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Zhang L, Sun S, Gong W, Thompson L, Cruz J, Dukpa K, Gonzales RM, Tu Z, He B, Liu Y, Tu C, Feng Y. Large-scale phylogenetic analysis reveals genetic diversity and geographic distribution of rabies virus in South-East and South Asia. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105472. [PMID: 37353186 DOI: 10.1016/j.meegid.2023.105472] [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: 05/06/2023] [Revised: 06/14/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023]
Abstract
South-East Asia (SEA) and South Asia (SA) are two important geographic regions with the most severe enzootic rabies in the world. In these regions, phylogenetic analysis of rabies virus (RABV) has been conducted only at a country level; the results obtained from different countries are scattered and unequal, with a non-uniform system to name RABV genotypes. Therefore, it is difficult to undertake origin-tracking and compare inter-country RABV evolution and transmission. To avoid the confusion in understanding and to generate a panoramic picture of RABV genetic diversity, distribution, and transmission in SEA and SA, the present study conducted a systematic phylogenetic analysis by combining all sequences representing 2368 RABV strains submitted to GenBank by 14 rabies endemic SEA and SA countries. The results showed that RABVs circulating in two regions were classified into four major clades and many subclades: the Asia clade is circulating only in SEA, the Indian subcontinent, and Arctic-like clades only in SA, while the Cosmopolitan clade has been detected in both regions. The results also showed a wide range of hosts were infected by divergent RABV subclades, with dogs being the major transmission source. However, wildlife rabies was also found to be an important issue with 6 wild carnivore species identified as potential sources of spillover risk for sylvatic rabies to humans, domestic animals, and other wild animals. Current findings indicate that the two regions have separate virus clades circulating thus indicating the absence of cross-transmission between the regions. The study emphasizes the importance of phylogenetic analysis in the regions using uniform genotyping and naming systems for rabies surveillance, to coordinate actions of member countries to eliminate dog-mediated human rabies by 2030.
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Affiliation(s)
- Liang Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, China
| | - Sheng Sun
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, China
| | - Wenjie Gong
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, China; College of Animal Medicine, Jilin University, Changchun, Jilin Province, China
| | - Lesa Thompson
- World Organization for Animal Health Regional Representative for Asia and the Pacific, Tokyo, Japan
| | - Jeffrey Cruz
- Department of Agriculture Bureau of Animal Industry, Quezon, Philippines
| | - Kinzang Dukpa
- World Organization for Animal Health Regional Representative for Asia and the Pacific, Tokyo, Japan
| | | | - Zhongzhong Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, China
| | - Biao He
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, China
| | - Yan Liu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, China
| | - Changchun Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu Province, China.
| | - Ye Feng
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, China; State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
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Vagheshwari DH, Bhanderi BB, Mathakiya RA, Jhala MK. Sequencing and sequence analysis of partial nucleoprotein (N) gene and phylogenetic analysis of rabies virus field isolates from Gujarat state, India. Virusdisease 2018; 28:320-327. [PMID: 29291220 DOI: 10.1007/s13337-017-0387-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 06/20/2017] [Indexed: 11/28/2022] Open
Abstract
The present study was undertaken with an aim of characterization of rabies virus (genus Lyssavirus of the family Rhabdoviridae under the order Mononegavirales) by sequencing of partial nucleoprotein (N) gene of rabies virus and phylogenetic analysis to know the genotype and lineage of rabies virus present in Gujarat state of India. A total of 32 samples (18 brain samples and 14 saliva samples) were aseptically collected from live and dead animals (viz. dog, buffalo, cow, goat, donkey and hyena) for rabies virus detection. Out of 32 samples, 24 samples were found positive by Reverse Transcriptase Polymerase Chain Reactions and from these 24 positive samples, 20 samples were selected for sequencing having good concentration of gene product. ClustalW alignment of nucleotide sequences and amino acid sequences of field rabies isolates revealed 95.20-100 and 97.95-100% similarity among themselves, respectively. Multiple sequence alignment of field rabies isolates and reference vaccine strains [Pasteur strain and Challenge Virus Strain (CVS)] indicated single nucleotide mutations at total 91 positions and amino acid mutations at total 17 different positions. Phylogenetic analysis of N gene sequences using our 20 field rabies isolates and 21 other reported isolates in Genbank resulted in 3 phylogenetic clusters. All the field rabies isolates showed same genetic lineage among themselves and with other earlier reported Indian rabies isolates placing them in Arctic like lineage of Genotype 1 Rabies virus. However, they were at genetic distance with reference Pasteur and CVS strains, which grouped in different phylogenetic cluster.
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Affiliation(s)
- Dhaval H Vagheshwari
- Department of Veterinary Microbiology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat 388001 India
| | - Bharat B Bhanderi
- Department of Veterinary Microbiology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat 388001 India
| | - Rafyuddin A Mathakiya
- Department of Veterinary Microbiology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat 388001 India
| | - Mayurdhvaj K Jhala
- Department of Veterinary Microbiology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat 388001 India
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He W, Zhang H, Zhang Y, Wang R, Lu S, Ji Y, Liu C, Yuan P, Su S. Codon usage bias in the N gene of rabies virus. INFECTION GENETICS AND EVOLUTION 2017; 54:458-465. [PMID: 28818621 DOI: 10.1016/j.meegid.2017.08.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 08/11/2017] [Accepted: 08/12/2017] [Indexed: 12/17/2022]
Abstract
Since its emergence, rabies virus (RABV) has been a major worldwide concern especially in developing countries. The nucleoprotein (N) of RABV is highly conserved and key for genetic typing, thus a better understanding of the N gene evolutionary trajectory can assist the development of control measures. We found that the N gene of RABV has a low codon usage bias with a mean effective number of codons (ENC) value of 56.33 influenced by both mutation pressure and natural selection. However, neutrality analysis indicated that natural selection dominates over mutation pressure. Additionally, we found that dinucleotide bias partly contributed to RABV codon usage bias. On the other hand, based on the clades of phylogenetic tree, we found that the evolutionary rate of the Africa 2 clade was the highest with a mean value of 3.75×10-3 substitutions per site per year. Above all, our results regarding N gene of RABV codon usage will serve future RABV evolution research.
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Affiliation(s)
- Wanting He
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Hongyu Zhang
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yuchen Zhang
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Ruyi Wang
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Sijia Lu
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yanjie Ji
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Chang Liu
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Pengkun Yuan
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Shuo Su
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.
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