Molecular Characterization of the Major Open Reading Frames (ORFs) and Enhancer Elements From Four Geographically Distinct North American Equine Infectious Anemia Virus (EIAV) Isolates |
| |
| Affiliation: | 1. Department of Veterinary Science, Maxwell-Gluck Equine Research Center, University of Kentucky, Lexington, KY;2. NGS Unit, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, Ames, IA;1. TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, China;2. Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, China;3. Tianjin Key Laboratory of Microbial Functional Genomics, 23 Hongda Street, TEDA, Tianjin 300457, China;4. Nebraska Center for Virology and School of Biological Sciences, University of Nebraska, Lincoln, NE 68583, USA;1. Department of Veterinary Science, University of Kentucky, Lexington, KY, USA;2. Center for Vaccine Research and Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA;1. Division of Disease Model Innovation, Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan;2. Laboratory of Infectious Disease, School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan;3. Department of Biomedicine, Center of Biomedical Research, Research Center for Human Disease Modeling, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan |
| |
| Abstract: | Although the equine lentivirus (equine infectious anemia virus [EIAV]) poses a major threat to equid populations throughout most regions of the world, detailed knowledge concerning its molecular epidemiology is still in its infancy. Such information is important because the few studies conducted to date suggest there is extensive genetic variation between viral isolates that if confirmed has significant implications for future vaccine design and development of newer diagnostic procedures. Here, we avoid potential assembly artifacts inherent in composite sequencing techniques by using long-range PCR in conjunction with next-generation sequencing for the rapid molecular characterization of all major open reading frames (ORFs) and known transcription factor binding motifs within the long terminal repeats (LTRs) of four North American EIAV isolates from Pennsylvania (EIAVPA), Tennessee (EIAVTN), North Carolina (EIAVNC), and Florida (EIAVFL). These were compared with complete published EIAV field strain genomic sequences from Asia (EIAVLIA, EIAVMIY), Europe (EIAVIRE), and North America (EIAVWY) plus EIAVUK a laboratory variant of EIAVWY. Phylogenetic analysis using the long-range PCR products suggested all the New World EIAV isolates comprised a single monophyletic group associated with EIAVIRE. This is distinct from the Asian isolates and so consistent with known historical details concerning the reintroduction of equids into North America by European settlers. Nonetheless nucleotide sequence identity for example between EIAVPA and EIAVTN, EIAVNC, EIAVFL, EIAVWY, EIAVUK plus EIAVIRE was limited to 84.6%, 81.0%, 82.1%, 80.4%, 80.1%, and 77.6%, respectively, with some of these values being not too dissimilar to those between EIAVPA and EIAVLIA or EIAVMIY at 78.0% and 75.4%, respectively. Overall, these results suggest substantial genetic diversity exists even within North American EIAV isolates. Comparative alignment of predicted amino acid sequences from all strains provides increased understanding concerning the extent of permitted substitutions in each viral ORF and known transcriptional LTR control elements. |
| |
| Keywords: | EIAV Horse Long range PCR Next generation sequencing |
| 本文献已被 ScienceDirect 等数据库收录！ |
|
