Genome Analysis and Replication Studies of the African Green Monkey Simian Foamy Virus Serotype 3 Strain FV2014
Abstract
:1. Introduction
2. Materials and Methods
2.1. Virus Preparation
2.2. PCR Assays and Copy Number Standard
2.3. Infectivity Analysis
2.4. Preparation of Viral Nucleic Acid, Sequencing, and Bioinformatics Analysis
2.4.1. High-Throughput Sequencing
2.4.2. Sanger Sequencing
2.5. Sequence Comparison and Phylogenetic Analysis
3. Results
3.1. Characterization of SFVcae_FV2014 Virus Stock
3.2. Studies of SFVcae_FV2014 Replication
3.3. SFVcae_FV2014 Genome Analysis
3.3.1. Structure and Sequence Comparison
3.3.2. Phylogenetic Analysis
4. Discussion
Supplementary Materials
Author Contributions
Acknowledgments
Conflicts of Interest
References
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Cell Name | Source | Host Species | Tissue Origin | Cell Type |
---|---|---|---|---|
Mus dunni | [14] | wild mouse | tail | fibroblast |
MDCK (NBL-2) | ATCC, CCL-34 | dog | kidney | epithelial |
FRhK-4 | ATCC, CRL-1688 | rhesus macaque | fetal, kidney | epithelial |
Vero | ATCC, CCL-81 | African green | kidney | epithelial |
monkey | ||||
MRC-5 | ATCC, CCL-171 | human | lung, fetal | fibroblast, |
diploid | ||||
A549 | ATCC, CCL-185 | human | lung, carcinoma | epithelial |
Virus | Previous Designation | Species of Virus Isolation | Accession Number 1 |
---|---|---|---|
SFVmcy_FV21 | SFVmcy-1, (SFV serotype I) | Taiwanese macaque | NC_010819 |
SFVmcy_FV34[RF] | SFVmcy-2, (SFV serotype II) | Taiwanese macaque | KF026286 |
SFVmmu_K3T | SFVmmu-K3T | Rhesus macaque | KF026288 |
SFVmmu_R289HybAGM[RF] | SFV-R289HybAGM | Rhesus macaque | JN801175 |
SFVcae_FV2014 | SFV 3 | African green monkey | MF582544 |
(SFV serotype III) | |||
SFVcae_LK3 | SFVagm-3 | African green monkey | NC_010820 |
SFVcae_agm4 | agm4 | African green monkey | AJ244075 |
SFVcae_agm5 | agm5 | African green monkey | AJ244067 |
SFVcae_agm20 | agm20 | African green monkey | AJ244091 |
SFVcae_agm24 | agm24 | African green monkey | AJ244090 |
SFVpve | SFVcpz | Chimpanzee | NC_001364 |
SFVpsc_huHRSV.13 | HFV | Chimpanzee | KX08159 |
SFVggo | SFVgor | Gorilla | HM245790 |
BFVbta | BFV | Cow | NC_001831 |
EFVeca_1 | EFVeca | Equine | AF201902 |
FFVfca_FUV7 | FFVfca | Feline | Y08851 |
Viral Regions | Location 1 | SFVcae_FV2014 LTR/gene 2 | ORF 3 | Location 1 | SFVcae_LK3 LTR/gene 2 | ORF 3 |
---|---|---|---|---|---|---|
LTR | 1–1710 | 1710 | 1–1708 | 1708 | ||
gag | 1827–3758 | 1932 | 643 | 1825–3756 | 1932 | 643 |
pol | 3706–7137 | 3432 | 1143 | 3704–7135 | 3432 | 1143 |
env | 7085–10045 | 2961 | 986 | 7083–10031 | 2949 | 982 |
tas | 10,015–10,905 | 891 | 296 | 10,001–10,897 | 897 | 298 |
bet | 10,015–10,285, 10,581–11,824 | 1515 | 504 | 10,001–10,271, 10,567–11,705 | 1410 | 469 |
LTR | 11,418–13,127 | 1710 | 11,404–13,111 | 1708 |
SFV Isolates | % Sequence Identity | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
LTR | gag | pol | env | env-LP | env-SU | env-TM | tas | bet | ||
SFVcae_LK3 | nt | 88.71 | 81.5 | 86.3 | 79.1 | 79.6 | 71.1 | 86.6 | 90.2 | 88.8 |
aa | 85.4 | 91.6 | 81.5 | 86.5 | 67.3 | 93.9 | 91.3 | 88.5 | ||
SFVmcy_FV21 | nt | 66.9 | 68.1 | 81.7 | 75.0 | 71.4 | 73.8 | 77.0 | 66.1 | 61.8 |
aa | 65.8 | 86.1 | 78.2 | 73.0 | 73.5 | 84.8 | 52.2 | 51.4 | ||
SFVmcy_FV34(RF) | nt | 65.8 | 68.8 | 81.9 | 75.0 | 72.2 | 69.1 | 76.6 | 65.4 | 64.4 |
aa | 66.7 | 86.3 | 78.2 | 73.8 | 63.2 | 83.9 | 52.5 | 50.9 | ||
SFVmmu_R289(RF) | nt | 67.6 | 69.6 | 81.5 | 73.4 | 73.8 | 68.3 | 77.8 | 66.7 | 62.2 |
aa | 67.6 | 86.4 | 74.5 | 76.2 | 63.7 | 85.3 | 53.7 | 51.2 |
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Fuentes, S.M.; Bae, E.H.; Nandakumar, S.; Williams, D.K.; Khan, A.S. Genome Analysis and Replication Studies of the African Green Monkey Simian Foamy Virus Serotype 3 Strain FV2014. Viruses 2020, 12, 403. https://doi.org/10.3390/v12040403
Fuentes SM, Bae EH, Nandakumar S, Williams DK, Khan AS. Genome Analysis and Replication Studies of the African Green Monkey Simian Foamy Virus Serotype 3 Strain FV2014. Viruses. 2020; 12(4):403. https://doi.org/10.3390/v12040403
Chicago/Turabian StyleFuentes, Sandra M., Eunhae H. Bae, Subhiksha Nandakumar, Dhanya K. Williams, and Arifa S. Khan. 2020. "Genome Analysis and Replication Studies of the African Green Monkey Simian Foamy Virus Serotype 3 Strain FV2014" Viruses 12, no. 4: 403. https://doi.org/10.3390/v12040403
APA StyleFuentes, S. M., Bae, E. H., Nandakumar, S., Williams, D. K., & Khan, A. S. (2020). Genome Analysis and Replication Studies of the African Green Monkey Simian Foamy Virus Serotype 3 Strain FV2014. Viruses, 12(4), 403. https://doi.org/10.3390/v12040403