembrane domain of African swine fever virus B169L protein. J Virol 2024; 98:e0023124. [PMID: 38980063 PMCID: PMC11334534 DOI: 10.1128/jvi.00231-24] [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: 02/06/2024] [Accepted: 05/21/2024] [Indexed: 07/10/2024] Open
Abstract
African swine fever virus (ASFV) is the causative agent of a contagious disease affecting wild and domestic swine. The function of B169L protein, as a potential integral structural membrane protein, remains to be experimentally characterized. Using state-of-the-art bioinformatics tools, we confirm here earlier predictions indicating the presence of an integral membrane helical hairpin, and further suggest anchoring of this protein to the ER membrane, with both terminal ends facing the lumen of the organelle. Our evolutionary analysis confirmed the importance of purifying selection in the preservation of the identified domains during the evolution of B169L in nature. Also, we address the possible function of this hairpin transmembrane domain (HTMD) as a class IIA viroporin. Expression of GFP fusion proteins in the absence of a signal peptide supported B169L insertion into the ER as a Type III membrane protein and the formation of oligomers therein. Overlapping peptides that spanned the B169L HTMD were reconstituted into ER-like membranes and the adopted structures analyzed by infrared spectroscopy. Consistent with the predictions, B169L transmembrane sequences adopted α-helical conformations in lipid bilayers. Moreover, single vesicle permeability assays demonstrated the assembly of lytic pores in ER-like membranes by B169L transmembrane helices, a capacity confirmed by ion-channel activity measurements in planar bilayers. Emphasizing the relevance of these observations, pore-forming activities were not observed in the case of transmembrane helices derived from EP84R, another ASFV protein predicted to anchor to membranes through a α-helical HTMD. Overall, our results support predictions of viroporin-like function for the B169L HTMD.IMPORTANCEAfrican swine fever (ASF), a devastating disease affecting domestic swine, is widely spread in Eurasia, producing significant economic problems in the pork industry. Approaches to prevent/cure the disease are mainly restricted to the limited information concerning the role of most of the genes encoded by the large (160-170 kba) virus genome. In this report, we present the experimental data on the functional characterization of the African swine fever virus (ASFV) gene B169L. Data presented here indicates that the B169L gene encodes for an essential membrane-associated protein with a viroporin function.
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Affiliation(s)
- Douglas P. Gladue
- Plum Island Animal Disease Center, ARS, USDA, Greenport, New York, USA
| | - Lidia Gomez-Lucas
- Instituto Biofisika (CSIC-UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, Bilbao, Spain
| | - Eneko Largo
- Department of Immunology, Microbiology and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain
| | | | - Johana Torralba
- Instituto Biofisika (CSIC-UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, Bilbao, Spain
| | - Maria Queralt-Martín
- Laboratory of Molecular Biophysics. Department of Physics, University Jaume I, Castello, Castellón, Spain
| | - Antonio Alcaraz
- Laboratory of Molecular Biophysics. Department of Physics, University Jaume I, Castello, Castellón, Spain
| | | | - Jose L. Nieva
- Instituto Biofisika (CSIC-UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, Bilbao, Spain
| | - Manuel V. Borca
- Plum Island Animal Disease Center, ARS, USDA, Greenport, New York, USA
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26
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Misra S, Gilbride E, Ramasamy S, Pond SLK, Kuchipudi SV. Enhanced Diversifying Selection on Polymerase Genes in H5N1 Clade 2.3.4.4b: A Key Driver of Altered Species Tropism and Host Range Expansion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.19.606826. [PMID: 39229076 PMCID: PMC11370473 DOI: 10.1101/2024.08.19.606826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Highly pathogenic avian influenza H5N1 clade 2.3.4.4b viruses have shown unprecedented host range and pathogenicity, including infections in cattle, previously not susceptible to H5N1. We investigated whether selection pressures on clade 2.3.4.4b viral genes could shed light on their unique epidemiological features. Our analysis revealed that while the gene products of clade 2.3.4.4b H5N1 primarily undergo purifying selection, there are notable instances of episodic diversifying selection. Specifically, the polymerase genes PB2, PB1, and PA exhibit significantly greater selection pressures in clade 2.3.4.4b than all earlier H5N1 virus clades. Polymerases play critical roles in influenza virus adaptation, including viral fitness, interspecies transmission, and virulence. Our findings provide evidence that significant selection pressures have shaped the evolution of the H5N1 clade 2.3.4.4b viruses, facilitating their expanded host tropism and the potential for further adaptation to mammalian hosts. We discuss how exogenous factors, such as altered bird migration patterns and increased host susceptibility, may have contributed to the expanded host range. As H5N1 viruses continue to infect new hosts, there is a greater risk of emergent novel variants with increased pathogenicity in humans and animals. Thus, comprehensive One Health surveillance is critical to monitor transmission among avian and mammalian hosts.
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27
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Fay EJ, Isterabadi K, Rezanka CM, Le J, Daugherty MD. Evolutionary and functional analyses reveal a role for the RHIM in tuning RIPK3 activity across vertebrates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593370. [PMID: 39149247 PMCID: PMC11326134 DOI: 10.1101/2024.05.09.593370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Receptor interacting protein kinases (RIPK) RIPK1 and RIPK3 play important roles in diverse innate immune pathways. Despite this, some RIPK1/3-associated proteins are absent in specific vertebrate lineages, suggesting that some RIPK1/3 functions are conserved while others are more evolutionarily labile. Here, we perform comparative evolutionary analyses of RIPK1-5 and associated proteins in vertebrates to identify lineage-specific rapid evolution of RIPK3 and RIPK1 and recurrent loss of RIPK3-associated proteins. Despite this, diverse vertebrate RIPK3 proteins are able to activate NF-κB and cell death in human cells. Additional analyses revealed a striking conservation of the RIP homotypic interaction motif (RHIM) in RIPK3, as well as other human RHIM-containing proteins. Interestingly, diversity in the RIPK3 RHIM can tune activation of NF-κB while retaining the ability to activate cell death. Altogether, these data suggest that NF-κB activation is a core, conserved function of RIPK3, and the RHIM can tailor RIPK3 function to specific needs within and between species.
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Affiliation(s)
- Elizabeth J. Fay
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093
| | - Kolya Isterabadi
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093
| | - Charles M. Rezanka
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093
| | - Jessica Le
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093
| | - Matthew D. Daugherty
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093
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Mizukoshi F, Kimura H, Sugimoto S, Kimura R, Nagasawa N, Hayashi Y, Hashimoto K, Hosoya M, Shirato K, Ryo A. Molecular Evolutionary Analyses of the Fusion Genes in Human Parainfluenza Virus Type 4. Microorganisms 2024; 12:1633. [PMID: 39203475 PMCID: PMC11356533 DOI: 10.3390/microorganisms12081633] [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: 07/09/2024] [Revised: 07/31/2024] [Accepted: 08/08/2024] [Indexed: 09/03/2024] Open
Abstract
The human parainfluenza virus type 4 (HPIV4) can be classified into two distinct subtypes, 4a and 4b. The full lengths of the fusion gene (F gene) of 48 HPIV4 strains collected during the period of 1966-2022 were analyzed. Based on these gene sequences, the time-scaled evolutionary tree was constructed using Bayesian Markov chain Monte Carlo methods. A phylogenetic tree showed that the first division of the two subtypes occurred around 1823, and the most recent common ancestors of each type, 4a and 4b, existed until about 1940 and 1939, respectively. Although the mean genetic distances of all strains were relatively wide, the distances in each subtype were not wide, indicating that this gene was conserved in each subtype. The evolutionary rates of the genes were relatively low (4.41 × 10-4 substitutions/site/year). Moreover, conformational B-cell epitopes were predicted in the apex of the trimer fusion protein. These results suggest that HPIV4 subtypes diverged 200 years ago and the progenies further diverged and evolved.
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Affiliation(s)
- Fuminori Mizukoshi
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama-shi 208-0011, Tokyo, Japan; (S.S.); (K.S.); (A.R.)
| | - Hirokazu Kimura
- Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi 370-0006, Gunma, Japan; (N.N.); (Y.H.)
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, Shibukawa-shi 377-0008, Gunma, Japan
- Department of Clinical Engineering, Faculty of Medical Technology, Gunma Paz University, Takasaki-shi 370-0006, Gunma, Japan
| | - Satoko Sugimoto
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama-shi 208-0011, Tokyo, Japan; (S.S.); (K.S.); (A.R.)
- Research Center for Biosafety, Laboratory Animal and Pathogen Bank, National Institute of Infectious Diseases, Musashimurayama-shi 208-0011, Tokyo, Japan
| | - Ryusuke Kimura
- Department of Bacteriology, Graduate School of Medicine, Gunma University, Maebashi-shi 371-8511, Gunma, Japan;
| | - Norika Nagasawa
- Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi 370-0006, Gunma, Japan; (N.N.); (Y.H.)
| | - Yuriko Hayashi
- Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi 370-0006, Gunma, Japan; (N.N.); (Y.H.)
| | - Koichi Hashimoto
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima-shi 960-1295, Fukushima, Japan;
| | - Mitsuaki Hosoya
- Department of Perinatology and Pediatrics for Regional Medical Support, Fukushima Medical University, Fukushima-shi 960-1295, Fukushima, Japan;
| | - Kazuya Shirato
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama-shi 208-0011, Tokyo, Japan; (S.S.); (K.S.); (A.R.)
| | - Akihide Ryo
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama-shi 208-0011, Tokyo, Japan; (S.S.); (K.S.); (A.R.)
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29
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Nyakio M, Were M, Wekesa C, Lungayia H, Okoth P, Were H. Molecular Footprints of Potato Virus Y Isolate Infecting Potatoes ( Solanum tuberosum) in Kenya. Adv Virol 2024; 2024:2197725. [PMID: 39139708 PMCID: PMC11321891 DOI: 10.1155/2024/2197725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/06/2024] [Accepted: 07/05/2024] [Indexed: 08/15/2024] Open
Abstract
Potato virus Y (PVY) is a highly diverse and genetically variable virus with various strains. Differential evolutionary routes have been reported in the genus Potyvirus, caused by natural selection pressure, mutation, and recombination, with their virulence being dependent on different environmental conditions. Despite its significance and economic impact on Solanaceous species, the understanding of PVY's phylogeography in Kenya remains limited and inadequately documented. The study centers on the molecular characterization of a Kenyan PVY isolate, GenBank accession number PP069009. In-depth phylogenetic analysis unveiled a strong evolutionary association between the Kenyan isolate and isolate [JQ924287] from the United States of America, supported by a robust 92% probability. Recombinant analyses exposed a mosaic-like genetic architecture within the Kenyan isolate, indicating multiple gene recombination events. Selection pressure scrutiny identified specific sites under selective pressure, with evidence of positive/diversifying and negative/purifying selection. Population genetics analysis revealed a calculated nucleotide diversity (π) of 0.00354881, while analysis of molecular variance (AMOVA) unveiled a structured genetic landscape with an øST value of 0.45224. The extensive haplotype network depicted the possibility of diverse PVY strains occurring across continents. This analysis provides valuable insights into the genetic diversity and distribution of PVY globally, highlighting the importance of understanding evolutionary dynamics for effective management and control strategies of PVY on a global scale.
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Affiliation(s)
- Maryrose Nyakio
- Department of Biological SciencesSchool of Natural SciencesMasinde Muliro University of Science & Technology, P.O. Box 190, Kakamega 50100, Kenya
| | - Mariam Were
- Department of Biological SciencesSchool of Natural SciencesMasinde Muliro University of Science & Technology, P.O. Box 190, Kakamega 50100, Kenya
| | - Clabe Wekesa
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena 07745, Germany
| | - Henry Lungayia
- Department of Biological SciencesSchool of Natural SciencesMasinde Muliro University of Science & Technology, P.O. Box 190, Kakamega 50100, Kenya
| | - Patrick Okoth
- Department of Biological SciencesSchool of Natural SciencesMasinde Muliro University of Science & Technology, P.O. Box 190, Kakamega 50100, Kenya
| | - Hassan Were
- Department of Agriculture and Land Use ManagementSchool of AgricultureVeterinary Sciences and TechnologyMasinde Muliro University of Science and Technology, P.O. Box 190, Kakamega 50100, Kenya
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30
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Cagliani R, Forni D, Mozzi A, Fuchs R, Tussia-Cohen D, Arrigoni F, Pozzoli U, De Gioia L, Hagai T, Sironi M. Evolution of Virus-like Features and Intrinsically Disordered Regions in Retrotransposon-derived Mammalian Genes. Mol Biol Evol 2024; 41:msae154. [PMID: 39101471 PMCID: PMC11299033 DOI: 10.1093/molbev/msae154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 08/06/2024] Open
Abstract
Several mammalian genes have originated from the domestication of retrotransposons, selfish mobile elements related to retroviruses. Some of the proteins encoded by these genes have maintained virus-like features; including self-processing, capsid structure formation, and the generation of different isoforms through -1 programmed ribosomal frameshifting. Using quantitative approaches in molecular evolution and biophysical analyses, we studied 28 retrotransposon-derived genes, with a focus on the evolution of virus-like features. By analyzing the rate of synonymous substitutions, we show that the -1 programmed ribosomal frameshifting mechanism in three of these genes (PEG10, PNMA3, and PNMA5) is conserved across mammals and originates alternative proteins. These genes were targets of positive selection in primates, and one of the positively selected sites affects a B-cell epitope on the spike domain of the PNMA5 capsid, a finding reminiscent of observations in infectious viruses. More generally, we found that retrotransposon-derived proteins vary in their intrinsically disordered region content and this is directly associated with their evolutionary rates. Most positively selected sites in these proteins are located in intrinsically disordered regions and some of them impact protein posttranslational modifications, such as autocleavage and phosphorylation. Detailed analyses of the biophysical properties of intrinsically disordered regions showed that positive selection preferentially targeted regions with lower conformational entropy. Furthermore, positive selection introduces variation in binary sequence patterns across orthologues, as well as in chain compaction. Our results shed light on the evolutionary trajectories of a unique class of mammalian genes and suggest a novel approach to study how intrinsically disordered region biophysical characteristics are affected by evolution.
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Affiliation(s)
- Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Computational Biology Unit, Bosisio Parini 23842, Italy
| | - Diego Forni
- Scientific Institute IRCCS E. MEDEA, Computational Biology Unit, Bosisio Parini 23842, Italy
| | - Alessandra Mozzi
- Scientific Institute IRCCS E. MEDEA, Computational Biology Unit, Bosisio Parini 23842, Italy
| | - Rotem Fuchs
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dafna Tussia-Cohen
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan 20126, Italy
| | - Uberto Pozzoli
- Scientific Institute IRCCS E. MEDEA, Computational Biology Unit, Bosisio Parini 23842, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan 20126, Italy
| | - Tzachi Hagai
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Computational Biology Unit, Bosisio Parini 23842, Italy
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31
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Russell T, Lozano JM, Challinor C, Barry G. Diversifying selection identified in immune epitopes of bovine coronavirus isolates from Irish cattle. J Gen Virol 2024; 105:002019. [PMID: 39158563 PMCID: PMC11333106 DOI: 10.1099/jgv.0.002019] [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: 02/07/2024] [Accepted: 08/07/2024] [Indexed: 08/20/2024] Open
Abstract
Bovine betacoronavirus (BoCoV) is a pneumoenteric pathogen of cattle that is closely related to human coronavirus OC43. Vaccines are administered to protect against diseases caused by BoCoV, but knowledge gaps exist with regard to correlates of protection and the effect of immune evasion on driving evolution. In this study, immune epitopes were mapped onto BoCoV structural proteins, including spike and haemagglutinin esterase (HE), and then supported with targeted gene sequencing of Irish clinical isolates and selective pressure analysis. Increased prevalence of diversifying selection and amino acid changes in some mapped immune epitopes suggests that immune escape is selecting for non-synonymous mutations arising in these regions. Selection analysis and sequencing provided increased support for neutralising antibody (nAb) epitopes compared to others, suggesting that nAbs are an important arm of the immune response to BoCoV. Phylogenetic analysis of spike and HE sequences showed that Irish isolates from this study were in the European clade, except for one HE sequence that sat in the Asian/American clade, while the spike gene of this sample was in the European clade. Recombination between a European and an Asian/American isolate would give rise to such a sequence. This study has gathered evidence suggesting that pressure to evade the nAb response is contributing to BoCoV evolution.
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Affiliation(s)
- Tristan Russell
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- Centre for Experimental Pathogen Host Research (CEPHR), University College Dublin, Dublin, Dublin 4, Ireland
| | - Jose Maria Lozano
- Department of Agriculture, Food and the Marine, Central Veterinary Research Laboratory, Celbridge, Ireland
| | - Cailyn Challinor
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Gerald Barry
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
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32
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Suterio DG, Hunter JR, Tenore SB, Pimentel SR, Galinskas J, Dias DA, Bellini DC, Ferreira PA, Diaz RS. People living with HIV co-infected with the Kaposi Sarcoma-associated Herpes Virus have a distinct HIV Tat profile and higher rates of antiretroviral virologic failure, more evident among those with Kaposi's sarcoma. J Med Virol 2024; 96:e29840. [PMID: 39092805 DOI: 10.1002/jmv.29840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/04/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024]
Abstract
Kaposi sarcoma (KS) is a neoplasm of vascular origin that promotes angiogenesis and the growth of endothelial cells triggered by the Kaposi Sarcoma-associated Herpes Virus (KSHV). When associated with HIV, KSHV becomes more aggressive and rapidly evolves. The HIV-1 TAT protein can be essential in developing AIDS-associated KS by promoting angiogenesis and increasing KSHV replication. Therefore, we evaluated the genetic profile of the first exon of tat gene among groups of people living with HIV (PLHIV) with (case group, n = 36) or without KS, this later with (positive control group, n = 46) and without KSHV infection (negative control group, n = 24); all individuals under antiretroviral therapy. The genetic diversity, the DN/DS ratio, and the genetic entropy of the first exon of tat were higher in the case group, followed by the positive control group, which was higher than the negative control group. The number of tat codons under positive selection was seven in the case group, six in the positive control group, and one in the negative control group. The prevalence of HIV viral loads below the detection limit was equal in the case and positive control groups, which were lower than in the negative control group. The mean CD4+ T cell counts were higher in the negative control group, followed by the positive control group, and followed by the case group. These results emphasize the negative influence of KSHV in antiretroviral treatment, as well as the HIV-specific TAT profile among PLHIV who developed KS.
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Affiliation(s)
- Dalila G Suterio
- Retrovirology Laboratory, Infectious Diseases Division, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - James R Hunter
- Retrovirology Laboratory, Infectious Diseases Division, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - Simone B Tenore
- Retrovirology Laboratory, Infectious Diseases Division, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
- Assistência, Centro de Referência e Treinamento em DST/AIDS, São Paulo, São Paulo, SP, Brazil
| | - Sidnei R Pimentel
- Assistência, Centro de Referência e Treinamento em DST/AIDS, São Paulo, São Paulo, SP, Brazil
| | - Juliana Galinskas
- Retrovirology Laboratory, Infectious Diseases Division, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - Danilo A Dias
- Retrovirology Laboratory, Infectious Diseases Division, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - Débora C Bellini
- Retrovirology Laboratory, Infectious Diseases Division, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - Paulo A Ferreira
- Retrovirology Laboratory, Infectious Diseases Division, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - Ricardo Sobhie Diaz
- Retrovirology Laboratory, Infectious Diseases Division, Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
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Zaib K, Khan A, Khan MU, Ullah I, Võ TC, Kang JM, Lê HG, Na BK, Afridi SG. Genetic structure of apical membrane antigen-1 in Plasmodium falciparum isolates from Pakistan. PARASITES, HOSTS AND DISEASES 2024; 62:302-312. [PMID: 39218629 PMCID: PMC11366544 DOI: 10.3347/phd.24028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 07/03/2024] [Indexed: 09/04/2024]
Abstract
Plasmodium falciparum apical membrane antigen-1 (PfAMA-1) is a major candidate for the blood-stage malaria vaccine. Genetic polymorphisms of global pfama-1suggest that the genetic diversity of the gene can disturb effective vaccine development targeting this antigen. This study was conducted to explore the genetic diversity and gene structure of pfama-1 among P. falciparum isolates collected in the Khyber Pakhtunkhwa (KP) province of Pakistan. A total of 19 full-length pfama-1 sequences were obtained from KP-Pakistan P. falciparum isolates, and genetic polymorphism and natural selection were investigated. KP-Pakistan pfama-1 exhibited genetic diversity, wherein 58 amino acid changes were identified, most of which were located in ectodomains, and domains I, II, and III. The amino acid changes commonly found in the ectodomain of global pfama-1 were also detected in KP-Pakistan pfama-1. Interestingly, 13 novel amino acid changes not reported in the global population were identified in KP-Pakistan pfama-1. KP-Pakistan pfama-1 shared similar levels of genetic diversity with global pfama-1. Evidence of natural selection and recombination events were also detected in KP-Pakistan pfama-1.
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Affiliation(s)
- Komal Zaib
- Department of Biochemistry Abdul Wali Khan University, Mardan 23200,
Pakistan
| | - Asifullah Khan
- Department of Biochemistry Abdul Wali Khan University, Mardan 23200,
Pakistan
| | - Muhammad Umair Khan
- Department of Biochemistry Abdul Wali Khan University, Mardan 23200,
Pakistan
| | - Ibrar Ullah
- Department of Biochemistry Abdul Wali Khan University, Mardan 23200,
Pakistan
| | - Tuấn Cường Võ
- Department of Parasitology and Tropical Medicine, Department of Convergence Medical Science, and Institute of Medical Science, Gyeongsang National University College of Medicine, Jinju 52727,
Korea
| | - Jung-Mi Kang
- Department of Parasitology and Tropical Medicine, Department of Convergence Medical Science, and Institute of Medical Science, Gyeongsang National University College of Medicine, Jinju 52727,
Korea
| | - Hương Giang Lê
- Department of Parasitology and Tropical Medicine, Department of Convergence Medical Science, and Institute of Medical Science, Gyeongsang National University College of Medicine, Jinju 52727,
Korea
| | - Byoung-Kuk Na
- Department of Parasitology and Tropical Medicine, Department of Convergence Medical Science, and Institute of Medical Science, Gyeongsang National University College of Medicine, Jinju 52727,
Korea
| | - Sahib Gul Afridi
- Department of Biochemistry Abdul Wali Khan University, Mardan 23200,
Pakistan
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34
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Yusuf LH, Lemus YS, Thorpe P, Garcia CM, Ritchie MG. Evidence for gene flow and trait reversal during radiation of Mexican Goodeid fish. Heredity (Edinb) 2024; 133:78-87. [PMID: 38858547 PMCID: PMC11286751 DOI: 10.1038/s41437-024-00694-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/12/2024] Open
Abstract
Understanding the phylogeographic history of a group and identifying the factors contributing to speciation is an important challenge in evolutionary biology. The Goodeinae are a group of live-bearing fishes endemic to Mexico. Here, we develop genomic resources for species within the Goodeinae and use phylogenomic approaches to characterise their evolutionary history. We sequenced, assembled and annotated the genomes of four Goodeinae species, including Ataeniobius toweri, the only matrotrophic live-bearing fish without a trophotaenia in the group. We estimated timings of species divergence and examined the extent and timing of introgression between the species to assess if this may have occurred during an early radiation, or in more recent episodes of secondary contact. We used branch-site models to detect genome-wide positive selection across Goodeinae, and we specifically asked whether this differs in A. toweri, where loss of placental viviparity has recently occurred. We found evidence of gene flow between geographically isolated species, suggesting vicariant speciation was supplemented by limited post-speciation gene flow, and gene flow may explain previous uncertainties about Goodeid phylogeny. Genes under positive selection in the group are likely to be associated with the switch to live-bearing. Overall, our studies suggest that both volcanism-driven vicariance and changes in reproductive mode influenced radiation in the Goodeinae.
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Affiliation(s)
- Leeban H Yusuf
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK.
| | - Yolitzi Saldívar Lemus
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
- Department of Biology, Texas State University, San Marcos, TX, USA
| | - Peter Thorpe
- School of Life Sciences, University of Dundee, Dundee, UK
| | - Constantino Macías Garcia
- Instituto de Ecologia, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito exterior s/n anexo al Jardín Botánico C. P. 04510, Mexico City CdMx, Mexico
| | - Michael G Ritchie
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
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Huang S, Girdner J, Nguyen LP, Sandoval C, Fregoso OI, Enard D, Li MMH. Positive selection analyses identify a single WWE domain residue that shapes ZAP into a more potent restriction factor against alphaviruses. PLoS Pathog 2024; 20:e1011836. [PMID: 39207950 PMCID: PMC11361444 DOI: 10.1371/journal.ppat.1011836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 07/24/2024] [Indexed: 09/04/2024] Open
Abstract
The host interferon pathway upregulates intrinsic restriction factors in response to viral infection. Many of them block a diverse range of viruses, suggesting that their antiviral functions might have been shaped by multiple viral families during evolution. Host-virus conflicts have led to the rapid adaptation of host and viral proteins at their interaction hotspots. Hence, we can use evolutionary genetic analyses to elucidate antiviral mechanisms and domain functions of restriction factors. Zinc finger antiviral protein (ZAP) is a restriction factor against RNA viruses such as alphaviruses, in addition to other RNA, retro-, and DNA viruses, yet its precise antiviral mechanism is not fully characterized. Previously, an analysis of 13 primate ZAP orthologs identified three positively selected residues in the poly(ADP-ribose) polymerase-like domain. However, selective pressure from ancient alphaviruses and others likely drove ZAP adaptation in a wider representation of mammals. We performed positive selection analyses in 261 mammalian ZAP using more robust methods with complementary strengths and identified seven positively selected sites in all domains of the protein. We generated ZAP inducible cell lines in which the positively selected residues of ZAP are mutated and tested their effects on alphavirus replication and known ZAP activities. Interestingly, the mutant in the second WWE domain of ZAP (N658A) is dramatically better than wild-type ZAP at blocking replication of Sindbis virus and other ZAP-sensitive alphaviruses due to enhanced viral translation inhibition. The N658A mutant is adjacent to the previously reported poly(ADP-ribose) (PAR) binding pocket, but surprisingly has reduced binding to PAR. In summary, the second WWE domain is critical for engineering a more potent ZAP and fluctuations in PAR binding modulate ZAP antiviral activity. Our study has the potential to unravel the role of ADP-ribosylation in the host innate immune defense and viral evolutionary strategies that antagonize this post-translational modification.
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Affiliation(s)
- Serina Huang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Juliana Girdner
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, United States of America
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California, United States of America
| | - LeAnn P. Nguyen
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California, Los Angeles, California, United States of America
| | - Carina Sandoval
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California, United States of America
| | - Oliver I. Fregoso
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California, Los Angeles, California, United States of America
| | - David Enard
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Melody M. H. Li
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California, Los Angeles, California, United States of America
- AIDS Institute, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
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Golding ME, Wu G, Wilkie R, Picard-Meyer E, Servat A, Marston DA, Aegerter JN, Horton DL, McElhinney LM. Investigating the emergence of a zoonotic virus: phylogenetic analysis of European bat lyssavirus 1 in the UK. Virus Evol 2024; 10:veae060. [PMID: 39193178 PMCID: PMC11345707 DOI: 10.1093/ve/veae060] [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: 12/05/2023] [Revised: 06/27/2024] [Accepted: 07/25/2024] [Indexed: 08/29/2024] Open
Abstract
European bat lyssavirus 1 (EBLV-1, Lyssavirus hamburg) is predominantly detected in serotine bats (Eptesicus serotinus) and is responsible for the majority of bat rabies cases in mainland Europe. A passive bat rabies surveillance scheme detected the virus in a serotine bat in the UK for the first time in October 2018. As of May 2024, 34 cases have been reported, 20 of which involved contact with an animal and 5 reported human contact. We investigated the emergence of EBLV-1 by undertaking comprehensive sequence analysis and Bayesian phylogenetics, based on complete virus genomes of 33 UK sequences and 108 sequences covering six countries in mainland Europe (1968-2023), including 21 French EBLV-1-positive RNA samples sequenced for this study. Sequence analysis revealed extreme similarity among UK EBLV-1 sequences (99.9%-100%), implying a single source of introduction rather than multiple independent introductions. Bayesian analysis revealed that the UK EBLV-1 sequences shared their most recent common ancestor with an EBLV-1 sequence from a serotine bat detected in Brittany, France, in 2001, with an estimated date of divergence of 1997. Within the UK sequences, the earliest divergence was estimated to occur in 2007. This study provides valuable insights into the molecular epidemiology of an emerging zoonotic pathogen and improved understanding of the risks posed to public and animal health.
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Affiliation(s)
- Megan E Golding
- Department of Virology, Animal and Plant Health Agency, Woodham Lane, Addlestone KT15 3NB, United Kingdom
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom
| | - Guanghui Wu
- Department of Virology, Animal and Plant Health Agency, Woodham Lane, Addlestone KT15 3NB, United Kingdom
| | - Rebekah Wilkie
- Department of Virology, Animal and Plant Health Agency, Woodham Lane, Addlestone KT15 3NB, United Kingdom
| | | | - Alexandre Servat
- Nancy Laboratory for Rabies and Wildlife, ANSES, Malzéville 51220, France
| | - Denise A Marston
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom
- Department of Science, Strategy and Planning, Animal and Plant Health Agency, Woodham Lane, Addlestone KT15 3NB, United Kingdom
| | - James N Aegerter
- National Wildlife Management Centre, Wildlife Epidemiology and Modelling, Animal and Plant Health Agency, Sand Hutton, York YO41 1LZ, United Kingdom
| | - Daniel L Horton
- Department of Virology, Animal and Plant Health Agency, Woodham Lane, Addlestone KT15 3NB, United Kingdom
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom
| | - Lorraine M McElhinney
- Department of Virology, Animal and Plant Health Agency, Woodham Lane, Addlestone KT15 3NB, United Kingdom
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Liu Y, Qin Y, Hu Y, Chen W, Han Z, Yi C, Bi J, Huang H, Li Y, Zhang X, Lan T, Zheng M, Sun W. Epidemiological and evolutionary analysis of canine circovirus from 1996 to 2023. BMC Vet Res 2024; 20:328. [PMID: 39033103 PMCID: PMC11264901 DOI: 10.1186/s12917-024-04186-6] [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: 03/05/2024] [Accepted: 07/09/2024] [Indexed: 07/23/2024] Open
Abstract
BACKGROUND Canine circovirus (CanineCV), a non-enveloped virus with a circular DNA genome, has been identified in various avian and mammalian species, including domestic and wild canids. This study aimed to comprehensively analyze the prevalence of CanineCV across diverse animal species in 11 provinces of China. RESULTS A total of 1,666 serum samples were collected, revealing a 5.82% prevalence of CanineCV in dogs, with the highest rates being observed in southern and eastern China. Phylogenetic analysis of 266 global CanineCV genomes sourced from the NCBI identified six distinct genotypes, elucidating the complex dynamics of their evolution. Evidence suggested a potential bat origin for CanineCV, with positive selection and high rates of evolution being observed. Recombination analysis revealed dynamic genetic exchange, highlighting the intricate nature of CanineCV evolution. Mutational analysis identified key amino acid substitutions likely to influence the virus's adaptation. Additionally, glycosylation, palmitoylation, and SUMOylation sites were predicted, shedding light on crucial functional properties of the virus. CONCLUSIONS This study provides a global perspective on the origin, genetic diversity, and evolutionary dynamics of CanineCV. Understanding these factors is crucial for elucidating its epidemiology and potential health risks.
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Affiliation(s)
- Yumeng Liu
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Yan Qin
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, 325035, China
| | - Yanqing Hu
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, 325035, China
| | - Wei Chen
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, 325035, China
| | - Zhixiao Han
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Chizhe Yi
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, China
| | - Jingshan Bi
- Guangxi Centre for Animal Disease Control and Prevention, Nanning, 530001, China
| | - Haixin Huang
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, 325035, China
| | - Yuying Li
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, 325035, China
| | - XinYu Zhang
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, 325035, China
| | - Tian Lan
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, 325035, China.
| | - Min Zheng
- Guangxi Centre for Animal Disease Control and Prevention, Nanning, 530001, China.
| | - Wenchao Sun
- Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou, 325035, China.
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Tiwary BK. A positive selection at binding site 501 in the B.1 lineage might have triggered the highly infectious sub-lineages of SARS-CoV-2. Gene 2024; 915:148427. [PMID: 38575097 DOI: 10.1016/j.gene.2024.148427] [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: 02/21/2024] [Revised: 03/21/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
The descendants of the B lineage are the most predominant variants among the SARS-CoV-2 virus due to the incorporation of new mutations augmenting the infectivity of the virus. There is a substantial increase in the transition transversion bias, nucleotide diversity and purifying selection on the spike protein in the descendants of the B lineage of the SARS-CoV-2 virus on a temporal scale. A strong bias for C-to-U substitutions is found in the genes encoding spike protein in this lineage. The positive selection has operated on the spike gene of B lineages and its sub-lineages. The B.1 lineage has undergone positive selection on site 501 of the receptor binding domain ultimately reflected in a key substitution N501Y in its three descendant lineages namely B.1.1.7, B.1.351 and P.1. The intensity of purifying selection on the multiple sites of the spike gene has increased substantially in the sub-lineages of B.1 in a timescale. The binding site 501 on the spike protein in B lineage is found to coevolve with other amino acid sites. This study sheds light on the evolutionary trajectory of the B lineage into highly infectious descendants in the recent past under the influence of positive and purifying selection exerted by natural immunity and vaccination of the host.
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Affiliation(s)
- Basant K Tiwary
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry 605 014, India.
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Dankaona W, Nooroong P, Poolsawat N, Srionrod N, Techangamsuwan S, Anuracpreeda P. Molecular characterization of canine circovirus based on the Capsid gene in Thailand. BMC Vet Res 2024; 20:312. [PMID: 38997779 PMCID: PMC11245861 DOI: 10.1186/s12917-024-04120-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 06/07/2024] [Indexed: 07/14/2024] Open
Abstract
BACKGROUND Canine circovirus (CanineCV) is a single-stranded circular DNA virus that infects domestic and wild canids in many countries. CanineCV is associated with gastroenteritis and diarrhea, respiratory disease, and generalized vasculitis leading to a fatal event. The Capsid protein (Cap) is a structural protein of the virus which has high genetic variability and plays a role in the canine immune response. In this study, we cloned the full-length CanineCV Capsid gene (Cap). In-silico analyses were used to explore the genomic and amino acid variability and natural selection acting on the Cap gene. The immune relevance for T-cell and B-cell epitopes was predicted by the immunoinformatic approach. RESULTS According to the Cap gene, our results showed that CanineCV was separated into five phylogenetic groups. The obtained CanineCV strain from this study was grouped with the previously discovered Thai strain (MG737385), as supported by a haplotype network. Entropy analyses revealed high nucleotide and amino acid variability of the Capsid region. Selection pressure analysis revealed four codons at positions 24, 50, 103, and 111 in the Cap protein evolved under diversifying selection. Prediction of B-cell epitopes exhibited four consensus sequences based on physiochemical properties, and eleven peptide sequences were predicted as T-cell epitopes. In addition, the positive selection sites were located within T-cell and B-cell epitopes, suggesting the role of the host immune system as a driving force in virus evolution. CONCLUSIONS Our study provides knowledge of CanineCV genetic diversity, virus evolution, and potential epitopes for host cell immune response.
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Affiliation(s)
- Wichan Dankaona
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Parasitology Research Laboratory (PRL), Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Pornpiroon Nooroong
- Parasitology Research Laboratory (PRL), Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Napassorn Poolsawat
- Parasitology Research Laboratory (PRL), Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Nitipon Srionrod
- Parasitology Research Laboratory (PRL), Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Somporn Techangamsuwan
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Panat Anuracpreeda
- Parasitology Research Laboratory (PRL), Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand.
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Hernández-Zambrano LJ, Alfonso-González H, Buitrago SP, Castro-Cavadía CJ, Garzón-Ospina D. Exploring the genetic diversity pattern of PvEBP/DBP2: A promising candidate for an effective Plasmodium vivax vaccine. Acta Trop 2024; 255:107231. [PMID: 38685340 DOI: 10.1016/j.actatropica.2024.107231] [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: 02/22/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
Malaria remains a public health challenge. Since many control strategies have proven ineffective in eradicating this disease, new strategies are required, among which the design of a multivalent vaccine stands out. However, the effectiveness of this strategy has been hindered, among other reasons, by the genetic diversity observed in parasite antigens. In Plasmodium vivax, the Erythrocyte Binding Protein (PvEBP, also known as DBP2) is an alternate ligand to Duffy Binding Protein (DBP); given its structural resemblance to DBP, EBP/DBP2 is proposed as a promising antigen for inclusion in vaccine design. However, the extent of genetic diversity within the locus encoding this protein has not been comprehensively assessed. Thus, this study aimed to characterize the genetic diversity of the locus encoding the P. vivax EBP/DBP2 protein and to determine the evolutionary mechanisms modulating this diversity. Several intrapopulation genetic variation parameters were estimated using 36 gene sequences of PvEBP/DBP2 from Colombian P. vivax clinical isolates and 186 sequences available in databases. The study then evaluated the worldwide genetic structure and the evolutionary forces that may influence the observed patterns of genetic variation. It was found that the PvEBP/DBP2 gene exhibits one of the lowest levels of genetic diversity compared to other vaccine-candidate antigens. Four major haplotypes were shared worldwide. Analysis of the protein's 3D structure and epitope prediction identified five regions with potential antigenic properties. The results suggest that the PvEBP/DBP2 protein possesses ideal characteristics to be considered when designing a multivalent effective antimalarial vaccine against P. vivax.
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Affiliation(s)
- Laura J Hernández-Zambrano
- Grupo de Estudios en Genética y Biología Molecular (GEBIMOL), School of Biological Sciences, Universidad Pedagógica y Tecnológica de Colombia - UPTC, Tunja, Boyacá, Colombia; Population Genetics And Molecular Evolution (PGAME), Fundación Scient, Tunja, Boyacá, Colombia
| | - Heliairis Alfonso-González
- Grupo de Estudios en Genética y Biología Molecular (GEBIMOL), School of Biological Sciences, Universidad Pedagógica y Tecnológica de Colombia - UPTC, Tunja, Boyacá, Colombia; Population Genetics And Molecular Evolution (PGAME), Fundación Scient, Tunja, Boyacá, Colombia
| | - Sindy P Buitrago
- Grupo de Estudios en Genética y Biología Molecular (GEBIMOL), School of Biological Sciences, Universidad Pedagógica y Tecnológica de Colombia - UPTC, Tunja, Boyacá, Colombia; Population Genetics And Molecular Evolution (PGAME), Fundación Scient, Tunja, Boyacá, Colombia
| | - Carlos J Castro-Cavadía
- Grupo de Investigaciones Microbiológicas y Biomédicas de Córdoba (GIMBIC), School of Health Sciences, Universidad de Córdoba, Montería, Córdoba, Colombia
| | - Diego Garzón-Ospina
- Grupo de Estudios en Genética y Biología Molecular (GEBIMOL), School of Biological Sciences, Universidad Pedagógica y Tecnológica de Colombia - UPTC, Tunja, Boyacá, Colombia; Population Genetics And Molecular Evolution (PGAME), Fundación Scient, Tunja, Boyacá, Colombia.
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Lucaci AG, Brew WE, Lamanna J, Selberg A, Carnevale V, Moore AR, Kosakovsky Pond SL. The evolution of mammalian Rem2: unraveling the impact of purifying selection and coevolution on protein function, and implications for human disorders. FRONTIERS IN BIOINFORMATICS 2024; 4:1381540. [PMID: 38978817 PMCID: PMC11228553 DOI: 10.3389/fbinf.2024.1381540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 05/28/2024] [Indexed: 07/10/2024] Open
Abstract
Rad And Gem-Like GTP-Binding Protein 2 (Rem2), a member of the RGK family of Ras-like GTPases, is implicated in Huntington's disease and Long QT Syndrome and is highly expressed in the brain and endocrine cells. We examine the evolutionary history of Rem2 identified in various mammalian species, focusing on the role of purifying selection and coevolution in shaping its sequence and protein structural constraints. Our analysis of Rem2 sequences across 175 mammalian species found evidence for strong purifying selection in 70% of non-invariant codon sites which is characteristic of essential proteins that play critical roles in biological processes and is consistent with Rem2's role in the regulation of neuronal development and function. We inferred epistatic effects in 50 pairs of codon sites in Rem2, some of which are predicted to have deleterious effects on human health. Additionally, we reconstructed the ancestral evolutionary history of mammalian Rem2 using protein structure prediction of extinct and extant sequences which revealed the dynamics of how substitutions that change the gene sequence of Rem2 can impact protein structure in variable regions while maintaining core functional mechanisms. By understanding the selective pressures, protein- and gene - interactions that have shaped the sequence and structure of the Rem2 protein, we gain a stronger understanding of its biological and functional constraints.
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Affiliation(s)
- Alexander G Lucaci
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
- Weill Cornell Medicine, The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, United States
| | - William E Brew
- Department of Biology, Temple University, Philadelphia, PA, United States
| | - Jason Lamanna
- Department of Biology, Temple University, Philadelphia, PA, United States
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, United States
| | - Avery Selberg
- Department of Biology, Temple University, Philadelphia, PA, United States
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
| | - Vincenzo Carnevale
- Department of Biology, Temple University, Philadelphia, PA, United States
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, United States
| | - Anna R Moore
- Department of Biology, Temple University, Philadelphia, PA, United States
| | - Sergei L Kosakovsky Pond
- Department of Biology, Temple University, Philadelphia, PA, United States
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
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42
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Faustini G, Poletto F, Baston R, Tucciarone CM, Legnardi M, Dal Maso M, Genna V, Fiorentini L, Di Donato A, Perulli S, Cecchinato M, Drigo M, Franzo G. D for dominant: porcine circovirus 2d (PCV-2d) prevalence over other genotypes in wild boars and higher viral flows from domestic pigs in Italy. Front Microbiol 2024; 15:1412615. [PMID: 38952451 PMCID: PMC11215180 DOI: 10.3389/fmicb.2024.1412615] [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: 04/05/2024] [Accepted: 05/20/2024] [Indexed: 07/03/2024] Open
Abstract
Introduction Porcine circovirus 2 (PCV-2) is a key pathogen for the swine industry at a global level. Nine genotypes, differing in epidemiology and potentially virulence, emerged over time, with PCV-2a, -2b, and -2d being the most widespread and clinically relevant. Conversely, the distribution of minor genotypes appears geographically and temporally restricted, suggesting lower virulence and different epidemiological drivers. In 2022, PCV-2e, the most genetically and phenotypically divergent genotype, was identified in multiple rural farms in North-eastern Italy. Since rural pigs often have access to outdoor environment, the introduction from wild boars was investigated. Methods Through a molecular and spatial approach, this study investigated the epidemiology and genetic diversity of PCV-2 in 122 wild boars across different provinces of North-eastern Italy. Results Molecular analysis revealed a high PCV-2 frequency (81.1%, 99/122), and classified the majority of strains as PCV-2d (96.3%, 78/81), with sporadic occurrences of PCV-2a (1.2%, 1/81) and PCV-2b (2.5%, 2/81) genotypes. A viral flow directed primarily from domestic pigs to wild boars was estimated by phylogenetic and phylodynamic analyses. Discussion These findings attested that the genotype replacement so far described only in the Italian domestic swine sector occurred also in wild boars. and suggested that the current heterogeneity of PCV-2d strains in Italian wild boars likely depends more on different introduction events from the domestic population rather than the presence of independent evolutionary pressures. While this might suggest PCV-2 circulation in wild boars having a marginal impact in the industrial sector, the sharing of PCV-2d strains across distinct wild populations, in absence of a consistent geographical pattern, suggests a complex interplay between domestic and wild pig populations, emphasizing the importance of improved biosecurity measures to mitigate the risk of pathogen transmission.
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Affiliation(s)
- Giulia Faustini
- Department of Animal Medicine, Production and Health, University of Padova, Legnaro, Italy
| | - Francesca Poletto
- Department of Animal Medicine, Production and Health, University of Padova, Legnaro, Italy
| | - Riccardo Baston
- Department of Animal Medicine, Production and Health, University of Padova, Legnaro, Italy
| | | | - Matteo Legnardi
- Department of Animal Medicine, Production and Health, University of Padova, Legnaro, Italy
| | - Mariangela Dal Maso
- AULSS 8 Berica, Dipartimento di Prevenzione, Servizi Veterinari, Vicenza, Italy
| | | | - Laura Fiorentini
- Istituto Zooprofilattico Sperimentale Della Lombardia E Dell'Emilia Romagna (IZSLER), Forlì, Forlì-Cesena, Italy
| | | | - Simona Perulli
- Istituto Zooprofilattico Sperimentale Della Lombardia E Dell'Emilia Romagna (IZSLER), Forlì, Forlì-Cesena, Italy
| | - Mattia Cecchinato
- Department of Animal Medicine, Production and Health, University of Padova, Legnaro, Italy
| | - Michele Drigo
- Department of Animal Medicine, Production and Health, University of Padova, Legnaro, Italy
| | - Giovanni Franzo
- Department of Animal Medicine, Production and Health, University of Padova, Legnaro, Italy
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Lucaci AG, Pond SLK. AOC: Analysis of Orthologous Collections - an application for the characterization of natural selection in protein-coding sequences. ARXIV 2024:arXiv:2406.09522v1. [PMID: 38947939 PMCID: PMC11213150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Motivation Modern molecular sequence analysis increasingly relies on automated and robust software tools for interpretation, annotation, and biological insight. The Analysis of Orthologous Collections (AOC) application automates the identification of genomic sites and species/lineages influenced by natural selection in coding sequence analysis. AOC quantifies different types of selection: negative, diversifying or directional positive, or differential selection between groups of branches. We include all steps necessary to go from unaligned homologous sequences to complete results and interactive visualizations that are designed to aid in the useful interpretation and contextualization. Results We are motivated by a desire to make evolutionary analyses as simple as possible, and to close the disparity in the literature between genes which draw a significant amount of interest and those that are largely overlooked and underexplored. We believe that such underappreciated and understudied genetic datasets can hold rich biological information and offer substantial insights into the diverse patterns and processes of evolution, especially if domain experts are able to perform the analyses themselves. Availability and implementation A Snakemake [Mölder et al., 2021] application implementation is publicly available on GitHub at https://github.com/aglucaci/AnalysisOfOrthologousCollections and is accompanied by software documentation and a tutorial.
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Affiliation(s)
- Alexander G Lucaci
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
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Penteado AB, de Oliveira Ribeiro G, Lima Araújo EL, Kato RB, de Melo Freire CC, de Araújo JMG, da Luz Wallau G, Salvato RS, de Jesus R, Bosco GG, Franz HF, da Silva PEA, de Souza Leal E, Goulart Trossini GH, de Lima Neto DF. Binding Evolution of the Dengue Virus Envelope Against DC-SIGN: A Combined Approach of Phylogenetics and Molecular Dynamics Analyses Over 30 Years of Dengue Virus in Brazil. J Mol Biol 2024; 436:168577. [PMID: 38642883 DOI: 10.1016/j.jmb.2024.168577] [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: 01/09/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/22/2024]
Abstract
The Red Queen Hypothesis (RQH), derived from Lewis Carroll's "Through the Looking-Glass", postulates that organisms must continually adapt in response to each other to maintain relative fitness. Within the context of host-pathogen interactions, the RQH implies an evolutionary arms race, wherein viruses evolve to exploit hosts and hosts evolve to resist viral invasion. This study delves into the dynamics of the RQH in the context of virus-cell interactions, specifically focusing on virus receptors and cell receptors. We observed multiple virus-host systems and noted patterns of co-evolution. As viruses evolved receptor-binding proteins to effectively engage with cell receptors, cells countered by altering their receptor genes. This ongoing mutual adaptation cycle has influenced the molecular intricacies of receptor-ligand interactions. Our data supports the RQH as a driving force behind the diversification and specialization of both viral and host cell receptors. Understanding this co-evolutionary dance offers insights into the unpredictability of emerging viral diseases and potential therapeutic interventions. Future research is crucial to dissect the nuanced molecular changes and the broader ecological consequences of this ever-evolving battle. Here, we combine phylogenetic inferences, structural modeling, and molecular dynamics analyses to describe the epidemiological characteristics of major Brazilian DENV strains that circulated from 1990 to 2022 from a combined perspective, thus providing us with a more detailed picture on the dynamics of such interactions over time.
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MESH Headings
- Dengue Virus/genetics
- Dengue Virus/metabolism
- Receptors, Cell Surface/metabolism
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/chemistry
- Phylogeny
- Molecular Dynamics Simulation
- Humans
- Cell Adhesion Molecules/metabolism
- Cell Adhesion Molecules/genetics
- Cell Adhesion Molecules/chemistry
- Brazil
- Lectins, C-Type/metabolism
- Lectins, C-Type/genetics
- Lectins, C-Type/chemistry
- Evolution, Molecular
- Dengue/virology
- Host-Pathogen Interactions/genetics
- Protein Binding
- Viral Envelope/metabolism
- Receptors, Virus/metabolism
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Viral Envelope Proteins/genetics
- Viral Envelope Proteins/metabolism
- Viral Envelope Proteins/chemistry
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Affiliation(s)
- André Berndt Penteado
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Av. Prof. Lineu Prestes, 580, Cidade Universitária, São Paulo, SP 05508-000, Brazil
| | - Geovani de Oliveira Ribeiro
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil; Department of Cellular Biology, University of Brasilia (UNB), Brasilia, Distrito Federal, Brazil
| | - Emerson Luiz Lima Araújo
- General Coordination of Attention to Communicable Diseases in Primary Care of the Department of Comprehensive Care Management of the Secretariat of Primary Health Care of the Ministry of Health (CDTAP/DGCI/SAPS-MS), Brazil
| | - Rodrigo Bentes Kato
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Caio Cesar de Melo Freire
- Department of Genetics and Evolution, Centre of Biological and Health Sciences, Federal University of Sao Carlos, PO Box 676, Washington Luis Road, km 235, São Carlos, SP 13565-905, Brazil
| | - Joselio Maria Galvão de Araújo
- Federal University of Rio Grande do Norte, Biosciences Center, Department of Microbiology and Parasitology, Campus Universitário, S/N Lagoa Nova 59078900, Natal, RN, Brazil
| | - Gabriel da Luz Wallau
- Department of Entomology and Bioinformatics Center of the Aggeu Magalhães Institute - FIOCRUZ - IAM, Brazil
| | - Richard Steiner Salvato
- Center for Scientific and Technological Development, State Center for Health Surveillance of Rio Grande do Sul, State Department of Health of Rio Grande do Sul, Porto Alegre, Brazil
| | - Ronaldo de Jesus
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Geraldine Goés Bosco
- University of São Paulo, Faculty of Philosophy Sciences and Letters of Ribeirão Preto. Av. Bandeirantes, 3900 Ribeirão Preto, SP, Brazil
| | - Helena Ferreira Franz
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Pedro Eduardo Almeida da Silva
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Elcio de Souza Leal
- Federal University of Pará, Faculty of Biotechnology, Institute of Biological Sciences, Rua Augusto Corrêa, Guamá, 04039-032 Belem, PA, Brazil
| | - Gustavo Henrique Goulart Trossini
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Av. Prof. Lineu Prestes, 580, Cidade Universitária, São Paulo, SP 05508-000, Brazil
| | - Daniel Ferreira de Lima Neto
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Av. Prof. Lineu Prestes, 580, Cidade Universitária, São Paulo, SP 05508-000, Brazil.
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Li L, Qin R, Liu Y, Tseng YS, Zhang W, Yu L, Mietzsch M, Zou X, Liu H, Lu G, Hu H, Mckenna R, Yang J, Wei Y, Agbandje-Mckenna M, Hu J, Yang L. Dissecting positive selection events and immunological drives during the evolution of adeno-associated virus lineages. PLoS Pathog 2024; 20:e1012260. [PMID: 38885242 PMCID: PMC11182496 DOI: 10.1371/journal.ppat.1012260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 05/14/2024] [Indexed: 06/20/2024] Open
Abstract
Adeno-associated virus (AAV) serotypes from primates are being developed and clinically used as vectors for human gene therapy. However, the evolutionary mechanism of AAV variants is far from being understood, except that genetic recombination plays an important role. Furthermore, little is known about the interaction between AAV and its natural hosts, human and nonhuman primates. In this study, natural AAV capsid genes were subjected to systemic evolutionary analysis with a focus on selection drives during the diversification of AAV lineages. A number of positively selected sites were identified from these AAV lineages with functional relevance implied by their localization on the AAV structures. The selection drives of the two AAV2 capsid sites were further investigated in a series of biological experiments. These observations did not support the evolution of the site 410 of the AAV2 capsid driven by selection pressure from the human CD4+ T-cell response. However, positive selection on site 548 of the AAV2 capsid was directly related to host humoral immunity because of the profound effects of mutations at this site on the immune evasion of AAV variants from human neutralizing antibodies at both the individual and population levels. Overall, this work provides a novel interpretation of the genetic diversity and evolution of AAV lineages in their natural hosts, which may contribute to their further engineering and application in human gene therapy.
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Affiliation(s)
- Lirong Li
- Department of Cardiology and Laboratory of Gene Therapy for Heart Diseases, State Key Laboratory of Biotherapy, and Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Runkuan Qin
- Department of Cardiology and Laboratory of Gene Therapy for Heart Diseases, State Key Laboratory of Biotherapy, and Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yunbo Liu
- Department of Cardiology and Laboratory of Gene Therapy for Heart Diseases, State Key Laboratory of Biotherapy, and Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yu-Shan Tseng
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America
| | - Weihan Zhang
- General Surgery Department, Gastric Cancer Center and Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lin Yu
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America
| | - Xinkai Zou
- Center for Immunology and Hematology, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Haizhou Liu
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Guangwen Lu
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hongbo Hu
- Center for Immunology and Hematology, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Robert Mckenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America
| | - Jinliang Yang
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yuquan Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Mavis Agbandje-Mckenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America
| | - Jiankun Hu
- General Surgery Department, Gastric Cancer Center and Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lin Yang
- Department of Cardiology and Laboratory of Gene Therapy for Heart Diseases, State Key Laboratory of Biotherapy, and Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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Rojas Chávez RA, Fili M, Han C, Rahman SA, Bicar IGL, Gregory S, Helverson A, Hu G, Darbro BW, Das J, Brown GD, Haim H. Mapping the Evolutionary Space of SARS-CoV-2 Variants to Anticipate Emergence of Subvariants Resistant to COVID-19 Therapeutics. PLoS Comput Biol 2024; 20:e1012215. [PMID: 38857308 PMCID: PMC11192331 DOI: 10.1371/journal.pcbi.1012215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 06/21/2024] [Accepted: 05/30/2024] [Indexed: 06/12/2024] Open
Abstract
New sublineages of SARS-CoV-2 variants-of-concern (VOCs) continuously emerge with mutations in the spike glycoprotein. In most cases, the sublineage-defining mutations vary between the VOCs. It is unclear whether these differences reflect lineage-specific likelihoods for mutations at each spike position or the stochastic nature of their appearance. Here we show that SARS-CoV-2 lineages have distinct evolutionary spaces (a probabilistic definition of the sequence states that can be occupied by expanding virus subpopulations). This space can be accurately inferred from the patterns of amino acid variability at the whole-protein level. Robust networks of co-variable sites identify the highest-likelihood mutations in new VOC sublineages and predict remarkably well the emergence of subvariants with resistance mutations to COVID-19 therapeutics. Our studies reveal the contribution of low frequency variant patterns at heterologous sites across the protein to accurate prediction of the changes at each position of interest.
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Affiliation(s)
| | - Mohammad Fili
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Changze Han
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Syed A. Rahman
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Isaiah G. L. Bicar
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Sullivan Gregory
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Annika Helverson
- Department of Biostatistics, College of Public Health, The University of Iowa, Iowa City, Iowa, United States of America
| | - Guiping Hu
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Benjamin W. Darbro
- Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, Iowa, United States of America
| | - Jishnu Das
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Grant D. Brown
- Department of Biostatistics, College of Public Health, The University of Iowa, Iowa City, Iowa, United States of America
| | - Hillel Haim
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States of America
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47
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MacDonald N, Raven N, Diep W, Evans S, Pannipitiya S, Bramwell G, Vanbeek C, Thomas F, Russell T, Dujon AM, Telonis-Scott M, Ujvari B. The molecular evolution of cancer associated genes in mammals. Sci Rep 2024; 14:11650. [PMID: 38773187 PMCID: PMC11109183 DOI: 10.1038/s41598-024-62425-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 05/16/2024] [Indexed: 05/23/2024] Open
Abstract
Cancer is a disease that many multicellular organisms have faced for millions of years, and species have evolved various tumour suppression mechanisms to control oncogenesis. Although cancer occurs across the tree of life, cancer related mortality risks vary across mammalian orders, with Carnivorans particularly affected. Evolutionary theory predicts different selection pressures on genes associated with cancer progression and suppression, including oncogenes, tumour suppressor genes and immune genes. Therefore, we investigated the evolutionary history of cancer associated gene sequences across 384 mammalian taxa, to detect signatures of selection across categories of oncogenes (GRB2, FGL2 and CDC42), tumour suppressors (LITAF, Casp8 and BRCA2) and immune genes (IL2, CD274 and B2M). This approach allowed us to conduct a fine scale analysis of gene wide and site-specific signatures of selection across mammalian lineages under the lens of cancer susceptibility. Phylogenetic analyses revealed that for most species the evolution of cancer associated genes follows the species' evolution. The gene wide selection analyses revealed oncogenes being the most conserved, tumour suppressor and immune genes having similar amounts of episodic diversifying selection. Despite BRCA2's status as a key caretaker gene, episodic diversifying selection was detected across mammals. The site-specific selection analyses revealed that the two apoptosis associated domains of the Casp8 gene of bats (Chiroptera) are under opposing forces of selection (positive and negative respectively), highlighting the importance of site-specific selection analyses to understand the evolution of highly complex gene families. Our results highlighted the need to critically assess different types of selection pressure on cancer associated genes when investigating evolutionary adaptations to cancer across the tree of life. This study provides an extensive assessment of cancer associated genes in mammals with highly representative, and substantially large sample size for a comparative genomic analysis in the field and identifies various avenues for future research into the mechanisms of cancer resistance and susceptibility in mammals.
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Affiliation(s)
- Nick MacDonald
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Nynke Raven
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Wendy Diep
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Samantha Evans
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Senuri Pannipitiya
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Georgina Bramwell
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Caitlin Vanbeek
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Frédéric Thomas
- CREEC, UMR IRD 224-CNRS 5290, Université de Montpellier, Montpellier, France
- MIVEGEC, IRD, CNRS, Université Montpellier, Montpellier, France
| | - Tracey Russell
- Faculty of Science, School of Life and Environmental Sciences, Sydney, NSW, Australia
| | - Antoine M Dujon
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Marina Telonis-Scott
- School of Life and Environmental Sciences, Deakin University, Burwood, Burwood, VIC, 3125, Australia
| | - Beata Ujvari
- School of Life and Environmental Sciences, Deakin University, Geelong, Waurn Ponds, Geelong, VIC, 3216, Australia.
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Franzo G, Tucciarone CM, Faustini G, Poletto F, Baston R, Cecchinato M, Legnardi M. Reconstruction of Avian Reovirus History and Dispersal Patterns: A Phylodynamic Study. Viruses 2024; 16:796. [PMID: 38793677 PMCID: PMC11125613 DOI: 10.3390/v16050796] [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: 03/27/2024] [Revised: 05/11/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Avian reovirus (ARV) infection can cause significant losses to the poultry industry. Disease control has traditionally been attempted mainly through vaccination. However, the increase in clinical outbreaks in the last decades demonstrated the poor effectiveness of current vaccination approaches. The present study reconstructs the evolution and molecular epidemiology of different ARV genotypes using a phylodynamic approach, benefiting from a collection of more than one thousand sigma C (σC) sequences sampled over time at a worldwide level. ARVs' origin was estimated to occur several centuries ago, largely predating the first clinical reports. The origins of all genotypes were inferred at least one century ago, and their emergence and rise reflect the intensification of the poultry industry. The introduction of vaccinations had only limited and transitory effects on viral circulation and further expansion was observed, particularly after the 1990s, likely because of the limited immunity and the suboptimal and patchy vaccination application. In parallel, strong selective pressures acted with different strengths and directionalities among genotypes, leading to the emergence of new variants. While preventing the spread of new variants with different phenotypic features would be pivotal, a phylogeographic analysis revealed an intricate network of viral migrations occurring even over long distances and reflecting well-established socio-economic relationships.
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Affiliation(s)
- Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, 35020 Legnaro, Italy; (C.M.T.); (G.F.); (F.P.); (R.B.); (M.C.); (M.L.)
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49
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Chowdhury LM, Pr D, Mandal S, Ravi C, Mohindra V, Sarkar UK. Complete mitochondrial genome of critically endangered catfish Hemibagrus punctatus (Jerdon, 1849) and comparative analysis for insights into the phylogeny of hemibagrids through mitogenomic approach. Mol Biol Rep 2024; 51:601. [PMID: 38693276 DOI: 10.1007/s11033-024-09490-w] [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: 01/19/2024] [Accepted: 03/27/2024] [Indexed: 05/03/2024]
Abstract
BACKGROUND Hemibagrus punctatus (Jerdon, 1849) is a critically endangered bagrid catfish endemic to the Western Ghats of India, whose population is declining due to anthropogenic activities. The current study aims to compare the mitogenome of H. punctatus with that of other Bagrid catfishes and provide insights into their evolutionary relationships. METHODS AND RESULTS Samples were collected from Hemmige Karnataka, India. In the present study, the mitogenome of H. punctatus was successfully assembled, and its phylogenetic relationships with other Bagridae species were studied. The total genomic DNA of samples was extracted following the phenol-chloroform isoamyl alcohol method. Samples were sequenced, and the Illumina paired-end reads were assembled to a contig length of 16,517 bp. The mitochondrial genome was annotated using MitoFish and MitoAnnotator (Iwasaki et al., 2013). A robust phylogenetic analysis employing NJ (Maximum composite likelihood) and ASAP methods supports the classification of H. punctatus within the Bagridae family, which validates the taxonomic status of this species. In conclusion, this research enriches our understanding of H. punctatus mitogenome, shedding light on its evolutionary dynamics within the Bagridae family and contributing to the broader knowledge of mitochondrial genes in the context of evolutionary biology. CONCLUSIONS The study's findings contribute to a better understanding of the mitogenome of H. punctatus and provide insights into the evolutionary relationships within other Hemibagrids.
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Affiliation(s)
| | - Divya Pr
- Principal Scientist, Centre for PAGR, ICAR NBFGR, Cochin, 682018, India.
| | - Sangeeta Mandal
- Principal Scientist, Centre for PAGR, ICAR NBFGR, Cochin, 682018, India
| | - Charan Ravi
- Principal Scientist, Centre for PAGR, ICAR NBFGR, Cochin, 682018, India
| | - Vindhya Mohindra
- Principal Scientist, Centre for PAGR, ICAR NBFGR, Cochin, 682018, India
| | - U K Sarkar
- Principal Scientist, Centre for PAGR, ICAR NBFGR, Cochin, 682018, India
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50
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Ames M, Hamernik A, Behling W, Douches DS, Halterman DA, Bethke PC. A survey of the Sli gene in wild and cultivated potato. PLANT DIRECT 2024; 8:e589. [PMID: 38766508 PMCID: PMC11099725 DOI: 10.1002/pld3.589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/27/2024] [Accepted: 04/18/2024] [Indexed: 05/22/2024]
Abstract
Inbred-hybrid breeding of diploid potatoes necessitates breeding lines that are self-compatible. One way of incorporating self-compatibility into incompatible cultivated potato (Solanum tuberosum) germplasm is to introduce the S-locus inhibitor gene (Sli), which functions as a dominant inhibitor of gametophytic self-incompatibility. To learn more about Sli diversity and function in wild species relatives of cultivated potato, we obtained Sli gene sequences that extended from the 5'UTR to the 3'UTR from 133 individuals from 22 wild species relatives of potato and eight diverse cultivated potato clones. DNA sequence alignment and phylogenetic trees based on genomic and protein sequences show that there are two highly conserved groups of Sli sequences. DNA sequences in one group contain the 533 bp insertion upstream of the start codon identified previously in self-compatible potato. The second group lacks the insertion. Three diploid and four polyploid individuals of wild species collected from geographically disjointed localities contained Sli with the 533 bp insertion. For most of the wild species clones examined, however, Sli did not have the insertion. Phylogenetic analysis indicated that Sli sequences with the insertion, in wild species and in cultivated clones, trace back to a single origin. Some diploid wild potatoes that have Sli with the insertion were self-incompatible and some wild potatoes that lack the insertion were self-compatible. Although there is evidence of positive selection for some codon positions in Sli, there is no evidence of diversifying selection at the gene level. In silico analysis of Sli protein structure did not support the hypothesis that amino acid changes from wild-type (no insertion) to insertion-type account for changes in protein function. Our study demonstrated that genetic factors besides the Sli gene must be important for conditioning a switch in the mating system from self-incompatible to self-compatible in wild potatoes.
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Affiliation(s)
- Mercedes Ames
- US Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Department of HorticultureUniversity of WisconsinMadisonWisconsinUSA
| | - Andy Hamernik
- US Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Department of HorticultureUniversity of WisconsinMadisonWisconsinUSA
| | - William Behling
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - David S. Douches
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Dennis A. Halterman
- US Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Department of HorticultureUniversity of WisconsinMadisonWisconsinUSA
| | - Paul C. Bethke
- US Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Department of HorticultureUniversity of WisconsinMadisonWisconsinUSA
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