Genetic Analysis of the Full-Length gag Gene from the Earliest Korean Subclade B of HIV-1: An Outbreak among Korean Hemophiliacs
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Patients and Samples
2.2. RNA Preparation and gag Gene Amplification
2.3. Phylogenetic Tree Analysis
2.4. Viral Signature Pattern Analysis (VESPA)
2.5. Statistical Analysis
2.6. Nucleotide Sequence Data
3. Results
3.1. Origin of the KSB of Subtype B
3.2. Molecular Epidemiologic Data on the gag Gene
3.3. Nucleotide/Amino Acid Signature Patterns
3.4. Korean Signature Pattern Amino Acid Residues and Duplication of the PTAP Motif in the p6 Gag Protein
3.5. Comparison of the Frequency of 100%-Specific Nucleotides among the Nine Genes
3.6. Sequence Identities of Donors O and P
3.7. Correlation between Sampling Intervals and Number of Nucleotide Differences
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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14 Signature Nucleotide Positions | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Nucleotide positions in HXB2 | 807 | 823 | 940 | 1012 | 1151 | 1264 | 1281 | 1674 | 1707 | 1722 | 1897 | 1899 | 2155 | 2190 |
Nucleotide in HXB2 | A | A | T | C | A | A | C | C | C | G | G | A | A | A |
Signature nucleotide | G | T | T | T | A | A | G | T | G | |||||
Cluster-O (n = 9) | 1.0a | 1.0 | 1.0 | 1.0 | 1.0 | 0.89 | 1.0 | 1.0 | 1.0 | |||||
Other KSB (n = 85) | 0.04b | 0.13 | 0.05 | 0.11 | 0.05 | 0.02 | 0.00 | 0.13 | 0.13 | |||||
Signature nucleotide | G | C | A | G | G | |||||||||
Cluster-P (n = 13) | 0.85 | 1.0 | 0.92 | 1.0 | 0.92 | |||||||||
Other KSB (n = 81) | 0.25 | 0.04 | 0.12 | 0.30 | 0.40 |
Signature Pattern Amino Acids at 12 Residues | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Position in HXB2 | 30 | 34 | 62 | 94 | 102 | 114 | 119 | 138 | 389 | 403 | 483 | 490 |
KSB (n = 94) | R83 | L78 | G86 | I89 | E77 | K93 | T89 | L93 | T74 | K89 | L88 | R84 |
k11 | i14 | e5 | v5 | d14 | n1 | a5 | m1 | i10 | r5 | p3 | k20 | |
v2 | a2, r1 | k1, h1 | p10 | q2, k2, h1 | ||||||||
Non-KSB (n = 25) | k13 | I20 | g15 | V19 | e15 | k13 | A24 | l15 | i9 | r14 | l13 | k15 |
r9 | l4 | e6 | i5 | d10 | r7 | t1 | m5 | t6 | k11 | m9 | r10 | |
q3 | i2 | t4 | i3, v2 | n3, s3 | r2 | |||||||
v1 | n1 | m3, g1 | q1 |
10 Specific Nucleotides | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Gene | gag | pol | vif | vpr | tat, rev, vpu | env | nef | |||||
No. of KSB (n) | 94 | 91 [2] | 127 [3] | 52* | 52* | 77 [5] | 143 [4] | |||||
Nucleotide position | 1899 | 2321 | 4235 | 5070 | 5253 | 5621 | None | 6473 | 8252 | 8670 | 8774 | None |
Signature | G | G | A | A | T | C | T | |||||
Cluster-O (n = 9) | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | |||||
Other KSB (n = 85) | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | |||||
Signature | G | A | G | |||||||||
Cluster-P (n = 13) | 1.0 | 1.0 | 1.0 | |||||||||
Other KSB (n = 81) | 0.0 | 0.0 | 0.0 |
Gene | Cluster O (n = 9) | Cluster P (n = 13) | KSB (n = 19) [13] |
---|---|---|---|
pol | 99.1 ± 0.5 | 99.2 ± 0.4a | 97.1 |
gag | 98.9 ± 0.2 | 98.9 ± 0.5 | 95.2 |
vif | 98.9 ± 0.5 | 98.9 ± 0.7 | 96.2 |
nef | 97.6 ± 1.6 | 97.3 ± 2.1a, b | 95.6 |
env | 96.3 ± 1.7 | 94.5 ± 3.2b | 89.8 |
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Cho, Y.-K.; Kim, J.-E.; Foley, B.T. Genetic Analysis of the Full-Length gag Gene from the Earliest Korean Subclade B of HIV-1: An Outbreak among Korean Hemophiliacs. Viruses 2019, 11, 545. https://doi.org/10.3390/v11060545
Cho Y-K, Kim J-E, Foley BT. Genetic Analysis of the Full-Length gag Gene from the Earliest Korean Subclade B of HIV-1: An Outbreak among Korean Hemophiliacs. Viruses. 2019; 11(6):545. https://doi.org/10.3390/v11060545
Chicago/Turabian StyleCho, Young-Keol, Jung-Eun Kim, and Brian T. Foley. 2019. "Genetic Analysis of the Full-Length gag Gene from the Earliest Korean Subclade B of HIV-1: An Outbreak among Korean Hemophiliacs" Viruses 11, no. 6: 545. https://doi.org/10.3390/v11060545