|
1
|
Li X, Tamim S, Trovão NS. The emergence and circulation of human immunodeficiency virus (HIV)-1 subtype C. J Med Microbiol 2024; 73. [PMID: 38757423 DOI: 10.1099/jmm.0.001827] [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: 05/18/2024] Open
Abstract
Introduction. Human immunodeficiency virus (HIV)-1 subtype C is the most prevalent globally and is thought to have originated in non-human primates in the Democratic Republic of Congo.Hypothesis/Gap Statement. Although the global dominance of HIV-1 subtype C is well established, a thorough understanding of its evolutionary history and transmission dynamics across various risk populations remains elusive. The current knowledge is insufficient to fully capture the global diversification and dissemination of this subtype.Aim. We for the first time sought to investigate the global evolutionary history and spatiotemporal dynamics of HIV-1 subtype C using a selection of maximum-likelihood-based phylodynamic approaches on a total of 1210 near full-length genomic sequences sampled from 32 countries, collected in 4 continents, with sampling dates between 1986-2019 among various risk groups were analysed.Methodology. We subsampled the HIV-1 subtype C genomic datasets based on continent and risk group traits, and performed nucleotide substitution model selection analysis, maximum likelihood (ML) phylogenetic reconstruction, phylogenetic tree topology similarity analysis, temporal signal analysis and traced the timings of viral spread both geographically and by risk group.Results. Based on the phylodynamic analyses of four datasets (full1210, locrisk626, loc562 and risk393), we inferred the time to the most recent common ancestor (TMRCA) in the 1930s and an evolutionary rate of 0.0023 substitutions per site per year. The total number of introduction events of HIV-1 subtype C between continents and between risk groups is estimated to be 71 and 115, respectively. The largest number of introductions occurred from Africa to Europe (n=32), from not-recorded to heterosexual (n=40) and from heterosexual to not-recorded (n=51) risk groups.Conclusion. Our results emphasize that HIV subtype C has mainly spread from Africa to Europe, likely through heterosexual transmission.
Collapse
Affiliation(s)
- Xingguang Li
- Guoke Ningbo Life Science and Health Industry Research Institute, Ningbo, 315000, PR China
| | - Sana Tamim
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Nídia S Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892, USA
| |
Collapse
|
|
2
|
Pamornchainavakul N, Makau DN, Paploski IAD, Corzo CA, VanderWaal K. Unveiling invisible farm-to-farm PRRSV-2 transmission links and routes through transmission tree and network analysis. Evol Appl 2023; 16:1721-1734. [PMID: 38020873 PMCID: PMC10660809 DOI: 10.1111/eva.13596] [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: 06/20/2022] [Revised: 08/04/2023] [Accepted: 09/01/2023] [Indexed: 12/01/2023] Open
Abstract
The United States (U.S.) swine industry has struggled to control porcine reproductive and respiratory syndrome (PRRS) for decades, yet the causative virus, PRRSV-2, continues to circulate and rapidly diverges into new variants. In the swine industry, the farm is typically the epidemiological unit for monitoring, prevention, and control; breaking transmission among farms is a critical step in containing disease spread. Despite this, our understanding of farm transmission still is inadequate, precluding the development of tailored control strategies. Therefore, our objective was to infer farm-to-farm transmission links, estimate farm-level transmissibility as defined by reproduction numbers (R), and identify associated risk factors for transmission using PRRSV-2 open reading frame 5 (ORF5) gene sequences, animal movement records, and other data from farms in a swine-dense region of the U.S. from 2014 to 2017. Timed phylogenetic and transmission tree analyses were performed on three sets of sequences (n = 206) from 144 farms that represented the three largest genetic variants of the virus in the study area. The length of inferred pig-to-pig infection chains that corresponded to pairs of farms connected via direct animal movement was used as a threshold value for identifying other feasible transmission links between farms; these links were then transformed into farm-to-farm transmission networks and calculated farm-level R-values. The median farm-level R was one (IQR = 1-2), whereas the R value of 28% of farms was more than one. Exponential random graph models were then used to evaluate the influence of farm attributes and/or farm relationships on the occurrence of farm-to-farm transmission links. These models showed that, even though most transmission events cannot be directly explained by animal movement, movement was strongly associated with transmission. This study demonstrates how integrative techniques may improve disease traceability in a data-rich era by providing a clearer picture of regional disease transmission.
Collapse
|
|
3
|
Variations in the NSP4 gene of the type 2 porcine reproductive and respiratory syndrome virus isolated in China from 1996 to 2021. Virus Genes 2023; 59:109-120. [PMID: 36383275 PMCID: PMC9667009 DOI: 10.1007/s11262-022-01957-x] [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: 09/20/2022] [Accepted: 11/05/2022] [Indexed: 11/17/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) has continuously mutated since its first isolation in China in 1996, leading to difficulties in infection prevention and control. Infections caused by PRRSV-2 strains are the main epidemic strains in China, as determined by phylogenetic analysis. In this study, we focused on the prevalence and genetic variations of the non-structural protein 4 (NSP4) from PRRSV-2 over the past 20 years in China. The fundamental biological properties of the NSP4 were predicted, and an analysis and comparison of NSP4 homology at the nucleotide and amino acid levels was conducted using 123 PRRSV-2 strains. The predicted molecular weight of the NSP4 protein was determined to be 21.1 kDa, and it was predicted to be a stable hydrophobic protein that lacks a signal peptide. NSP4 from different strains exhibited a high degree of amino acid (85.8-100%) and nucleotide sequence homology (81.0-100%). Multiple amino acid substitutions were identified in NSP4 among 15 representative PRRSV-2 strains. Phylogenetic analysis showed that the lineage 8 and 1 strains, the most prevalent strains in China, were indifferent clades with a long genetic distance. This analysis will help fully elucidate the parameters of the PRRSV NSP4 epidemic in China to lay a foundation for adequate understanding of the function of NSP4. Genetic information results from the accumulation of conserved and non-conserved sequences. The high conservation of the NSP4 gene determines the most basic life traits and functions of PRRSV. Analyzing the spatial structure of NSP4 protein and studying the genetic evolution of NSP4 not only provide the theoretical basis for how NSP4 participates in the regulation of the innate response of the host but also provide a target for genetic manipulation and a reasonable target molecule and structure for new drug molecules.
Collapse
|
|
4
|
Li C, Gong B, Sun Q, Xu H, Zhao J, Xiang L, Tang YD, Leng C, Li W, Guo Z, Fu J, Peng J, Wang Q, Zhou G, Yu Y, Meng F, An T, Cai X, Tian ZJ, Zhang H. First Detection of NADC34-like PRRSV as a Main Epidemic Strain on a Large Farm in China. Pathogens 2021; 11:pathogens11010032. [PMID: 35055980 PMCID: PMC8778757 DOI: 10.3390/pathogens11010032] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/27/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022] Open
Abstract
The newly emerged sublineage 1.5 (NADC34-like) porcine reproductive and respiratory syndrome virus (PRRSV) has posed a direct threat to the Chinese pig industry since 2018. However, the prevalence and impact of NADC34-like PRRSV on Chinese pig farms is unclear. In the present study, we continuously monitored pathogens—including PRRSV, African swine fever virus (ASFV), classical swine fever virus (CSFV), pseudorabies virus (PRV), and porcine circovirus 2 (PCV2)—on a fattening pig farm with strict biosecurity practices located in Heilongjiang Province, China, from 2020 to 2021. The results showed that multiple types of PRRSV coexisted on a single pig farm. NADC30-like and NADC34-like PRRSVs were the predominant strains on this pig farm. Importantly, NADC34-like PRRSV—detected during the period of peak mortality—was one of the predominant strains on this pig farm. Sequence alignment suggested that these strains shared the same 100 aa deletion in the NSP2 protein as IA/2014/NADC34 isolated from the United States (U.S.) in 2014. Phylogenetic analysis based on open reading frame 5 (ORF5) showed that the genetic diversity of NADC34-like PRRSV on this farm was relatively singular, but it had a relatively high rate of evolution. Restriction fragment length polymorphism (RFLP) pattern analysis showed that almost all ORF5 RFLPs were 1-7-4, with one 1-4-4. In addition, two complete genomes of NADC34-like PRRSVs were sequenced. Recombination analysis and sequence alignment demonstrated that both viruses, with 98.9% nucleotide similarity, were non-recombinant viruses. This study reports the prevalence and characteristics of NADC34-like PRRSVs on a large-scale breeding farm in northern China for the first time. These results will help to reveal the impact of NADC34-like PRRSVs on Chinese pig farms, and provide a reference for the detection and further prevention and control of NADC34-like PRRSVs.
Collapse
Affiliation(s)
- Chao Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Bangjun Gong
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Qi Sun
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Hu Xu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Jing Zhao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Lirun Xiang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Yan-Dong Tang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Chaoliang Leng
- Henan Key Laboratory of Insect Biology in Funiu Mountain, Henan Provincial Engineering Laboratory of Insects Bio-Reactor, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang 473061, China;
| | - Wansheng Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Zhenyang Guo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Jun Fu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Jinmei Peng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Qian Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Guohui Zhou
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Ying Yu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China;
| | - Fandan Meng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Tongqing An
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Xuehui Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Zhi-Jun Tian
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
| | - Hongliang Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.L.); (B.G.); (Q.S.); (H.X.); (J.Z.); (L.X.); (Y.-D.T.); (W.L.); (Z.G.); (J.F.); (J.P.); (Q.W.); (G.Z.); (F.M.); (T.A.); (X.C.); (Z.-J.T.)
- Correspondence: ; Tel.: +86-13624503578
| |
Collapse
|