1
|
Zhao H, Qin L, Deng X, Wang Z, Jiang R, Reitz SR, Wu S, He Z. Nucleotide and dinucleotide preference of segmented viruses are shaped more by segment: In case study of tomato spotted wilt virus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 122:105608. [PMID: 38796047 DOI: 10.1016/j.meegid.2024.105608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/16/2024] [Accepted: 05/21/2024] [Indexed: 05/28/2024]
Abstract
Several studies have showed that the nucleotide and dinucleotide composition of viruses possibly follows their host species or protein coding region. Nevertheless, the influence of viral segment on viral nucleotide and dinucleotide composition is still unknown. Here, we explored through tomato spotted wilt virus (TSWV), a segmented virus that seriously threatens the production of tomatoes all over the world. Through nucleotide composition analysis, we found the same over-representation of A across all viral segments at the first and second codon position, but it exhibited distinct in segments at the third codon position. Interestingly, the protein coding regions which encoded by the same or different segments exhibit obvious distinct nucleotide preference. Then, we found that the dinucleotides UpG and CpU were overrepresented and the dinucleotides UpA, CpG and GpU were underrepresented, not only in the complete genomic sequences, but also in different segments, protein coding regions and host species. Notably, 100% of the data investigated here were predicted to the correct viral segment and protein coding region, despite the fact that only 67% of the data analyzed here were predicted to the correct viral host species. In conclusion, in case study of TSWV, nucleotide composition and dinucleotide preference of segment viruses are more strongly dependent on segment and protein coding region than on host species. This research provides a novel perspective on the molecular evolutionary mechanisms of TSWV and provides reference for future research on genetic diversity of segmented viruses.
Collapse
Affiliation(s)
- Haiting Zhao
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Lang Qin
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Xiaolong Deng
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Zhilei Wang
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Runzhou Jiang
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Stuart R Reitz
- Malheur Experiment Station, Oregon State University, Ontario, OR, USA
| | - Shengyong Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Zhen He
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China.
| |
Collapse
|
2
|
Hakim MS, Gazali FM, Widyaningsih SA, Parvez MK. Driving forces of continuing evolution of rotaviruses. World J Virol 2024; 13:93774. [DOI: 10.5501/wjv.v13.i2.93774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/06/2024] [Accepted: 05/17/2024] [Indexed: 06/24/2024] Open
Abstract
Rotaviruses are non-enveloped double-stranded RNA virus that causes acute diarrheal diseases in children (< 5 years). More than 90% of the global rotavirus infection in humans was caused by Rotavirus group A. Rotavirus infection has caused more than 200000 deaths annually and predominantly occurs in the low-income countries. Rotavirus evolution is indicated by the strain dynamics or the emergence of the unprecedented strain. The major factors that drive the rotavirus evolution include the genetic shift that is caused by the reassortment mechanism, either in the intra- or the inter-genogroup. However, other factors are also known to have an impact on rotavirus evolution. This review discusses the structure and types, epidemiology, and evolution of rotaviruses. This article also reviews other supplemental factors of rotavirus evolution, such as genetic reassortment, mutation rate, glycan specificity, vaccine introduction, the host immune responses, and antiviral drugs.
Collapse
Affiliation(s)
- Mohamad Saifudin Hakim
- Postgraduate School of Molecular Medicine, Erasmus MC-University Medical Center, Rotterdam 3015GD, Netherlands
- Viral Infection Working Group, International Society of Antimicrobial Chemotherapy, London EC4R 9AN, United Kingdom
| | - Faris Muhammad Gazali
- Master Program in Biotechnology, Postgraduate School, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Suci Ardini Widyaningsih
- Master of Medical Sciences in Clinical Investigation, Harvard Medical School, Boston, MA 02115, United States
| | - Mohammad Khalid Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| |
Collapse
|
3
|
Singhal S, Balitactac AK, Nayagam AG, Pour Bahrami P, Nayeem S, Turner PE. Experimental Evolution Studies in Φ6 Cystovirus. Viruses 2024; 16:977. [PMID: 38932268 PMCID: PMC11209170 DOI: 10.3390/v16060977] [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: 04/27/2024] [Revised: 06/05/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
Experimental evolution studies, in which biological populations are evolved in a specific environment over time, can address questions about the nature of spontaneous mutations, responses to selection, and the origins and maintenance of novel traits. Here, we review more than 30 years of experimental evolution studies using the bacteriophage (phage) Φ6 cystovirus. Similar to many lab-studied bacteriophages, Φ6 has a high mutation rate, large population size, fast generation time, and can be genetically engineered or cryogenically frozen, which facilitates its rapid evolution in the laboratory and the subsequent characterization of the effects of its mutations. Moreover, its segmented RNA genome, outer membrane, and capacity for multiple phages to coinfect a single host cell make Φ6 a good non-pathogenic model for investigating the evolution of RNA viruses that infect humans. We describe experiments that used Φ6 to address the fitness effects of spontaneous mutations, the consequences of evolution in the presence of coinfection, the evolution of host ranges, and mechanisms and consequences of the evolution of thermostability. We highlight open areas of inquiry where further experimentation on Φ6 could inform predictions for pathogenic viruses.
Collapse
Affiliation(s)
- Sonia Singhal
- Department of Biological Sciences, San José State University, San José, CA 95192, USA; (A.K.B.); (A.G.N.); (P.P.B.); (S.N.)
| | - Akiko K. Balitactac
- Department of Biological Sciences, San José State University, San José, CA 95192, USA; (A.K.B.); (A.G.N.); (P.P.B.); (S.N.)
| | - Aruna G. Nayagam
- Department of Biological Sciences, San José State University, San José, CA 95192, USA; (A.K.B.); (A.G.N.); (P.P.B.); (S.N.)
| | - Parnian Pour Bahrami
- Department of Biological Sciences, San José State University, San José, CA 95192, USA; (A.K.B.); (A.G.N.); (P.P.B.); (S.N.)
| | - Sara Nayeem
- Department of Biological Sciences, San José State University, San José, CA 95192, USA; (A.K.B.); (A.G.N.); (P.P.B.); (S.N.)
| | - Paul E. Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA;
- Program in Microbiology, Yale School of Medicine, New Haven, CT 06520, USA
- Center for Phage Biology and Therapy, Yale University, New Haven, CT 06511, USA
| |
Collapse
|
4
|
Carter MH, Gribble J, Diller JR, Denison MR, Mirza SA, Chappell JD, Halasa NB, Ogden KM. Human Rotaviruses of Multiple Genotypes Acquire Conserved VP4 Mutations during Serial Passage. Viruses 2024; 16:978. [PMID: 38932271 PMCID: PMC11209247 DOI: 10.3390/v16060978] [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: 05/14/2024] [Revised: 06/06/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Human rotaviruses exhibit limited tropism and replicate poorly in most cell lines. Attachment protein VP4 is a key rotavirus tropism determinant. Previous studies in which human rotaviruses were adapted to cultured cells identified mutations in VP4. However, most such studies were conducted using only a single human rotavirus genotype. In the current study, we serially passaged 50 human rotavirus clinical specimens representing five of the genotypes most frequently associated with severe human disease, each in triplicate, three to five times in primary monkey kidney cells then ten times in the MA104 monkey kidney cell line. From 13 of the 50 specimens, we obtained 25 rotavirus antigen-positive lineages representing all five genotypes, which tended to replicate more efficiently in MA104 cells at late versus early passage. We used Illumina next-generation sequencing and analysis to identify variants that arose during passage. In VP4, variants encoded 28 mutations that were conserved for all P[8] rotaviruses and 12 mutations that were conserved for all five genotypes. These findings suggest there may be a conserved mechanism of human rotavirus adaptation to MA104 cells. In the future, such a conserved adaptation mechanism could be exploited to study human rotavirus biology or efficiently manufacture vaccines.
Collapse
Affiliation(s)
- Maximilian H. Carter
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jennifer Gribble
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Julia R. Diller
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Mark R. Denison
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Sara A. Mirza
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - James D. Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Natasha B. Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kristen M. Ogden
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| |
Collapse
|
5
|
Maio N, Heffner AL, Rouault TA. Iron‑sulfur clusters in viral proteins: Exploring their elusive nature, roles and new avenues for targeting infections. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119723. [PMID: 38599324 PMCID: PMC11139609 DOI: 10.1016/j.bbamcr.2024.119723] [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: 01/25/2024] [Revised: 03/13/2024] [Accepted: 04/01/2024] [Indexed: 04/12/2024]
Abstract
Viruses have evolved complex mechanisms to exploit host factors for replication and assembly. In response, host cells have developed strategies to block viruses, engaging in a continuous co-evolutionary battle. This dynamic interaction often revolves around the competition for essential resources necessary for both host cell and virus replication. Notably, iron, required for the biosynthesis of several cofactors, including iron‑sulfur (FeS) clusters, represents a critical element in the ongoing competition for resources between infectious agents and host. Although several recent studies have identified FeS cofactors at the core of virus replication machineries, our understanding of their specific roles and the cellular processes responsible for their incorporation into viral proteins remains limited. This review aims to consolidate our current knowledge of viral components that have been characterized as FeS proteins and elucidate how viruses harness these versatile cofactors to their benefit. Its objective is also to propose that viruses may depend on incorporation of FeS cofactors more extensively than is currently known. This has the potential to revolutionize our understanding of viral replication, thereby carrying significant implications for the development of strategies to target infections.
Collapse
Affiliation(s)
- Nunziata Maio
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA.
| | - Audrey L Heffner
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tracey A Rouault
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| |
Collapse
|
6
|
Bourke BP, Dusek RJ, Ergunay K, Linton YM, Drovetski SV. Viral pathogen detection in U.S. game-farm mallard ( Anas platyrhynchos) flags spillover risk to wild birds. Front Vet Sci 2024; 11:1396552. [PMID: 38860005 PMCID: PMC11163284 DOI: 10.3389/fvets.2024.1396552] [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: 03/05/2024] [Accepted: 05/06/2024] [Indexed: 06/12/2024] Open
Abstract
The threat posed by emerging infectious diseases is a major concern for global public health, animal health and food security, and the role of birds in transmission is increasingly under scrutiny. Each year, millions of mass-reared game-farm birds are released into the wild, presenting a unique and a poorly understood risk to wild and susceptible bird populations, and to human health. In particular, the shedding of enteric pathogens through excrement into bodies of water at shared migratory stop-over sites, and breeding and wintering grounds, could facilitate multi-species long-distance pathogen dispersal and infection of high numbers of naive endemic birds annually. The Mallard (Anas platyrhynchos) is the most abundant of all duck species, migratory across much of its range, and an important game species for pen-rearing and release. Major recent population declines along the US Atlantic coast has been attributed to game-farm and wild mallard interbreeding and the introduction maladaptive traits into wild populations. However, pathogen transmission and zoonosis among game-farms Mallard may also impact these populations, as well as wildlife and human health. Here, we screened 16 game-farm Mallard from Wisconsin, United States, for enteric viral pathogens using metatranscriptomic data. Four families of viral pathogens were identified - Picobirnaviridae (Genogroup I), Caliciviridae (Duck Nacovirus), Picornaviridae (Duck Aalivirus) and Sedoreoviridae (Duck Rotavirus G). To our knowledge, this is the first report of Aalivirus in the Americas, and the first report of Calicivirus outside domestic chicken and turkey flocks in the United States. Our findings highlight the risk of viral pathogen spillover from peri-domestically reared game birds to naive wild bird populations.
Collapse
Affiliation(s)
- Brian P. Bourke
- Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD, United States
- One Health Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
- Department of Entomology, Smithsonian Institution—National Museum of Natural History, Washington, DC, United States
| | - Robert J. Dusek
- U.S. Geological Survey, National Wildlife Health Center, Madison, WI, United States
| | - Koray Ergunay
- Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD, United States
- One Health Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
- Department of Entomology, Smithsonian Institution—National Museum of Natural History, Washington, DC, United States
- Hacettepe University, Department of Medical Microbiology, Ankara, Türkiye
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD, United States
- One Health Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
- Department of Entomology, Smithsonian Institution—National Museum of Natural History, Washington, DC, United States
| | - Sergei V. Drovetski
- U.S. Geological Survey, Eastern Ecological Science Center at the Patuxent Research Refuge, Laurel, MD, United States
| |
Collapse
|
7
|
Sabsay KR, te Velthuis AJ. Using structure prediction of negative sense RNA virus nucleoproteins to assess evolutionary relationships. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.16.580771. [PMID: 38405982 PMCID: PMC10888975 DOI: 10.1101/2024.02.16.580771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Negative sense RNA viruses (NSV) include some of the most detrimental human pathogens, including the influenza, Ebola and measles viruses. NSV genomes consist of one or multiple single-stranded RNA molecules that are encapsidated into one or more ribonucleoprotein (RNP) complexes. These RNPs consist of viral RNA, a viral RNA polymerase, and many copies of the viral nucleoprotein (NP). Current evolutionary relationships within the NSV phylum are based on alignment of conserved RNA-directed RNA polymerase (RdRp) domain amino acid sequences. However, the RdRp domain-based phylogeny does not address whether NP, the other core protein in the NSV genome, evolved along the same trajectory or whether several RdRp-NP pairs evolved through convergent evolution in the segmented and non-segmented NSV genomes architectures. Addressing how NP and the RdRp domain evolved may help us better understand NSV diversity. Since NP sequences are too short to infer robust phylogenetic relationships, we here used experimentally-obtained and AlphaFold 2.0-predicted NP structures to probe whether evolutionary relationships can be estimated using NSV NP sequences. Following flexible structure alignments of modeled structures, we find that the structural homology of the NSV NPs reveals phylogenetic clusters that are consistent with RdRp-based clustering. In addition, we were able to assign viruses for which RdRp sequences are currently missing to phylogenetic clusters based on the available NP sequence. Both our RdRp-based and NP-based relationships deviate from the current NSV classification of the segmented Naedrevirales, which cluster with the other segmented NSVs in our analysis. Overall, our results suggest that the NSV RdRp and NP genes largely evolved along similar trajectories and that even short pieces of genetic, protein-coding information can be used to infer evolutionary relationships, potentially making metagenomic analyses more valuable.
Collapse
Affiliation(s)
- Kimberly R. Sabsay
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States
- Lewis Sigler Institute, Princeton University, Princeton, NJ 08544, United States
| | - Aartjan J.W. te Velthuis
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States
| |
Collapse
|
8
|
Tan CCS, van Dorp L, Balloux F. The evolutionary drivers and correlates of viral host jumps. Nat Ecol Evol 2024; 8:960-971. [PMID: 38528191 DOI: 10.1038/s41559-024-02353-4] [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: 01/11/2024] [Accepted: 01/29/2024] [Indexed: 03/27/2024]
Abstract
Most emerging and re-emerging infectious diseases stem from viruses that naturally circulate in non-human vertebrates. When these viruses cross over into humans, they can cause disease outbreaks, epidemics and pandemics. While zoonotic host jumps have been extensively studied from an ecological perspective, little attention has gone into characterizing the evolutionary drivers and correlates underlying these events. To address this gap, we harnessed the entirety of publicly available viral genomic data, employing a comprehensive suite of network and phylogenetic analyses to investigate the evolutionary mechanisms underpinning recent viral host jumps. Surprisingly, we find that humans are as much a source as a sink for viral spillover events, insofar as we infer more viral host jumps from humans to other animals than from animals to humans. Moreover, we demonstrate heightened evolution in viral lineages that involve putative host jumps. We further observe that the extent of adaptation associated with a host jump is lower for viruses with broader host ranges. Finally, we show that the genomic targets of natural selection associated with host jumps vary across different viral families, with either structural or auxiliary genes being the prime targets of selection. Collectively, our results illuminate some of the evolutionary drivers underlying viral host jumps that may contribute to mitigating viral threats across species boundaries.
Collapse
Affiliation(s)
- Cedric C S Tan
- UCL Genetics Institute, University College London, London, UK.
- The Francis Crick Institute, London, UK.
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, UK
| | | |
Collapse
|
9
|
Wu H, Zhou HY, Zheng H, Wu A. Towards Understanding and Identification of Human Viral Co-Infections. Viruses 2024; 16:673. [PMID: 38793555 PMCID: PMC11126107 DOI: 10.3390/v16050673] [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: 04/05/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Viral co-infections, in which a host is infected with multiple viruses simultaneously, are common in the human population. Human viral co-infections can lead to complex interactions between the viruses and the host immune system, affecting the clinical outcome and posing challenges for treatment. Understanding the types, mechanisms, impacts, and identification methods of human viral co-infections is crucial for the prevention and control of viral diseases. In this review, we first introduce the significance of studying human viral co-infections and summarize the current research progress and gaps in this field. We then classify human viral co-infections into four types based on the pathogenic properties and species of the viruses involved. Next, we discuss the molecular mechanisms of viral co-infections, focusing on virus-virus interactions, host immune responses, and clinical manifestations. We also summarize the experimental and computational methods for the identification of viral co-infections, emphasizing the latest advances in high-throughput sequencing and bioinformatics approaches. Finally, we highlight the challenges and future directions in human viral co-infection research, aiming to provide new insights and strategies for the prevention, control, diagnosis, and treatment of viral diseases. This review provides a comprehensive overview of the current knowledge and future perspectives on human viral co-infections and underscores the need for interdisciplinary collaboration to address this complex and important topic.
Collapse
Affiliation(s)
- Hui Wu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 211100, China;
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Hang-Yu Zhou
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Heng Zheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 211100, China;
| | - Aiping Wu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| |
Collapse
|
10
|
Li T, Liu R, Wang Q, Rao J, Liu Y, Dai Z, Gooneratne R, Wang J, Xie Q, Zhang X. A review of the influence of environmental pollutants (microplastics, pesticides, antibiotics, air pollutants, viruses, bacteria) on animal viruses. JOURNAL OF HAZARDOUS MATERIALS 2024; 468:133831. [PMID: 38402684 DOI: 10.1016/j.jhazmat.2024.133831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 02/09/2024] [Accepted: 02/17/2024] [Indexed: 02/27/2024]
Abstract
Microorganisms, especially viruses, cause disease in both humans and animals. Environmental chemical pollutants including microplastics, pesticides, antibiotics sand air pollutants arisen from human activities affect both animal and human health. This review assesses the impact of chemical and biological contaminants (virus and bacteria) on viruses including its life cycle, survival, mutations, loads and titers, shedding, transmission, infection, re-assortment, interference, abundance, viral transfer between cells, and the susceptibility of the host to viruses. It summarizes the sources of environmental contaminants, interactions between contaminants and viruses, and methods used to mitigate such interactions. Overall, this review provides a perspective of environmentally co-occurring contaminants on animal viruses that would be useful for future research on virus-animal-human-ecosystem harmony studies to safeguard human and animal health.
Collapse
Affiliation(s)
- Tong Li
- State Key Laboratory of Swine and Poultry Breeding Industry & Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangdong, Guangzhou 510642, China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, China
| | - Ruiheng Liu
- State Key Laboratory of Swine and Poultry Breeding Industry & Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangdong, Guangzhou 510642, China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, China
| | - Qian Wang
- State Key Laboratory of Swine and Poultry Breeding Industry & Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangdong, Guangzhou 510642, China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, China
| | - Jiaqian Rao
- State Key Laboratory of Swine and Poultry Breeding Industry & Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangdong, Guangzhou 510642, China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, China
| | - Yuanjia Liu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Zhenkai Dai
- State Key Laboratory of Swine and Poultry Breeding Industry & Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangdong, Guangzhou 510642, China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, China
| | - Ravi Gooneratne
- Department of Wine, Food and Molecular Biosciences, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Jun Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China.
| | - Qingmei Xie
- State Key Laboratory of Swine and Poultry Breeding Industry & Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangdong, Guangzhou 510642, China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, China.
| | - Xinheng Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry & Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangdong, Guangzhou 510642, China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, China; Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, China.
| |
Collapse
|
11
|
Valusenko-Mehrkens R, Schilling-Loeffler K, Johne R, Falkenhagen A. VP4 Mutation Boosts Replication of Recombinant Human/Simian Rotavirus in Cell Culture. Viruses 2024; 16:565. [PMID: 38675907 PMCID: PMC11054354 DOI: 10.3390/v16040565] [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: 02/23/2024] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Rotavirus A (RVA) is the leading cause of diarrhea requiring hospitalization in children and causes over 100,000 annual deaths in Sub-Saharan Africa. In order to generate next-generation vaccines against African RVA genotypes, a reverse genetics system based on a simian rotavirus strain was utilized here to exchange the antigenic capsid proteins VP4, VP7 and VP6 with those of African human rotavirus field strains. One VP4/VP7/VP6 (genotypes G9-P[6]-I2) triple-reassortant was successfully rescued, but it replicated poorly in the first cell culture passages. However, the viral titer was enhanced upon further passaging. Whole genome sequencing of the passaged virus revealed a single point mutation (A797G), resulting in an amino acid exchange (E263G) in VP4. After introducing this mutation into the VP4-encoding plasmid, a VP4 mono-reassortant as well as the VP4/VP7/VP6 triple-reassortant replicated to high titers already in the first cell culture passage. However, the introduction of the same mutation into the VP4 of other human RVA strains did not improve the rescue of those reassortants, indicating strain specificity. The results show that specific point mutations in VP4 can substantially improve the rescue and replication of recombinant RVA reassortants in cell culture, which may be useful for the development of novel vaccine strains.
Collapse
Affiliation(s)
| | | | | | - Alexander Falkenhagen
- Department of Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany; (R.V.-M.); (K.S.-L.); (R.J.)
| |
Collapse
|
12
|
Solarte-Murillo L, Reyes H, Ojeda L, Cárcamo JG, Pontigo JP, Loncoman CA. Analyses and Insights into Genetic Reassortment and Natural Selection as Key Drivers of Piscine orthoreovirus Evolution. Viruses 2024; 16:556. [PMID: 38675898 PMCID: PMC11053957 DOI: 10.3390/v16040556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 04/28/2024] Open
Abstract
Piscine orthoreovirus (PRV) is a pathogen that causes heart and skeletal muscle inflammation in Salmo salar and has also been linked to circulatory disorders in other farmed salmonids, such as Oncorhynchus kisutch and Oncorhynchus mykiss. The virus has a segmented, double-stranded RNA genome, which makes it possible to undergo genetic reassortment and increase its genomic diversity through point mutations. In this study, genetic reassortment in PRV was assessed using the full genome sequences available in public databases. This study used full genome sequences that were concatenated and genome-wide reassortment events, and phylogenetic analyses were performed using the recombination/reassortment detection program version 5 (RDP5 V 5.5) software. Additionally, each segment was aligned codon by codon, and overall mean distance and selection was tested using the Molecular Evolutionary Genetics Analysis X software, version 10.2 (MEGA X version 10.2). The results showed that there were 17 significant reassortment events in 12 reassortant sequences, involving genome exchange between low and highly virulent genotypes. PRV sequences from different salmonid host species did not appear to limit the reassortment. This study found that PRV frequently undergoes reassortment events to increase the diversity of its segmented genome, leading to antigenic variation and increased virulence. This study also noted that to date, no reassortment events have been described between PRV-1 and PRV-3 genotypes. However, the number of complete genomic sequences within each genotype is uneven. This is important because PRV-3 induces cross-protection against PRV-1, making it a potential vaccine candidate.
Collapse
Affiliation(s)
- Laura Solarte-Murillo
- Laboratorio de Virología Molecular, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile;
| | - Humberto Reyes
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile;
| | - Loreto Ojeda
- Laboratorio de Bioquímica Farmacológica, Virología y Biotecnología, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile
- Interdisciplinary Center for Aquaculture Research, INCAR, Concepción 4030000, Chile
| | - Juan G. Cárcamo
- Laboratorio de Bioquímica Farmacológica, Virología y Biotecnología, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile
- Interdisciplinary Center for Aquaculture Research, INCAR, Concepción 4030000, Chile
| | - Juan Pablo Pontigo
- Laboratorio Institucional, Facultad de Ciencias de la Naturaleza, Escuela de Medicina Veterinaria, Universidad San Sebastián, Puerto Montt 5400000, Chile;
| | - Carlos A. Loncoman
- Laboratorio de Virología Molecular, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile;
| |
Collapse
|
13
|
Mustafa MI, Mohammed A. Developing recombinant antibodies by phage display technology to neutralize viral infectious diseases. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100140. [PMID: 38182043 DOI: 10.1016/j.slasd.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/07/2024]
Abstract
The use of recombinant antibodies developed through phage display technology offers a promising approach for combating viral infectious diseases. By specifically targeting antigens on viral surfaces, these antibodies have the potential to reduce the severity of infections or even prevent them altogether. With the emergence of new and more virulent strains of viruses, it is crucial to develop innovative methods to counteract them. Phage display technology has proven successful in generating recombinant antibodies capable of targeting specific viral antigens, thereby providing a powerful tool to fight viral infections. In this mini-review article, we examine the development of these antibodies using phage display technology, and discuss the associated challenges and opportunities in developing novel treatments for viral infectious diseases. Furthermore, we provide an overview of phage display technology. As these methods continue to evolve and improve, novel and sophisticated tools based on phage display and peptide display systems are constantly emerging, offering exciting prospects for solving scientific, medical, and technological problems related to viral infectious diseases in the near future.
Collapse
Affiliation(s)
- Mujahed I Mustafa
- Department of Biotechnology, College of Applied and Industrial Sciences, University of Bahri, Khartoum, Sudan.
| | - Ahmed Mohammed
- Department of Biotechnology, School of Life Sciences and Technology, Omdurman Islamic university, Omdurman, Sudan
| |
Collapse
|
14
|
Zhou Q, Cui Y, Wang C, Wu H, Xiong H, Qi K, Liu H. Characterization of natural co-infection with goose astrovirus genotypes I and II in gout affected goslings. Avian Pathol 2024; 53:146-153. [PMID: 38088166 DOI: 10.1080/03079457.2023.2295341] [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: 08/16/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
RESEARCH HIGHLIGHTS Urate tophi were found in the kidneys, liver, spleen and lungs.IFA confirmed the co-expression of GoAstV-I and II antigens in the same kidney.
Collapse
Affiliation(s)
- Qian Zhou
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, People's Republic of China
| | - Yaqian Cui
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, People's Republic of China
| | - Chenxiao Wang
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, People's Republic of China
| | - Hanwen Wu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, People's Republic of China
| | - Haifeng Xiong
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, People's Republic of China
| | - Kezong Qi
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, People's Republic of China
| | - Hongmei Liu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, People's Republic of China
| |
Collapse
|
15
|
Belluccini G, Lin Q, Williams B, Lou Y, Vatansever Z, López-García M, Lythe G, Leitner T, Romero-Severson E, Molina-París C. A story of viral co-infection, co-transmission and co-feeding in ticks: how to compute an invasion reproduction number. ARXIV 2024:arXiv:2403.15282v1. [PMID: 38562445 PMCID: PMC10983997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
With a single circulating vector-borne virus, the basic reproduction number incorporates contributions from tick-to-tick (co-feeding), tick-to-host and host-to-tick transmission routes. With two different circulating vector-borne viral strains, resident and invasive, and under the assumption that co-feeding is the only transmission route in a tick population, the invasion reproduction number depends on whether the model system of ordinary differential equations possesses the property of neutrality. We show that a simple model, with two populations of ticks infected with one strain, resident or invasive, and one population of co-infected ticks, does not have Alizon's neutrality property. We present model alternatives that are capable of representing the invasion potential of a novel strain by including populations of ticks dually infected with the same strain. The invasion reproduction number is analysed with the next-generation method and via numerical simulations.
Collapse
Affiliation(s)
- Giulia Belluccini
- T-6, Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
- School of Mathematics, University of Leeds, Leeds, LS2 9JT, UK
| | - Qianying Lin
- T-6, Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | | | - Yijun Lou
- Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Zati Vatansever
- Department of Parasitology, Faculty of Veterinary Medicine, Kafkas University, Kars, Turkey
| | | | - Grant Lythe
- School of Mathematics, University of Leeds, Leeds, LS2 9JT, UK
| | - Thomas Leitner
- T-6, Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | - Ethan Romero-Severson
- T-6, Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | - Carmen Molina-París
- T-6, Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| |
Collapse
|
16
|
Do HQ, Yeom M, Moon S, Lee H, Chung CU, Chung HC, Park JW, Na W, Song D. Genetic characterization and pathogenicity in a mouse model of newly isolated bat-originated mammalian orthoreovirus in South Korea. Microbiol Spectr 2024; 12:e0176223. [PMID: 38289932 PMCID: PMC10913406 DOI: 10.1128/spectrum.01762-23] [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: 04/28/2023] [Accepted: 12/29/2023] [Indexed: 02/01/2024] Open
Abstract
Mammalian orthoreoviruses (MRVs) infect a wide range of hosts, including humans, livestock, and wildlife. In the present study, we isolated a novel Mammalian orthoreovirus from the intestine of a microbat (Myotis aurascens) and investigated its biological and pathological characteristics. Phylogenetic analysis indicated that the new isolate was serotype 2, sharing the segments with those from different hosts. Our results showed that it can infect a wide range of cell lines from different mammalian species, including human, swine, and non-human primate cell lines. Additionally, media containing trypsin, yeast extract, and tryptose phosphate broth promoted virus propagation in primate cell lines and most human cell lines, but not in A549 and porcine cell lines. Mice infected with this strain via the intranasal route, but not via the oral route, exhibited weight loss and respiratory distress. The virus is distributed in a broad range of organs and causes lung damage. In vitro and in vivo experiments also suggested that the new virus could be a neurotropic infectious strain that can infect a neuroblastoma cell line and replicate in the brains of infected mice. Additionally, it caused a delayed immune response, as indicated by the high expression levels of cytokines and chemokines only at 14 days post-infection (dpi). These data provide an important understanding of the genetics and pathogenicity of mammalian orthoreoviruses in bats at risk of spillover infections.IMPORTANCEMammalian orthoreoviruses (MRVs) have a broad range of hosts and can cause serious respiratory and gastroenteritis diseases in humans and livestock. Some strains infect the central nervous system, causing severe encephalitis. In this study, we identified BatMRV2/SNU1/Korea/2021, a reassortment of MRV serotype 2, isolated from bats with broad tissue tropism, including the neurological system. In addition, it has been shown to cause respiratory syndrome in mouse models. The given data will provide more evidence of the risk of mammalian orthoreovirus transmission from wildlife to various animal species and the sources of spillover infections.
Collapse
Affiliation(s)
- Hai Quynh Do
- Department of Virology, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Minjoo Yeom
- Department of Virology, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Suyun Moon
- College of Veterinary Medicine, Chonnam National University, Gwangju, South Korea
| | - Hanbyeul Lee
- Department of Virology, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Chul-un Chung
- Department of Life Science, Dongguk University, Gyeongju, South Korea
| | - Hee-chun Chung
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
| | - Jun Won Park
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, South Korea
| | - Woonsung Na
- College of Veterinary Medicine, Chonnam National University, Gwangju, South Korea
| | - Daesub Song
- Department of Virology, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| |
Collapse
|
17
|
Ferguson C, Ali A. Global Genetic Diversity of Tobacco Ringspot Virus Including Newly Reported Isolates from Cotton ( Gossypium hirsutum) in Oklahoma. PLANT DISEASE 2024; 108:635-646. [PMID: 37773330 DOI: 10.1094/pdis-07-23-1251-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
Cotton is one of the most salient cash crops globally and in the United States. Lately, several virus-like diseases have been reported from cotton in the United States such as the tobacco ringspot virus (TRSV) in Oklahoma. TRSV has been reported from various hosts worldwide with minimal phylogenetic examination. In this study, complete genome sequences of four TRSV isolates from cotton were isolated, and the genetic diversity was investigated along with additional available TRSV isolates retrieved from GenBank. Phylogenetic analysis based on the complete RNA1 and RNA2 sequences distributed all TRSV isolates into three major phylogenetic clades exhibiting a differential clade composition depending on the segment. The TRSV cotton isolates exhibited differential grouping between the RNA1 and RNA2 analyses. Additionally, monophyletic subclades of isolates appeared to be conserved between both segments. Thirty-five recombination events in RNA1 and 23 in RNA2 were identified with implications in the variation of the phylogenetic analyses. Furthermore, multiple hypotheses of TRSV evolution were generated based on the phylogenetic analyses, but to test them, more complete genomes of TRSV will be needed. This study provides the first complete genome analysis of TRSV isolates infecting cotton in the United States and a detailed analysis of global TRSV isolates.
Collapse
Affiliation(s)
- Connor Ferguson
- Department of Biological Science, The University of Tulsa, Tulsa, OK 74104
| | - Akhtar Ali
- Department of Biological Science, The University of Tulsa, Tulsa, OK 74104
| |
Collapse
|
18
|
Torralba B, Blanc S, Michalakis Y. Reassortments in single-stranded DNA multipartite viruses: Confronting expectations based on molecular constraints with field observations. Virus Evol 2024; 10:veae010. [PMID: 38384786 PMCID: PMC10880892 DOI: 10.1093/ve/veae010] [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: 07/31/2023] [Revised: 11/23/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024] Open
Abstract
Single-stranded DNA multipartite viruses, which mostly consist of members of the genus Begomovirus, family Geminiviridae, and all members of the family Nanoviridae, partly resolve the cost of genomic integrity maintenance through two remarkable capacities. They are able to systemically infect a host even when their genomic segments are not together in the same host cell, and these segments can be separately transmitted by insect vectors from host to host. These capacities potentially allow such viruses to reassort at a much larger spatial scale, since reassortants could arise from parental genotypes that do not co-infect the same cell or even the same host. To assess the limitations affecting reassortment and their implications in genome integrity maintenance, the objective of this review is to identify putative molecular constraints influencing reassorted segments throughout the infection cycle and to confront expectations based on these constraints with empirical observations. Trans-replication of the reassorted segments emerges as the major constraint, while encapsidation, viral movement, and transmission compatibilities appear more permissive. Confronting the available molecular data and the resulting predictions on reassortments to field population surveys reveals notable discrepancies, particularly a surprising rarity of interspecific natural reassortments within the Nanoviridae family. These apparent discrepancies unveil important knowledge gaps in the biology of ssDNA multipartite viruses and call for further investigation on the role of reassortment in their biology.
Collapse
Affiliation(s)
- Babil Torralba
- PHIM, Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Avenue du Campus d’Agropolis - ZAC de Baillarguet, Montpellier 34980, France
| | - Stéphane Blanc
- PHIM, Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Avenue du Campus d’Agropolis - ZAC de Baillarguet, Montpellier 34980, France
| | - Yannis Michalakis
- MIVEGEC, Université Montpellier, CNRS, IRD, 911, Avenue Agropolis, Montpellier 34394, France
| |
Collapse
|
19
|
Okamoto A, Takemae H, Nagai M, Hashimoto S, Mizutani T, Furuya T. First report of the whole-genome sequence analysis of avian rotavirus A from Japanese chickens. Virus Genes 2024; 60:25-31. [PMID: 38102511 DOI: 10.1007/s11262-023-02040-9] [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: 07/29/2023] [Accepted: 11/11/2023] [Indexed: 12/17/2023]
Abstract
Rotavirus A infects many mammalian species, including humans and causes diarrhea and gastrointestinal diseases. The virus also infects various bird species, including chickens, although information of avian rotavirus A (ARVA) infection in chicken populations in Japan is scarce. In this study, we report for the first time the whole-genome sequences of ARVA strains from Japanese chicken populations. The virus strains were inoculated to MA104 cells and cultured viruses were used to obtain the sequences with the MiSeq system, and genetic analysis demonstrated the genotype constellation of G19-P[30]-I11-R6-C6-M7-A16-N6-T8-E10-H8 of the Japanese chicken ARVA isolates. Phylogenetic analyses demonstrated that the VP1, VP2, VP3, VP4, VP7, NSP2, and NSP4 coding gene sequences of the Japanese strains were closer to those of Korean than the European ARVA strains, although such relationship was not clear for other genes. The data suggest that the Japanese ARVA strains and the ones in Korea have genetically close relationship, although the origin is not clear at this point. Further information including the whole-genome sequences of the Korean strains and sequences of other Japanese chicken ARVA strains will be necessary for elucidation of their origin.
Collapse
Affiliation(s)
- Ayana Okamoto
- Laboratory of Veterinary Infectious Diseases, Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Hitoshi Takemae
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
- Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Makoto Nagai
- Department of Large Animal Clinic, Azabu University, Veterinary Teaching Hospital, Azabu University, Sagamihara, Kanagawa, 252-5201, Japan
| | - Shinichiro Hashimoto
- Wellfam Foods Corporation, 1-6-5 Kudan Minami, Chiyoda-ku, Tokyo, 102-0074, Japan
| | - Tetsuya Mizutani
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
- Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Tetsuya Furuya
- Laboratory of Veterinary Infectious Diseases, Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan.
- Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan.
| |
Collapse
|
20
|
Acevedo AM, Postic L, Curiel M, Gondard M, Bréard E, Zientara S, Vorimore F, Tran ML, Turpaud M, Savini G, Lorusso A, Marcacci M, Vitour D, Dujardin P, Perera CL, Díaz C, Obret Y, Sailleau C. Detection, Characterization and Sequencing of BTV Serotypes Circulating in Cuba in 2022. Viruses 2024; 16:164. [PMID: 38275974 PMCID: PMC10819738 DOI: 10.3390/v16010164] [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: 12/05/2023] [Revised: 01/19/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
In Cuba, despite a high sero-prevalence of bluetongue virus (BTV), circulating serotypes remain unknown. The aim of this study was to identify circulating BTV serotypes in farms throughout the western region of Cuba. Blood samples were collected from 200 young cattle and sheep between May and July 2022 for virological analyses (PCR, viral isolation and virus neutralization) and genome sequencing. The results confirmed viral circulation, with viro-prevalence of 25% for BTV. The virus was isolated from 18 blood samples and twelve BTV serotypes were identified by sequencing RT-PCR products targeting the segment 2 of the BTV genome (BTV-1, 2, 3, 6, 10, 12, 13, 17, 18, 19, 22 and 24). Finally, the full genome sequences of 17 Cuban BTV isolates were recovered using a Sequence Independent Single Primer Amplification (SISPA) approach combined to MinION Oxford Nanopore sequencing technology. All together, these results highlight the co-circulation of a wide diversity of BTV serotypes in a quite restricted area and emphasize the need for entomological and livestock surveillance, particularly in light of recent changes in the global distribution and nature of BTV infections.
Collapse
Affiliation(s)
- Ana María Acevedo
- National Center for Animal and Plant Health (CENSA), Carretera de Tapaste y Autopista Nacional, Apartado Postal 10, San José de las Lajas, San José de las Lajas 32700, Cuba; (A.M.A.); (M.C.); (C.L.P.); (C.D.); (Y.O.)
| | - Lydie Postic
- ANSES/INRAE/ENVA-UPEC, UMR 1161 Virology, Laboratoire de santé animale, 14 rue Pierre et Marie Curie, 94700 Maisons Alfort, France; (L.P.); (M.G.); (E.B.); (S.Z.); (M.T.); (D.V.); (P.D.)
| | - Maray Curiel
- National Center for Animal and Plant Health (CENSA), Carretera de Tapaste y Autopista Nacional, Apartado Postal 10, San José de las Lajas, San José de las Lajas 32700, Cuba; (A.M.A.); (M.C.); (C.L.P.); (C.D.); (Y.O.)
| | - Mathilde Gondard
- ANSES/INRAE/ENVA-UPEC, UMR 1161 Virology, Laboratoire de santé animale, 14 rue Pierre et Marie Curie, 94700 Maisons Alfort, France; (L.P.); (M.G.); (E.B.); (S.Z.); (M.T.); (D.V.); (P.D.)
| | - Emmanuel Bréard
- ANSES/INRAE/ENVA-UPEC, UMR 1161 Virology, Laboratoire de santé animale, 14 rue Pierre et Marie Curie, 94700 Maisons Alfort, France; (L.P.); (M.G.); (E.B.); (S.Z.); (M.T.); (D.V.); (P.D.)
| | - Stéphan Zientara
- ANSES/INRAE/ENVA-UPEC, UMR 1161 Virology, Laboratoire de santé animale, 14 rue Pierre et Marie Curie, 94700 Maisons Alfort, France; (L.P.); (M.G.); (E.B.); (S.Z.); (M.T.); (D.V.); (P.D.)
| | - Fabien Vorimore
- Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (F.V.); (M.-L.T.)
| | - Mai-Lan Tran
- Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (F.V.); (M.-L.T.)
| | - Mathilde Turpaud
- ANSES/INRAE/ENVA-UPEC, UMR 1161 Virology, Laboratoire de santé animale, 14 rue Pierre et Marie Curie, 94700 Maisons Alfort, France; (L.P.); (M.G.); (E.B.); (S.Z.); (M.T.); (D.V.); (P.D.)
| | - Giovanni Savini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy; (G.S.); (A.L.); (M.M.)
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy; (G.S.); (A.L.); (M.M.)
| | - Maurilia Marcacci
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy; (G.S.); (A.L.); (M.M.)
| | - Damien Vitour
- ANSES/INRAE/ENVA-UPEC, UMR 1161 Virology, Laboratoire de santé animale, 14 rue Pierre et Marie Curie, 94700 Maisons Alfort, France; (L.P.); (M.G.); (E.B.); (S.Z.); (M.T.); (D.V.); (P.D.)
| | - Pascal Dujardin
- ANSES/INRAE/ENVA-UPEC, UMR 1161 Virology, Laboratoire de santé animale, 14 rue Pierre et Marie Curie, 94700 Maisons Alfort, France; (L.P.); (M.G.); (E.B.); (S.Z.); (M.T.); (D.V.); (P.D.)
| | - Carmen Laura Perera
- National Center for Animal and Plant Health (CENSA), Carretera de Tapaste y Autopista Nacional, Apartado Postal 10, San José de las Lajas, San José de las Lajas 32700, Cuba; (A.M.A.); (M.C.); (C.L.P.); (C.D.); (Y.O.)
| | - Cristian Díaz
- National Center for Animal and Plant Health (CENSA), Carretera de Tapaste y Autopista Nacional, Apartado Postal 10, San José de las Lajas, San José de las Lajas 32700, Cuba; (A.M.A.); (M.C.); (C.L.P.); (C.D.); (Y.O.)
| | - Yalainne Obret
- National Center for Animal and Plant Health (CENSA), Carretera de Tapaste y Autopista Nacional, Apartado Postal 10, San José de las Lajas, San José de las Lajas 32700, Cuba; (A.M.A.); (M.C.); (C.L.P.); (C.D.); (Y.O.)
| | - Corinne Sailleau
- ANSES/INRAE/ENVA-UPEC, UMR 1161 Virology, Laboratoire de santé animale, 14 rue Pierre et Marie Curie, 94700 Maisons Alfort, France; (L.P.); (M.G.); (E.B.); (S.Z.); (M.T.); (D.V.); (P.D.)
| |
Collapse
|
21
|
Labutin A, Heckel G. Genome-wide support for incipient Tula hantavirus species within a single rodent host lineage. Virus Evol 2024; 10:veae002. [PMID: 38361825 PMCID: PMC10868551 DOI: 10.1093/ve/veae002] [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: 03/14/2023] [Revised: 11/08/2023] [Accepted: 01/04/2024] [Indexed: 02/17/2024] Open
Abstract
Evolutionary divergence of viruses is most commonly driven by co-divergence with their hosts or through isolation of transmission after host shifts. It remains mostly unknown, however, whether divergent phylogenetic clades within named virus species represent functionally equivalent byproducts of high evolutionary rates or rather incipient virus species. Here, we test these alternatives with genomic data from two widespread phylogenetic clades in Tula orthohantavirus (TULV) within a single evolutionary lineage of their natural rodent host, the common vole Microtus arvalis. We examined voles from forty-two locations in the contact region between clades for TULV infection by reverse transcription (RT)-PCR. Sequencing yielded twenty-three TULV Central North and twenty-one TULV Central South genomes, which differed by 14.9-18.5 per cent at the nucleotide and 2.2-3.7 per cent at the amino acid (AA) level without evidence of recombination or reassortment between clades. Geographic cline analyses demonstrated an abrupt (<1 km wide) transition between the parapatric TULV clades in continuous landscape. This transition was located within the Central mitochondrial lineage of M. arvalis, and genomic single nucleotide polymorphisms showed gradual mixing of host populations across it. Genomic differentiation of hosts was much weaker across the TULV Central North to South transition than across the nearby hybrid zone between two evolutionary lineages in the host. We suggest that these parapatric TULV clades represent functionally distinct, incipient species, which are likely differently affected by genetic polymorphisms in the host. This highlights the potential of natural viral contact zones as systems for investigating the genetic and evolutionary factors enabling or restricting the transmission of RNA viruses.
Collapse
Affiliation(s)
- Anton Labutin
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern 3012, Switzerland
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern 3012, Switzerland
| |
Collapse
|
22
|
Dall'Ara M, Guo Y, Poli D, Gilmer D, Ratti C. Analysis of the relative frequencies of the multipartite BNYVV genomic RNAs in different plants and tissues. J Gen Virol 2024; 105. [PMID: 38197877 DOI: 10.1099/jgv.0.001950] [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: 01/11/2024] Open
Abstract
Multipartite virus genomes are composed of two or more segments, each packaged into an independent viral particle. A potential advantage of multipartitism is the regulation of gene expression through changes in the segment copy number. Soil-borne beet necrotic yellow vein virus (BNYVV) is a typical example of multipartism, given its high number of genomic positive-sense RNAs (up to five). Here we analyse the relative frequencies of the four genomic RNAs of BNYVV type B during infection of different host plants (Chenopodium quinoa, Beta macrocarpa and Spinacia oleracea) and organs (leaves and roots). By successfully validating a two-step reverse-transcriptase digital droplet PCR protocol, we show that RNA1 and -2 genomic segments always replicate at low and comparable relative frequencies. In contrast, RNA3 and -4 accumulate with variable relative frequencies, resulting in distinct RNA1 : RNA2 : RNA3 : RNA4 ratios, depending on the infected host species and organ.
Collapse
Affiliation(s)
- M Dall'Ara
- DISTAL-Plant pathology, University of Bologna, Viale G. Fanin, 40, 40127 Bologna, Italy
| | - Y Guo
- DISTAL-Plant pathology, University of Bologna, Viale G. Fanin, 40, 40127 Bologna, Italy
| | - D Poli
- DISTAL-Plant pathology, University of Bologna, Viale G. Fanin, 40, 40127 Bologna, Italy
| | - D Gilmer
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, France
| | - C Ratti
- DISTAL-Plant pathology, University of Bologna, Viale G. Fanin, 40, 40127 Bologna, Italy
| |
Collapse
|
23
|
Wu Q, Kinoti WM, Habili N, Tyerman SD, Rinaldo A, Constable FE. Genetic Diversity of Grapevine Virus A in Three Australian Vineyards Using Amplicon High Throughput Sequencing (Amplicon-HTS). Viruses 2023; 16:42. [PMID: 38257742 PMCID: PMC10819895 DOI: 10.3390/v16010042] [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: 11/03/2023] [Revised: 12/18/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Shiraz disease (SD) is one of the most destructive viral diseases of grapevines in Australia and is known to cause significant economic loss to local growers. Grapevine virus A (GVA) was reported to be the key pathogen associated with this disease. This study aimed to better understand the diversity of GVA variants both within and between individual SD and grapevine leafroll disease (LRD) affected grapevines located at vineyards in South Australia. Amplicon high throughput sequencing (Amplicon-HTS) combined with median-joining networks (MJNs) was used to analyze the variability in specific gene regions of GVA variants. Several GVAII variant groups contain samples from both vineyards studied, suggesting that these GVAII variants were from a common origin. Variant groups analyzed by MJNs using the overall data set denote that there may be a possible relationship between variant groups of GVA and the geographical location of the grapevines.
Collapse
Affiliation(s)
- Qi Wu
- School of Agriculture, Food and Wine, University of Adelaide, Waite Precinct, PMB 1, Glen Osmond, SA 5064, Australia (S.D.T.)
- Australian Wine Research Institute, Wine Innovation Central Building, Hartley Grove crn Paratoo Road, Urrbrae, SA 5064, Australia
| | - Wycliff M. Kinoti
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia
| | - Nuredin Habili
- School of Agriculture, Food and Wine, University of Adelaide, Waite Precinct, PMB 1, Glen Osmond, SA 5064, Australia (S.D.T.)
- Australian Wine Research Institute, Wine Innovation Central Building, Hartley Grove crn Paratoo Road, Urrbrae, SA 5064, Australia
| | - Stephen D. Tyerman
- School of Agriculture, Food and Wine, University of Adelaide, Waite Precinct, PMB 1, Glen Osmond, SA 5064, Australia (S.D.T.)
| | - Amy Rinaldo
- Australian Wine Research Institute, Wine Innovation Central Building, Hartley Grove crn Paratoo Road, Urrbrae, SA 5064, Australia
| | - Fiona E. Constable
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3086, Australia
| |
Collapse
|
24
|
Damayo JE, McKee RC, Buchmann G, Norton AM, Ashe A, Remnant EJ. Virus replication in the honey bee parasite, Varroa destructor. J Virol 2023; 97:e0114923. [PMID: 37966226 PMCID: PMC10746231 DOI: 10.1128/jvi.01149-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/06/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE The parasitic mite Varroa destructor is a significant driver of worldwide colony losses of our most important commercial pollinator, the Western honey bee Apis mellifera. Declines in honey bee health are frequently attributed to the viruses that mites vector to honey bees, yet whether mites passively transmit viruses as a mechanical vector or actively participate in viral amplification and facilitate replication of honey bee viruses is debated. Our work investigating the antiviral RNA interference response in V. destructor demonstrates that key viruses associated with honey bee declines actively replicate in mites, indicating that they are biological vectors, and the host range of bee-associated viruses extends to their parasites, which could impact virus evolution, pathogenicity, and spread.
Collapse
Affiliation(s)
- James E. Damayo
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Rebecca C. McKee
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Gabriele Buchmann
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
- Institute of Plant Genetics, Heinrich-Heine University, Duesseldorf, Germany
| | - Amanda M. Norton
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
- Academic Support Unit, Research and Advanced Instrumentation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Alyson Ashe
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Emily J. Remnant
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| |
Collapse
|
25
|
Heymann JB. Structural Studies of Bacteriophage Φ6 and Its Transformations during Its Life Cycle. Viruses 2023; 15:2404. [PMID: 38140645 PMCID: PMC10747372 DOI: 10.3390/v15122404] [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: 10/24/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
From the first isolation of the cystovirus bacteriophage Φ6 from Pseudomonas syringae 50 years ago, we have progressed to a better understanding of the structure and transformations of many parts of the virion. The three-layered virion, encapsulating the tripartite double-stranded RNA (dsRNA) genome, breaches the cell envelope upon infection, generates its own transcripts, and coopts the bacterial machinery to produce its proteins. The generation of a new virion starts with a procapsid with a contracted shape, followed by the packaging of single-stranded RNA segments with concurrent expansion of the capsid, and finally replication to reconstitute the dsRNA genome. The outer two layers are then added, and the fully formed virion released by cell lysis. Most of the procapsid structure, composed of the proteins P1, P2, P4, and P7 is now known, as well as its transformations to the mature, packaged nucleocapsid. The outer two layers are less well-studied. One additional study investigated the binding of the host protein YajQ to the infecting nucleocapsid, where it enhances the transcription of the large RNA segment that codes for the capsid proteins. Finally, I relate the structural aspects of bacteriophage Φ6 to those of other dsRNA viruses, noting the similarities and differences.
Collapse
Affiliation(s)
- J. Bernard Heymann
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, 50 South Dr., Bethesda, MD 20892, USA; ; Tel.: +1-301-846-6924
- National Cryo-EM Program, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| |
Collapse
|
26
|
Jiang X, Wei F, He D, Niu X, Wu B, Wu Q, Tang Y, Diao Y. Co-circulation of multiple genotypes of ARV in poultry in Anhui, China. Avian Pathol 2023; 52:389-400. [PMID: 37314823 DOI: 10.1080/03079457.2023.2226081] [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: 09/01/2022] [Revised: 05/19/2023] [Accepted: 06/12/2023] [Indexed: 06/15/2023]
Abstract
ABSTRACTPoultry production in China has been experiencing a high incidence of broiler arthritis /tenosynovitis caused by avian orthoreovirus (ARV) since 2013. In the spring of 2020 severe arthritis cases from broiler flocks were identified in a large-scale commercial poultry company in Anhui Province, China. Diseased organs from dead birds were sent for diagnosis to our laboratory. ARVs, including seven broiler-isolates and two breeder-isolates, were successfully harvested and sequenced. Interestingly, the genotypes of ARVs isolated from infected chickens were inconsistent between different flocks, or even between different houses on the same flocks. Pathogenicity testing in chicks confirmed that the seven broiler-isolates were pathogenic strains, which could cause arthritis in infected chickens. Subsequently, a total of 89.66% serum samples collected from apparently healthy adult broiler flocks not vaccinated against ARV tested positive for ARV antibodies, suggesting that low and high virulence reovirus strains may be co-circulating in the farm. To this end, we collected dead embryos of unhatched chicken eggs for pathogen tracing, and the two ARV breeder-isolates isolated indicated that vertical transmission from breeders to progeny should not be underestimated for the prevalence of ARV within broiler flocks. The findings have implications for the evidenced-based formulation of prevention and control strategies.
Collapse
Affiliation(s)
- Xiaoning Jiang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong Province, People's Republic of China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong, People's Republic of China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong, People's Republic of China
| | - Feng Wei
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong Province, People's Republic of China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong, People's Republic of China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong, People's Republic of China
| | - Dalin He
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong Province, People's Republic of China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong, People's Republic of China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong, People's Republic of China
| | - Xing Niu
- Linyi Vocational University of Science and Technology, Linyi, Shandong, People's Republic of China
| | - Bingrong Wu
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong Province, People's Republic of China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong, People's Republic of China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong, People's Republic of China
| | - Qiong Wu
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong Province, People's Republic of China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong, People's Republic of China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong, People's Republic of China
| | - Yi Tang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong Province, People's Republic of China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong, People's Republic of China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong, People's Republic of China
| | - Youxiang Diao
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong Province, People's Republic of China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong, People's Republic of China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong, People's Republic of China
| |
Collapse
|
27
|
Cintron R, Whitmer SLM, Moscoso E, Campbell EM, Kelly R, Talundzic E, Mobley M, Chiu KW, Shedroff E, Shankar A, Montgomery JM, Klena JD, Switzer WM. HantaNet: A New MicrobeTrace Application for Hantavirus Classification, Genomic Surveillance, Epidemiology and Outbreak Investigations. Viruses 2023; 15:2208. [PMID: 38005885 PMCID: PMC10675615 DOI: 10.3390/v15112208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Hantaviruses zoonotically infect humans worldwide with pathogenic consequences and are mainly spread by rodents that shed aerosolized virus particles in urine and feces. Bioinformatics methods for hantavirus diagnostics, genomic surveillance and epidemiology are currently lacking a comprehensive approach for data sharing, integration, visualization, analytics and reporting. With the possibility of hantavirus cases going undetected and spreading over international borders, a significant reporting delay can miss linked transmission events and impedes timely, targeted public health interventions. To overcome these challenges, we built HantaNet, a standalone visualization engine for hantavirus genomes that facilitates viral surveillance and classification for early outbreak detection and response. HantaNet is powered by MicrobeTrace, a browser-based multitool originally developed at the Centers for Disease Control and Prevention (CDC) to visualize HIV clusters and transmission networks. HantaNet integrates coding gene sequences and standardized metadata from hantavirus reference genomes into three separate gene modules for dashboard visualization of phylogenetic trees, viral strain clusters for classification, epidemiological networks and spatiotemporal analysis. We used 85 hantavirus reference datasets from GenBank to validate HantaNet as a classification and enhanced visualization tool, and as a public repository to download standardized sequence data and metadata for building analytic datasets. HantaNet is a model on how to deploy MicrobeTrace-specific tools to advance pathogen surveillance, epidemiology and public health globally.
Collapse
Affiliation(s)
- Roxana Cintron
- Laboratory Branch, Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (A.S.); (W.M.S.)
| | - Shannon L. M. Whitmer
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (M.M.); (E.S.); (J.D.K.)
| | - Evan Moscoso
- General Dynamics Information Technology, Atlanta, GA 30329, USA; (E.M.); (R.K.)
| | - Ellsworth M. Campbell
- Laboratory Branch, Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (A.S.); (W.M.S.)
| | - Reagan Kelly
- General Dynamics Information Technology, Atlanta, GA 30329, USA; (E.M.); (R.K.)
| | - Emir Talundzic
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (M.M.); (E.S.); (J.D.K.)
| | - Melissa Mobley
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (M.M.); (E.S.); (J.D.K.)
| | - Kuo Wei Chiu
- General Dynamics Information Technology, Atlanta, GA 30329, USA; (E.M.); (R.K.)
| | - Elizabeth Shedroff
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (M.M.); (E.S.); (J.D.K.)
| | - Anupama Shankar
- Laboratory Branch, Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (A.S.); (W.M.S.)
| | - Joel M. Montgomery
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (M.M.); (E.S.); (J.D.K.)
| | - John D. Klena
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (M.M.); (E.S.); (J.D.K.)
| | - William M. Switzer
- Laboratory Branch, Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (A.S.); (W.M.S.)
| |
Collapse
|
28
|
Li W, Li R, Tang X, Cheng J, Zhan L, Shang Z, Wu J. Genomics evolution of Jingmen viruses associated with ticks and vertebrates. Genomics 2023; 115:110734. [PMID: 37890641 DOI: 10.1016/j.ygeno.2023.110734] [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: 08/30/2023] [Revised: 10/08/2023] [Accepted: 10/24/2023] [Indexed: 10/29/2023]
Abstract
Jingmen virus (JMV) associated with ticks and vertebrates have been found to be related to human disease. We obtained the genome of a Jingmen tick virus (JMTV) strain from Rhipicephalus microplus in Guizhou province and compared the genomes of seven JMV species associated with ticks and vertebrates to understand the evolutionary relationships. The topology of the phylogenetic tree of segment 1 and segment 3 is similar, and segment 2 and segment 4 formed two different topologies, with the main differences being between Alongshan virus (ALSV), Takachi virus, Yanggou tick virus and Pteropus lylei jingmen virus (PLJV), and the possibility of genetic reassortment among these viruses. Moreover, we detected recombination within JMTV and between PLJV and ALSV. The genetic reassortment and recombination that occurs during cross-species transmission of these JMV associated with ticks and vertebrates not only complicates their evolutionary relationships, but also raises the risk of these viruses to humans.
Collapse
Affiliation(s)
- Weiyi Li
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, China; Key Laboratory of Modern Pathogen Biology and Characteristics, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Rongting Li
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, China; Key Laboratory of Modern Pathogen Biology and Characteristics, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Xiaomin Tang
- Key Laboratory of Modern Pathogen Biology and Characteristics, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China; Department of Human Parasitology, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Jinzhi Cheng
- Key Laboratory of Modern Pathogen Biology and Characteristics, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China; Department of Human Parasitology, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Lin Zhan
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, China; Central Laboratory, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, China
| | - Zhengling Shang
- Department of Immunology, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Jiahong Wu
- Key Laboratory of Modern Pathogen Biology and Characteristics, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China; Department of Human Parasitology, Basic Medical College, Guizhou Medical University, Guiyang, Guizhou 550025, China.
| |
Collapse
|
29
|
Shi P, Xu Y, Zhu Z, Zhou C, Wu M, He Y, Zhao H, Liu L, Zhao L, Li X, Qin C. Manganese Mineralization of Pathogenic Viruses as a Universal Vaccine Platform. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303615. [PMID: 37867242 PMCID: PMC10667830 DOI: 10.1002/advs.202303615] [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: 06/04/2023] [Revised: 09/12/2023] [Indexed: 10/24/2023]
Abstract
Biomimetic viral mineralization improves viral vaccine stability and immunogenicity using inorganic metals such as Ca, Al, or Fe. Mn is a metal found in high concentrations in mammalian tissues; however, under natural or laboratory conditions, Mn mineralization by medical viruses has yet to be established. Herein, a single IAV particle is successfully encapsulated with manganese phosphate (MnP) under specific conditions using the human influenza A virus (IAV). MnP-mineralized IAVs (IAV@Mn) exhibited physiochemical and in vitro properties similar to Ca-mineralized IAVs. In animal models, IAV@Mn shows limited replication in immune-competent cells and a significant attenuation compared to naïve cells. Moreover, a single-dose vaccination with IAV@Mn induced robust humoral and cellular immune responses and conferred significant protection against a wild-type IAV challenge in mice. Thus, Mn mineralization in pathogenic viruses provides a rapid and universal strategy for generating an emergency vaccine in response to emerging viruses.
Collapse
Affiliation(s)
- Pan‐Deng Shi
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAcademy of Military Medical SciencesBeijing100071China
| | - Yan‐Peng Xu
- Laboratory of VirologyBeijing Key Laboratory of Etiology of Viral Diseases in ChildrenCapital Institute of PediatricsBeijing100020China
| | - Zhu Zhu
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAcademy of Military Medical SciencesBeijing100071China
- School of MedicineTsinghua UniversityBeijing100091China
| | - Chao Zhou
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAcademy of Military Medical SciencesBeijing100071China
| | - Mei Wu
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAcademy of Military Medical SciencesBeijing100071China
| | - Yangzhige He
- Department of Medical Research CenterState Key Laboratory of Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Science & Peking Union Medical CollegeBeijing100730China
| | - Hui Zhao
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAcademy of Military Medical SciencesBeijing100071China
| | - Liying Liu
- Laboratory of VirologyBeijing Key Laboratory of Etiology of Viral Diseases in ChildrenCapital Institute of PediatricsBeijing100020China
| | - Linqing Zhao
- Laboratory of VirologyBeijing Key Laboratory of Etiology of Viral Diseases in ChildrenCapital Institute of PediatricsBeijing100020China
| | - Xiao‐Feng Li
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAcademy of Military Medical SciencesBeijing100071China
| | - Cheng‐Feng Qin
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAcademy of Military Medical SciencesBeijing100071China
| |
Collapse
|
30
|
Borodavka A, Acker J. Seeing Biomolecular Condensates Through the Lens of Viruses. Annu Rev Virol 2023; 10:163-182. [PMID: 37040799 DOI: 10.1146/annurev-virology-111821-103226] [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] [Indexed: 04/13/2023]
Abstract
Phase separation of viral biopolymers is a key factor in the formation of cytoplasmic viral inclusions, known as sites of virus replication and assembly. This review describes the mechanisms and factors that affect phase separation in viral replication and identifies potential areas for future research. Drawing inspiration from studies on cellular RNA-rich condensates, we compare the hierarchical coassembly of ribosomal RNAs and proteins in the nucleolus to the coordinated coassembly of viral RNAs and proteins taking place within viral factories in viruses containing segmented RNA genomes. We highlight the common characteristics of biomolecular condensates in viral replication and how this new understanding is reshaping our views of virus assembly mechanisms. Such studies have the potential to uncover unexplored antiviral strategies targeting these phase-separated states.
Collapse
Affiliation(s)
- Alexander Borodavka
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom;
| | - Julia Acker
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom;
| |
Collapse
|
31
|
Kim EH, Park SJ. Emerging Tick-Borne Dabie bandavirus: Virology, Epidemiology, and Prevention. Microorganisms 2023; 11:2309. [PMID: 37764153 PMCID: PMC10536723 DOI: 10.3390/microorganisms11092309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/09/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Severe Fever with Thrombocytopenia Syndrome (SFTS), caused by Dabie bandavirus (SFTSV), is an emerging infectious disease first identified in China. Since its discovery, infections have spread throughout East Asian countries primarily through tick bites but also via transmission between animals and humans. The expanding range of ticks, the primary vectors for SFTSV, combined with migration patterns of tick-carrying birds, sets the stage for the global spread of this virus. SFTSV rapidly evolves due to continuous mutation and reassortment; currently, no approved vaccines or antiviral drugs are available. Thus, the threat this virus poses to global health is unmistakable. This review consolidates the most recent research on SFTSV, including its molecular characteristics, transmission pathways through ticks and other animals, as well as the progress in antiviral drug and vaccine development, encompassing animal models and clinical trials.
Collapse
Affiliation(s)
- Eun-Ha Kim
- Center for Study of Emerging and Re-Emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea;
| | - Su-Jin Park
- Division of Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| |
Collapse
|
32
|
Degiuseppe JI, Martelli A, Barrios Mathieur C, Stupka JA. Genetic diversity of rotavirus A in Argentina during 2019-2022: detection of G6 strains and insights regarding its dissemination. Arch Virol 2023; 168:251. [PMID: 37702836 DOI: 10.1007/s00705-023-05874-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/11/2023] [Indexed: 09/14/2023]
Abstract
One of the challenges associated with introducing a vaccine is monitoring its impact through clinical and molecular surveillance. The aims of this study were to analyze the genetic diversity of rotavirus A in Argentina between 2019 and 2022 and to assess the phylogenetic and phylodynamic features of the unusual G6 strains detected. A significant decline in the Wa-like genogroup strains was observed, and G6 strains were detected for the first time in Argentina, in association with P[8] and P[9]. Spatiotemporal analysis showed that the G6-lineage I strains detected recently in Argentina and Brazil might have emerged from European strains. This study provides recent evidence of the genetic diversity of rotaviruses in isolated cases. It is considered important to support continuous surveillance of rotavirus in the post-vaccine scenario, mainly to evaluate potential changes that may occur after the COVID-19 pandemic.
Collapse
Affiliation(s)
- Juan Ignacio Degiuseppe
- Argentine Reference Laboratory for Rotavirus and Norovirus, INEI-ANLIS "Dr. Carlos G. Malbrán", Avenida Vélez Sársfield 563, Buenos Aires, Argentina.
| | - Antonella Martelli
- Laboratory of Clinical Virology, Centro de Educación Médica e Investigaciones Clínicas "Dr. Norberto Quirno" (CEMIC), Galván 4102, Buenos Aires, Argentina
| | - Christian Barrios Mathieur
- Argentine Reference Laboratory for Rotavirus and Norovirus, INEI-ANLIS "Dr. Carlos G. Malbrán", Avenida Vélez Sársfield 563, Buenos Aires, Argentina
| | - Juan Andrés Stupka
- Argentine Reference Laboratory for Rotavirus and Norovirus, INEI-ANLIS "Dr. Carlos G. Malbrán", Avenida Vélez Sársfield 563, Buenos Aires, Argentina
| |
Collapse
|
33
|
Jaccard A, Dubuis N, Kellenberger I, Brodard J, Schnee S, Gindro K, Schumpp O. New viruses of Cladosporium sp. expand considerably the taxonomic structure of Gammapartitivirus genus. J Gen Virol 2023; 104:001879. [PMID: 37549001 PMCID: PMC10539651 DOI: 10.1099/jgv.0.001879] [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: 06/13/2023] [Accepted: 07/25/2023] [Indexed: 08/08/2023] Open
Abstract
Despite the fact that Cladosporium sp. are ubiquitous fungi, their viromes have been little studied. By analysing a collection of Cladosporium fungi, two new partitiviruses named Cladosporium cladosporioides partitivirus 1 (CcPV1) and Cladosporium cladosporioides partitivirus 2 (CcPV2) co-infecting a strain of Cladosporium cladosporioides were identified. Their complete genome consists of two monocistronic dsRNA segments (RNA1 and RNA2) with a high percentage of pairwise identity on 5' and 3' end. The RNA directed RNA polymerase (RdRp) of both viruses and the capsid protein (CP) of CcPV1 display the classic characteristics required for their assignment to the Gammapartitivirus genus. In contrast, CcPV2 RNA2 encodes for a 41 KDa CP that is unusually smaller when aligned to CPs of other viruses classified in this genus. The structural role of this protein is confirmed by electrophoresis on acrylamide gel of purified viral particles. Despite the low percentage of identity between the capsid proteins of CcPV1 and CcPV2, their three-dimensional structures predicted by AlphaFold2 show strong similarities and confirm functional proximity. Fifteen similar viral sequences of unknown function were annotated using the CcPV2 CP sequence. The phylogeny of the CP was highly consistent with the phylogeny of their corresponding RdRp, supporting the organization of Gammapartitiviruses into three distinct clades despite stretching the current demarcation criteria. It is proposed that a new subgenus be created within the genus Gammapartitivirus for this new group.
Collapse
Affiliation(s)
| | - Nathalie Dubuis
- Department of Plant Protection, Agroscope, Nyon, Switzerland
| | | | - Justine Brodard
- Department of Plant Protection, Agroscope, Nyon, Switzerland
| | - Sylvain Schnee
- Department of Plant Protection, Agroscope, Nyon, Switzerland
| | - Katia Gindro
- Department of Plant Protection, Agroscope, Nyon, Switzerland
| | - Olivier Schumpp
- Department of Plant Protection, Agroscope, Nyon, Switzerland
| |
Collapse
|
34
|
Garcia ML, Danthi P. The Reovirus σ1 Attachment Protein Influences the Stability of Its Entry Intermediate. J Virol 2023; 97:e0058523. [PMID: 37167564 PMCID: PMC10231251 DOI: 10.1128/jvi.00585-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/13/2023] Open
Abstract
Structural metastability of viral capsids is pivotal for viruses to survive in harsh environments and to undergo timely conformational changes required for cell entry. Mammalian orthoreovirus (reovirus) is a model to study capsid metastability. Following initial disassembly of the reovirus particle mediated by proteases, a metastable intermediate called the infectious subvirion particle (ISVP) is generated. Using a σ1 monoreassortant virus, we recently showed that σ1 properties affect its encapsidation on particles and the metastability of ISVPs. How metastability is impacted by σ1 and whether the lower encapsidation level of σ1 is connected to this property is unknown. To define a correlation between encapsidation of σ1 and ISVP stability, we generated mutant viruses with single amino acid polymorphisms in σ1 or those that contain chimeric σ1 molecules composed of σ1 portions from type 1 and type 3 reovirus strains. We found that under most conditions where σ1 encapsidation on the particle was lower, ISVPs displayed lower stability. Characterization of mutant viruses selected for enhanced stability via a forward genetic approach also revealed that in some cases, σ1 properties influence stability without influencing σ1 encapsidation. These data indicate that σ1 can also influence ISVP stability independent of its level of incorporation. Together, our work reveals an underappreciated effect of the σ1 attachment protein on the properties of the reovirus capsid. IMPORTANCE Reovirus particles are comprised of eight proteins. Among them, the reovirus σ1 protein functions engages cellular receptors. σ1 also influences the stability of an entry intermediate called ISVP. Here, we sought to define the basis of the link between σ1 properties and stability of ISVPs. Using variety of mutant strains, we determined that when virus preparations contain particles with a high amount of encapsidated σ1, ISVP stability is higher. Additionally, we identified portions of σ1 that impact its encapsidation and consequently the stability of ISVPs. We also determined that in some cases, σ1 properties alter stability of ISVPs without affecting encapsidation. This work highlights that proteins of these complex particles are arranged in an intricate, interconnected manner such that changing the properties of these proteins has a profound impact on the remainder of the particle.
Collapse
Affiliation(s)
| | - Pranav Danthi
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| |
Collapse
|
35
|
Kunić V, Mikuletič T, Kogoj R, Koritnik T, Steyer A, Šoprek S, Tešović G, Konjik V, Roksandić Križan I, Prišlin M, Jemeršić L, Brnić D. Interspecies transmission of porcine-originated G4P[6] rotavirus A between pigs and humans: a synchronized spatiotemporal approach. Front Microbiol 2023; 14:1194764. [PMID: 37283926 PMCID: PMC10239803 DOI: 10.3389/fmicb.2023.1194764] [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: 03/27/2023] [Accepted: 04/25/2023] [Indexed: 06/08/2023] Open
Abstract
As a leading viral cause of acute gastroenteritis in both humans and pigs, rotavirus A (RVA) poses a potential public health concern. Although zoonotic spillover of porcine RVA strains to humans is sporadic, it has been detected worldwide. The origin of chimeric human-animal strains of RVA is closely linked to the crucial role of mixed genotypes in driving reassortment and homologous recombination, which play a major role in shaping the genetic diversity of RVA. To better understand how genetically intertwined porcine and zoonotic human-derived G4P[6] RVA strains are, the present study employed a spatiotemporal approach to whole-genome characterization of RVA strains collected during three consecutive RVA seasons in Croatia (2018-2021). Notably, sampled children under 2 years of age and weanling piglets with diarrhea were included in the study. In addition to samples tested by real-time RT-PCR, genotyping of VP7 and VP4 gene segments was conducted. The unusual genotype combinations detected in the initial screening, including three human and three porcine G4P[6] strains, were subjected to next-generation sequencing, followed by phylogenetic analysis of all gene segments, and intragenic recombination analysis. Results showed a porcine or porcine-like origin for each of the eleven gene segments in all six RVA strains. The G4P[6] RVA strains detected in children most likely resulted from porcine-to-human interspecies transmission. Furthermore, the genetic diversity of Croatian porcine and porcine-like human G4P[6] strains was propelled by reassortment events between porcine and porcine-like human G4P[6] RVA strains, along with homologous intragenotype and intergenotype recombinations in VP4, NSP1, and NSP3 segments. Described concurrent spatiotemporal approach in investigating autochthonous human and animal RVA strains is essential in drawing relevant conclusions about their phylogeographical relationship. Therefore, continuous surveillance of RVA, following the One Health principles, may provide relevant data for assessing the impact on the protectiveness of currently available vaccines.
Collapse
Affiliation(s)
- Valentina Kunić
- Virology Department, Croatian Veterinary Institute, Zagreb, Croatia
| | - Tina Mikuletič
- School of Medicine, Institute for Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - Rok Kogoj
- School of Medicine, Institute for Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - Tom Koritnik
- Public Health Microbiology Department, National Laboratory of Health, Environment, and Food, Ljubljana, Slovenia
| | - Andrej Steyer
- Public Health Microbiology Department, National Laboratory of Health, Environment, and Food, Ljubljana, Slovenia
| | - Silvija Šoprek
- Department for Pediatric Infectious Diseases, University Hospital for Infectious Diseases “Dr. Fran Mihaljević”, Zagreb, Croatia
| | - Goran Tešović
- Department for Pediatric Infectious Diseases, University Hospital for Infectious Diseases “Dr. Fran Mihaljević”, Zagreb, Croatia
- School of Medicine, University of Zagreb, Zagreb, Croatia
| | | | | | - Marina Prišlin
- Virology Department, Croatian Veterinary Institute, Zagreb, Croatia
| | - Lorena Jemeršić
- Virology Department, Croatian Veterinary Institute, Zagreb, Croatia
| | - Dragan Brnić
- Virology Department, Croatian Veterinary Institute, Zagreb, Croatia
| |
Collapse
|
36
|
Liu B, Zhu J, He T, Zhang Z. Genetic variants of Dabie bandavirus: classification and biological/clinical implications. Virol J 2023; 20:68. [PMID: 37060090 PMCID: PMC10103499 DOI: 10.1186/s12985-023-02033-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/07/2023] [Indexed: 04/16/2023] Open
Abstract
Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease caused by Dabie bandavirus (DBV), a novel Bandavirus in the family Phenuiviridae. The first case of SFTS was reported in China, followed by cases in Japan, South Korea, Taiwan and Vietnam. With clinical manifestations including fever, leukopenia, thrombocytopenia, and gastrointestinal symptoms, SFTS has a fatality rate of approximately 10%. In recent years, an increasing number of viral strains have been isolated and sequenced, and several research groups have attempted to classify the different genotypes of DBV. Additionally, accumulating evidence indicates certain correlations between the genetic makeup and biological/clinical manifestations of the virus. Here, we attempted to evaluate the genetic classification of different groups, align the genotypic nomenclature in different studies, summarize the distribution of different genotypes, and review the biological and clinical implications of DBV genetic variations.
Collapse
Affiliation(s)
- Bingyan Liu
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Furong Road 678, Hefei, 230601, China
| | - Jie Zhu
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Furong Road 678, Hefei, 230601, China
| | - Tengfei He
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Furong Road 678, Hefei, 230601, China
| | - Zhenhua Zhang
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Furong Road 678, Hefei, 230601, China.
| |
Collapse
|
37
|
Wang S, Liang B, Wang W, Li L, Feng N, Zhao Y, Wang T, Yan F, Yang S, Xia X. Viral vectored vaccines: design, development, preventive and therapeutic applications in human diseases. Signal Transduct Target Ther 2023; 8:149. [PMID: 37029123 PMCID: PMC10081433 DOI: 10.1038/s41392-023-01408-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/06/2023] [Accepted: 03/14/2023] [Indexed: 04/09/2023] Open
Abstract
Human diseases, particularly infectious diseases and cancers, pose unprecedented challenges to public health security and the global economy. The development and distribution of novel prophylactic and therapeutic vaccines are the prioritized countermeasures of human disease. Among all vaccine platforms, viral vector vaccines offer distinguished advantages and represent prominent choices for pathogens that have hampered control efforts based on conventional vaccine approaches. Currently, viral vector vaccines remain one of the best strategies for induction of robust humoral and cellular immunity against human diseases. Numerous viruses of different families and origins, including vesicular stomatitis virus, rabies virus, parainfluenza virus, measles virus, Newcastle disease virus, influenza virus, adenovirus and poxvirus, are deemed to be prominent viral vectors that differ in structural characteristics, design strategy, antigen presentation capability, immunogenicity and protective efficacy. This review summarized the overall profile of the design strategies, progress in advance and steps taken to address barriers to the deployment of these viral vector vaccines, simultaneously highlighting their potential for mucosal delivery, therapeutic application in cancer as well as other key aspects concerning the rational application of these viral vector vaccines. Appropriate and accurate technological advances in viral vector vaccines would consolidate their position as a leading approach to accelerate breakthroughs in novel vaccines and facilitate a rapid response to public health emergencies.
Collapse
Affiliation(s)
- Shen Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Bo Liang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Weiqi Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - Ling Li
- China National Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Na Feng
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yongkun Zhao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Tiecheng Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Feihu Yan
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.
| | - Songtao Yang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.
| | - Xianzhu Xia
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.
| |
Collapse
|
38
|
Wasberg A, Faria IR, Bergholm J, Petric PP, Mostafa A, Pleschka S, Schwemmle M, Lundkvist Å, Ellström P, Naguib MM. Assessing compatibility and viral fitness between poultry-adapted H9N2 and wild bird-derived neuraminidases. Sci Rep 2023; 13:4476. [PMID: 36934147 PMCID: PMC10024770 DOI: 10.1038/s41598-023-31653-1] [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: 01/16/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Exchange of viral segments between one or more influenza virus subtypes can contribute to a shift in virulence and adaptation to new hosts. Among several influenza subtypes, H9N2 is widely circulating in poultry populations worldwide and has the ability to infect humans. Here, we studied the reassortant compatibility between chicken H9N2 with N1-N9 gene segments of wild bird origin, either with an intact or truncated stalk. Naturally occurring amino acid deletions in the NA stalk of the influenza virus can lead to increased virulence in both mallard ducks and chickens. Our findings show extended genetic compatibility between chicken H9Nx gene segments and the wild-bird NA with and without 20 amino acid stalk deletion. Replication kinetics in avian, mammalian and human cell lines revealed that parental chH9N2 and rH9N6 viruses with intact NA-stalk replicated significantly better in avian DF1 cells compared to human A549 cells. After introducing a stalk deletion, an enhanced preference for replication in mammalian and human cell lines could be observed for rH9N2Δ(H6), rH9N6Δ and rH9N9Δ compared to the parental chH9N2 virus. This highlights the potential emergence of novel viruses with variable phenotypic traits, warranting the continuous monitoring of H9N2 and co-circulating subtypes in avian hosts.
Collapse
Affiliation(s)
- Anishia Wasberg
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Inês R Faria
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Julia Bergholm
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07, Uppsala, Sweden
| | - Philipp P Petric
- Institute of Virology, Medical Center, University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
| | - Stephan Pleschka
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF),partner site Giessen-Marburg-Langen, Giessen, Germany
| | - Martin Schwemmle
- Institute of Virology, Medical Center, University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Åke Lundkvist
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Patrik Ellström
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Mahmoud M Naguib
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
| |
Collapse
|
39
|
Strain-Specific Interactions between the Viral Capsid Proteins VP4, VP7 and VP6 Influence Rescue of Rotavirus Reassortants by Reverse Genetics. Int J Mol Sci 2023; 24:ijms24065670. [PMID: 36982745 PMCID: PMC10054668 DOI: 10.3390/ijms24065670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/06/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
Rotavirus A (RVA) genome segments can reassort upon co-infection of target cells with two different RVA strains. However, not all reassortants are viable, which limits the ability to generate customized viruses for basic and applied research. To gain insight into the factors that restrict reassortment, we utilized reverse genetics and tested the generation of simian RVA strain SA11 reassortants carrying the human RVA strain Wa capsid proteins VP4, VP7, and VP6 in all possible combinations. VP7-Wa, VP6-Wa, and VP7/VP6-Wa reassortants were effectively rescued, but the VP4-Wa, VP4/VP7-Wa, and VP4/VP6-Wa reassortants were not viable, suggesting a limiting effect of VP4-Wa. However, a VP4/VP7/VP6-Wa triple-reassortant was successfully generated, indicating that the presence of homologous VP7 and VP6 enabled the incorporation of VP4-Wa into the SA11 backbone. The replication kinetics of the triple-reassortant and its parent strain Wa were comparable, while the replication of all other rescued reassortants was similar to SA11. Analysis of the predicted structural protein interfaces identified amino acid residues, which might influence protein interactions. Restoring the natural VP4/VP7/VP6 interactions may therefore improve the rescue of RVA reassortants by reverse genetics, which could be useful for the development of next generation RVA vaccines.
Collapse
|
40
|
Diller JR, Thoner TW, Ogden KM. Mammalian orthoreoviruses exhibit rare genotype variability in genome constellations. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 110:105421. [PMID: 36871695 PMCID: PMC10112866 DOI: 10.1016/j.meegid.2023.105421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/21/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
Mammalian orthoreoviruses (reoviruses) are currently classified based on properties of the attachment protein, σ1. Four reovirus serotypes have been identified, three of which are represented by well-studied prototype human reovirus strains. Reoviruses contain ten segments of double-stranded RNA that encode 12 proteins and can reassort during coinfection. To understand the breadth of reovirus genetic diversity and its potential influence on reassortment, the sequence of the entire genome should be considered. While much is known about the prototype strains, a thorough analysis of all ten reovirus genome segment sequences has not previously been conducted. We analyzed phylogenetic relationships and nucleotide sequence conservation for each of the ten segments of more than 60 complete or nearly complete reovirus genome sequences, including those of the prototype strains. Using these relationships, we defined genotypes for each segment, with minimum nucleotide identities of 77-88% for most genotypes that contain several representative sequences. We applied segment genotypes to determine reovirus genome constellations, and we propose implementation of an updated reovirus genome classification system that incorporates genotype information for each segment. For most sequenced reoviruses, segments other than S1, which encodes σ1, cluster into a small number of genotypes and a limited array of genome constellations that do not differ greatly over time or based on animal host. However, a small number of reoviruses, including prototype strain Jones, have constellations in which segment genotypes differ from those of most other sequenced reoviruses. For these reoviruses, there is little evidence of reassortment with the major genotype. Future basic research studies that focus on the most genetically divergent reoviruses may provide new insights into reovirus biology. Analysis of available partial sequences and additional complete reovirus genome sequencing may also reveal reassortment biases, host preferences, or infection outcomes that are based on reovirus genotype.
Collapse
Affiliation(s)
- Julia R Diller
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Timothy W Thoner
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kristen M Ogden
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
| |
Collapse
|
41
|
Taylor KY, Agu I, José I, Mäntynen S, Campbell AJ, Mattson C, Chou TW, Zhou B, Gresham D, Ghedin E, Díaz Muñoz SL. Influenza A virus reassortment is strain dependent. PLoS Pathog 2023; 19:e1011155. [PMID: 36857394 PMCID: PMC10010518 DOI: 10.1371/journal.ppat.1011155] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/13/2023] [Accepted: 01/26/2023] [Indexed: 03/02/2023] Open
Abstract
RNA viruses can exchange genetic material during coinfection, an interaction that creates novel strains with implications for viral evolution and public health. Influenza A viral genetic exchange can occur when genome segments from distinct strains reassort in coinfected cells. Predicting potential genomic reassortment between influenza strains has been a long-standing goal. Experimental coinfection studies have shed light on factors that limit or promote reassortment. However, determining the reassortment potential between diverse Influenza A strains has remained elusive. To address this challenge, we developed a high throughput genotyping approach to quantify reassortment among a diverse panel of human influenza virus strains encompassing two pandemics (swine and avian origin), three specific epidemics, and both circulating human subtypes A/H1N1 and A/H3N2. We found that reassortment frequency (the proportion of reassortants generated) is an emergent property of specific pairs of strains where strain identity is a predictor of reassortment frequency. We detect little evidence that antigenic subtype drives reassortment as intersubtype (H1N1xH3N2) and intrasubtype reassortment frequencies were, on average, similar. Instead, our data suggest that certain strains bias the reassortment frequency up or down, independently of the coinfecting partner. We observe that viral productivity is also an emergent property of coinfections, but uncorrelated to reassortment frequency; thus viral productivity is a separate factor affecting the total number of reassortants produced. Assortment of individual segments among progeny and pairwise segment combinations within progeny generally favored homologous combinations. These outcomes were not related to strain similarity or shared subtype but reassortment frequency was closely correlated to the proportion of both unique genotypes and of progeny with heterologous pairwise segment combinations. We provide experimental evidence that viral genetic exchange is potentially an individual social trait subject to natural selection, which implies the propensity for reassortment is not evenly shared among strains. This study highlights the need for research incorporating diverse strains to discover the traits that shift the reassortment potential to realize the goal of predicting influenza virus evolution resulting from segment exchange.
Collapse
Affiliation(s)
- Kishana Y. Taylor
- Department of Microbiology and Molecular Genetics University of California, Davis Davis, California
| | - Ilechukwu Agu
- Department of Microbiology and Molecular Genetics University of California, Davis Davis, California
| | - Ivy José
- Department of Microbiology and Molecular Genetics University of California, Davis Davis, California
| | - Sari Mäntynen
- Department of Microbiology and Molecular Genetics University of California, Davis Davis, California
| | - A. J. Campbell
- Department of Microbiology and Molecular Genetics University of California, Davis Davis, California
| | - Courtney Mattson
- Department of Microbiology and Molecular Genetics University of California, Davis Davis, California
| | - Tsui-Wen Chou
- Center for Genomics and Systems Biology + Department of Biology New York University New York, United States of America
| | - Bin Zhou
- Center for Genomics and Systems Biology + Department of Biology New York University New York, United States of America
| | - David Gresham
- Center for Genomics and Systems Biology + Department of Biology New York University New York, United States of America
| | - Elodie Ghedin
- Center for Genomics and Systems Biology + Department of Biology New York University New York, United States of America
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, United States of America
| | - Samuel L. Díaz Muñoz
- Department of Microbiology and Molecular Genetics University of California, Davis Davis, California
- Genome Center University of California, Davis Davis, California
- * E-mail:
| |
Collapse
|
42
|
Whitlock AOB, Bird BH, Ghersi B, Davison AJ, Hughes J, Nichols J, Vučak M, Amara E, Bangura J, Lavalie EG, Kanu MC, Kanu OT, Sjodin A, Remien CH, Nuismer SL. Identifying the genetic basis of viral spillover using Lassa virus as a test case. ROYAL SOCIETY OPEN SCIENCE 2023; 10:221503. [PMID: 36968239 PMCID: PMC10031424 DOI: 10.1098/rsos.221503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
The rate at which zoonotic viruses spill over into the human population varies significantly over space and time. Remarkably, we do not yet know how much of this variation is attributable to genetic variation within viral populations. This gap in understanding arises because we lack methods of genetic analysis that can be easily applied to zoonotic viruses, where the number of available viral sequences is often limited, and opportunistic sampling introduces significant population stratification. Here, we explore the feasibility of using patterns of shared ancestry to correct for population stratification, enabling genome-wide association methods to identify genetic substitutions associated with spillover into the human population. Using a combination of phylogenetically structured simulations and Lassa virus sequences collected from humans and rodents in Sierra Leone, we demonstrate that existing methods do not fully correct for stratification, leading to elevated error rates. We also demonstrate, however, that the Type I error rate can be substantially reduced by confining the analysis to a less-stratified region of the phylogeny, even in an already-small dataset. Using this method, we detect two candidate single-nucleotide polymorphisms associated with spillover in the Lassa virus polymerase gene and provide generalized recommendations for the collection and analysis of zoonotic viruses.
Collapse
Affiliation(s)
| | - Brian H. Bird
- One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Bruno Ghersi
- One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | | | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Jenna Nichols
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Matej Vučak
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Emmanuel Amara
- University of Makeni and University of California, Davis One Health Program, Makeni, Sierra Leone
| | - James Bangura
- University of Makeni and University of California, Davis One Health Program, Makeni, Sierra Leone
| | - Edwin G. Lavalie
- University of Makeni and University of California, Davis One Health Program, Makeni, Sierra Leone
| | - Marilyn C. Kanu
- University of Makeni and University of California, Davis One Health Program, Makeni, Sierra Leone
| | - Osman T. Kanu
- University of Makeni and University of California, Davis One Health Program, Makeni, Sierra Leone
| | - Anna Sjodin
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Christopher H. Remien
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID, USA
| | - Scott L. Nuismer
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| |
Collapse
|
43
|
Hellert J, Aebischer A, Haouz A, Guardado-Calvo P, Reiche S, Beer M, Rey FA. Structure, function, and evolution of the Orthobunyavirus membrane fusion glycoprotein. Cell Rep 2023; 42:112142. [PMID: 36827185 DOI: 10.1016/j.celrep.2023.112142] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/29/2022] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
La Crosse virus, responsible for pediatric encephalitis in the United States, and Schmallenberg virus, a highly teratogenic veterinary virus in Europe, belong to the large Orthobunyavirus genus of zoonotic arthropod-borne pathogens distributed worldwide. Viruses in this under-studied genus cause CNS infections or fever with debilitating arthralgia/myalgia syndromes, with no effective treatment. The main surface antigen, glycoprotein Gc (∼1,000 residues), has a variable N-terminal half (GcS) targeted by the patients' antibody response and a conserved C-terminal moiety (GcF) responsible for membrane fusion during cell entry. Here, we report the X-ray structure of post-fusion La Crosse and Schmallenberg virus GcF, revealing the molecular determinants for hairpin formation and trimerization required to drive membrane fusion. We further experimentally confirm the role of residues in the fusion loops and in a vestigial endoplasmic reticulum (ER) translocation sequence at the GcS-GcF junction. The resulting knowledge provides essential molecular underpinnings for future development of potential therapeutic treatments and vaccines.
Collapse
Affiliation(s)
- Jan Hellert
- Structural Virology Unit, Institut Pasteur - Université Paris-Cité, CNRS UMR 3569, 25-28 rue du Dr. Roux, 75015 Paris, France; Centre for Structural Systems Biology (CSSB), Leibniz-Institut für Virologie (LIV), Notkestraße 85, 22607 Hamburg, Germany
| | - Andrea Aebischer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald, Germany; Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald, Germany
| | - Ahmed Haouz
- Crystallography Platform C2RT, Institut Pasteur, CNRS UMR 3528, 25-28 rue du Dr. Roux, 75015 Paris, France
| | - Pablo Guardado-Calvo
- Structural Virology Unit, Institut Pasteur - Université Paris-Cité, CNRS UMR 3569, 25-28 rue du Dr. Roux, 75015 Paris, France
| | - Sven Reiche
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald, Germany.
| | - Félix A Rey
- Structural Virology Unit, Institut Pasteur - Université Paris-Cité, CNRS UMR 3569, 25-28 rue du Dr. Roux, 75015 Paris, France.
| |
Collapse
|
44
|
Zhao M, Plough LV, Behringer DC, Bojko J, Kough AS, Alper NW, Xu L, Schott EJ. Cross-Hemispheric Genetic Diversity and Spatial Genetic Structure of Callinectes sapidus Reovirus 1 (CsRV1). Viruses 2023; 15:v15020563. [PMID: 36851777 PMCID: PMC9962310 DOI: 10.3390/v15020563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The movement of viruses in aquatic systems is rarely studied over large geographic scales. Oceanic currents, host migration, latitude-based variation in climate, and resulting changes in host life history are all potential drivers of virus connectivity, adaptation, and genetic structure. To expand our understanding of the genetic diversity of Callinectes sapidus reovirus 1 (CsRV1) across a broad spatial and host life history range of its blue crab host (Callinectes sapidus), we obtained 22 complete and 96 partial genomic sequences for CsRV1 strains from the US Atlantic coast, Gulf of Mexico, Caribbean Sea, and the Atlantic coast of South America. Phylogenetic analyses of CsRV1 genomes revealed that virus genotypes were divided into four major genogroups consistent with their host geographic origins. However, some CsRV1 sequences from the US mid-Atlantic shared high genetic similarity with the Gulf of Mexico genotypes, suggesting potential human-mediated movement of CsRV1 between the US mid-Atlantic and Gulf coasts. This study advances our understanding of how climate, coastal geography, host life history, and human activity drive patterns of genetic structure and diversity of viruses in marine animals and contributes to the capacity to infer broadscale host population connectivity in marine ecosystems from virus population genetic data.
Collapse
Affiliation(s)
- Mingli Zhao
- Institute of Marine and Environmental Technology, University of Maryland Baltimore County, Baltimore, MD 21202, USA
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London AL9 7TA, UK
| | - Louis V. Plough
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD 21613, USA
| | - Donald C. Behringer
- Fisheries and Aquatic Sciences, University of Florida, Gainesville, FL 32653, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32608, USA
| | - Jamie Bojko
- School of Health and Life Sciences, Teesside University, Middlesbrough TS1 3BA, UK
| | - Andrew S. Kough
- John G. Shedd Aquarium, Haerther Center for Conservation Research, Chicago, IL 60605, USA
| | - Nathaniel W. Alper
- Baltimore Polytechnic Institute, Columbia University, New York, NY 20027, USA
| | - Lan Xu
- Department of Marine Biotechnology and Institute of Marine and Environmental Technology, University of Maryland, Baltimore County, Baltimore, MD 21202, USA
| | - Eric J. Schott
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
- Correspondence:
| |
Collapse
|
45
|
Foster JE, López K, Eastwood G, Guzman H, Carrington CVF, Tesh RB, Auguste AJ. Phylogenetic characterization of Orthobunyaviruses isolated from Trinidad shows evidence of natural reassortment. Virus Genes 2023; 59:473-478. [PMID: 36763228 DOI: 10.1007/s11262-023-01973-5] [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: 10/18/2022] [Accepted: 01/29/2023] [Indexed: 02/11/2023]
Abstract
The genus Orthobunyavirus is a diverse group of viruses in the family Peribunyaviridae, recently classified into 20 serogroups, and 103 virus species. Although most viruses within these serogroups are phylogenetically distinct, the absence of complete genome sequences has left several viruses incompletely characterized. Here we report the complete genome sequences for 11 orthobunyaviruses isolated from Trinidad, French Guiana, Guatemala, and Panama that were serologically classified into six serogroups and 10 species. Phylogenetic analyses of these 11 newly derived sequences indicate that viruses belonging to the Patois, Capim, Guama, and Group C serocomplexes all have a close genetic origin. We show that three of the 11 orthobunyaviruses characterized (belonging to the Group C and Bunyamwera serogroups) have evidence of histories of natural reassortment through the M genome segment. Our data also suggests that two distinct lineages of Group C viruses concurrently circulate in Trinidad and are transmitted by the same mosquito vectors. This study also highlights the importance of complementing serological identification with nucleotide sequencing when characterizing orthobunyaviruses.
Collapse
Affiliation(s)
- Jerome E Foster
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Krisangel López
- Department of Entomology, College of Agriculture and Life Sciences, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Gillian Eastwood
- Department of Entomology, College of Agriculture and Life Sciences, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.,Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.,Global Change Center at Virginia Tech, Blacksburg, VA, 24061, USA
| | - Hilda Guzman
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Christine V F Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago
| | - Robert B Tesh
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Albert J Auguste
- Department of Entomology, College of Agriculture and Life Sciences, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA. .,Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
| |
Collapse
|
46
|
Reddy MV, Gupta V, Nayak A, Tiwari SP. Picobirnaviruses in animals: a review. Mol Biol Rep 2023; 50:1785-1797. [PMID: 36462086 PMCID: PMC9734933 DOI: 10.1007/s11033-022-08133-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/16/2022] [Indexed: 12/04/2022]
Abstract
Picobirnaviruses (PBVs) are small non enveloped viruses with bi-segmented ds RNA. They have been observed in a wide variety of vertebrates, including mammals and birds with or without diarrhoea, as well as in sewage samples since its discovery (1988). The source of the viruses is uncertain. True hosts of PBVs and their role as primary pathogens or secondary opportunistic agents or innocuous viruses in the gut remains alien. The mechanisms by which they play a role in pathogenicity are still unclear based on the fact that they can be found in both symptomatic and asymptomatic cases. There is a need to determine their tropism since they have not only been associated with viral gastroenteritis but also been reported in the respiratory tracts of pigs. As zoonotic agents with diverse hosts, the importance of epidemiological and surveillance studies cannot be overstated. The segmented genome of PBV might pose a serious public health issue because of the possibility of continuous genetic reassortment. Aware of the growing attention being given to emerging RNA viruses, we reviewed the current knowledge on PBVs and described the current status of PBVs in animals.
Collapse
Affiliation(s)
- Mareddy Vineetha Reddy
- Department of Veterinary Microbiology, College of Veterinary Science & Animal Husbandry, Nanaji Deshmukh Veterinary Science University, Jabalpur, M.P India
| | - Vandana Gupta
- Department of Veterinary Microbiology, College of Veterinary Science & Animal Husbandry, Nanaji Deshmukh Veterinary Science University, Jabalpur, M.P India
| | - Anju Nayak
- Department of Veterinary Microbiology, College of Veterinary Science & Animal Husbandry, Nanaji Deshmukh Veterinary Science University, Jabalpur, M.P India
| | | |
Collapse
|
47
|
Molecular Engineering of a Mammarenavirus with Unbreachable Attenuation. J Virol 2023; 97:e0138522. [PMID: 36533953 PMCID: PMC9888291 DOI: 10.1128/jvi.01385-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Several mammarenaviruses cause severe hemorrhagic fever (HF) disease in humans and pose important public health problems in their regions of endemicity. There are no United States (US) Food and Drug Administration (FDA)-approved mammarenavirus vaccines, and current anti-mammarenavirus therapy is limited to an off-label use of ribavirin that has limited efficacy. Mammarenaviruses are enveloped viruses with a bi-segmented negative-strand RNA genome. Each genome segment contains two open reading frames (ORF) separated by a noncoding intergenic region (IGR). The large (L) segment encodes the RNA dependent RNA polymerase, L protein, and the Z matrix protein, whereas the small (S) segment encodes the surface glycoprotein precursor (GPC) and nucleoprotein (NP). In the present study, we document the generation of a recombinant form of the prototypic mammarenavirus lymphocytic choriomeningitis virus (LCMV) expressing a codon deoptimized (CD) GPC and containing the IGR of the S segment in both the S and L segments (rLCMV/IGR-CD). We show that rLCMV/IGR-CD is fully attenuated in C57BL/6 (B6) mice but able to provide complete protection upon a single administration against a lethal challenge with LCMV. Importantly, rLCMV/IGR-CD exhibited an unbreachable attenuation for its safe implementation as a live-attenuated vaccine (LAV). IMPORTANCE Several mammarenaviruses cause severe disease in humans and pose important public health problems in their regions of endemicity. Currently, no FDA-licensed mammarenavirus vaccines are available, and anti-mammarenaviral therapy is limited to an off-label use of ribavirin whose efficacy is controversial. Here, we describe the generation of recombinant version of the prototypic mammarenavirus lymphocytic choriomeningitis virus (rLCMV) combining the features of a codon deoptimized (CD) GPC and the noncoding intergenic region (IGR) of the S segment in both S and L genome segments, called rLCMV/IGR-CD. We present evidence that rLCMV/IGR-CD has excellent safety and protective efficacy features as live-attenuated vaccine (LAV). Importantly, rLCMV/IGR-CD prevents, in coinfected mice, the generation of LCMV reassortants with increased virulence. Our findings document a well-defined molecular strategy for the generation of mammarenavirus LAV candidates able to trigger long-term protective immunity, upon a single immunization, while exhibiting unique enhanced safety features, including unbreachable attenuation.
Collapse
|
48
|
Abbadi M, Basso A, Biasini L, Quartesan R, Buratin A, Davidovich N, Toffan A. Tilapia lake virus: A structured phylogenetic approach. Front Genet 2023; 14:1069300. [PMID: 37144122 PMCID: PMC10151519 DOI: 10.3389/fgene.2023.1069300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/31/2023] [Indexed: 05/06/2023] Open
Abstract
Tilapia Lake Virus (TiLV), also known as Tilapia tilapinevirus, is an emerging pathogen affecting both wild and farmed tilapia (Oreochromis spp.), which is considered one of the most important fish species for human consumption. Since its first report in Israel in 2014, Tilapia Lake Virus has spread globally causing mortality rates up to 90%. Despite the huge socio-economic impact of this viral species, to date the scarce availability of Tilapia Lake Virus complete genomes is severely affecting the knowledge on the origin, evolution and epidemiology of this virus. Herein, along with the identification, isolation and complete genome sequencing of two Israeli Tilapia Lake Virus deriving from outbreaks occurred in tilapia farms in Israel in 2018, we performed a bioinformatics multifactorial approach aiming to characterize each genetic segment before carrying out phylogenetic analysis. Results highlighted the suitability of using the concatenated ORFs 1, 3, and 5 in order to obtain the most reliable, fixed and fully supported tree topology. Finally, we also attempted to investigate the presence of potential reassortment events in all the studied isolates. As a result, we report a reassortment event detected in segment 3 of isolate TiLV/Israel/939-9/2018 involved in the present study, and confirmed almost all the other events previously reported.
Collapse
Affiliation(s)
- Miriam Abbadi
- National Reference Laboratory for fish diseases, Istituto Zooprofilattico Sperimentale Delle Venezie, Legnaro, Padova, Italy
- *Correspondence: Miriam Abbadi,
| | - Andrea Basso
- National Reference Laboratory for fish diseases, Istituto Zooprofilattico Sperimentale Delle Venezie, Legnaro, Padova, Italy
| | - Lorena Biasini
- National Reference Laboratory for fish diseases, Istituto Zooprofilattico Sperimentale Delle Venezie, Legnaro, Padova, Italy
| | - Rosita Quartesan
- National Reference Laboratory for fish diseases, Istituto Zooprofilattico Sperimentale Delle Venezie, Legnaro, Padova, Italy
| | - Alessandra Buratin
- National Reference Laboratory for fish diseases, Istituto Zooprofilattico Sperimentale Delle Venezie, Legnaro, Padova, Italy
| | | | - Anna Toffan
- National Reference Laboratory for fish diseases, Istituto Zooprofilattico Sperimentale Delle Venezie, Legnaro, Padova, Italy
| |
Collapse
|
49
|
Šimičić P, Židovec-Lepej S. A Glimpse on the Evolution of RNA Viruses: Implications and Lessons from SARS-CoV-2. Viruses 2022; 15:1. [PMID: 36680042 PMCID: PMC9866536 DOI: 10.3390/v15010001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
RNA viruses are characterised by extremely high genetic variability due to fast replication, large population size, low fidelity, and (usually) a lack of proofreading mechanisms of RNA polymerases leading to high mutation rates. Furthermore, viral recombination and reassortment may act as a significant evolutionary force among viruses contributing to greater genetic diversity than obtainable by mutation alone. The above-mentioned properties allow for the rapid evolution of RNA viruses, which may result in difficulties in viral eradication, changes in virulence and pathogenicity, and lead to events such as cross-species transmissions, which are matters of great interest in the light of current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemics. In this review, we aim to explore the molecular mechanisms of the variability of viral RNA genomes, emphasising the evolutionary trajectory of SARS-CoV-2 and its variants. Furthermore, the causes and consequences of coronavirus variation are explored, along with theories on the origin of human coronaviruses and features of emergent RNA viruses in general. Finally, we summarise the current knowledge on the circulating variants of concern and highlight the many unknowns regarding SARS-CoV-2 pathogenesis.
Collapse
Affiliation(s)
| | - Snježana Židovec-Lepej
- Department of Immunological and Molecular Diagnostics, University Hospital for Infectious Diseases “Dr. Fran Mihaljević”, HR-10000 Zagreb, Croatia
| |
Collapse
|
50
|
Omatola CA, Olaniran AO. Genetic heterogeneity of group A rotaviruses: a review of the evolutionary dynamics and implication on vaccination. Expert Rev Anti Infect Ther 2022; 20:1587-1602. [PMID: 36285575 DOI: 10.1080/14787210.2022.2139239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
INTRODUCTION Human rotavirus remains a major etiology of acute gastroenteritis among under 5-year children worldwide despite the availability of oral vaccines. The genetic instability of rotavirus and the ability to form different combinations from the different G- and P-types reshapes the antigenic landscape of emerging strains which often display limited or no antigen identities with the vaccine strain. As evidence also suggests, the selection of the antigenically distinct novel or rare strains and their successful spread in the human population has raised concerns regarding undermining the effectiveness of vaccination programs. AREAS COVERED We review aspects related to current knowledge about genetic and antigenic heterogeneity of rotavirus, the mechanism of genetic diversity and evolution, and the implication of genetic change on vaccination. EXPERT OPINION Genetic changes in the segmented genome of rotavirus can alter the antigenic landscape on the virion capsid and further promote viral fitness in a fully vaccinated population. Against this background, the potential risk of the appearance of new rotavirus strains over the long term would be better predicted by a continued and increased close monitoring of the variants across the globe to identify any change associated with disease dynamics.
Collapse
Affiliation(s)
- Cornelius A Omatola
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Durban, Republic of South Africa
| | - Ademola O Olaniran
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Durban, Republic of South Africa
| |
Collapse
|