Analysis of evolutionary and genetic patterns in structural genes of primate lentiviruses

Abstract

Background: Primate lentiviruses (HIV1, HIV2, and Simian immunodeficiency virus [SIV]) cause immune deficiency, encephalitis, and infectious anemia in mammals such as cattle, cat, goat, sheep, horse, and puma.

Objective: This study was designed and conducted with the main purpose of confirming the overall codon usage pattern of primate lentiviruses and exploring the evolutionary and genetic characteristics commonly or specifically expressed in HIV1, HIV2, and SIV.

Methods: The gag, pol, and env gene sequences of HIV1, HIV2, and SIV were analyzed to determine their evolutionary relationships, nucleotide compositions, codon usage patterns, neutrality, selection pressure (influence of mutational pressure and natural selection), and viral adaptation to human codon usage.

Results: A strong 'A' bias was confirmed in all three structural genes, consistent with previous findings regarding HIV. Notably, the ENC-GC3s plot and neutral evolution analysis showed that all primate lentiviruses were more affected by selection pressure than by mutation caused by the GC composition of the gene, consistent with prior reports regarding HIV1. The overall codon usage bias of pol was highest among the structural genes, while the codon usage bias of env was lowest. The virus groups showing high codon bias in all three genes were HIV1 and SIVcolobus. The codon adaptation index (CAI) and similarity D(A, B) values indicated that although there was a high degree of similarity to human codon usage in all three structural genes of HIV, this similarity was not caused by translation pressure. In addition, compared with HIV1, the codon usage of HIV2 is more similar to the human codon usage, but the overall codon usage bias is lower.

Conclusion: The origin viruses of HIV (SIVcpz_gor and SIVsmm) exhibit greater similarity to human codon usage in the gag gene, confirming their robust adaptability to human codon usage. Therefore, HIV1 and HIV2 may have evolved to avoid human codon usage by selection pressure in the gag gene after interspecies transmission from SIV hosts to humans. By overcoming safety and stability issues, information from codon usage analysis will be useful for attenuated HIV1 vaccine development. A recoded HIV1 variant can be used as a vaccine vector or in immunotherapy to induce specific innate immune responses. Further research regarding HIV1 dinucleotide usage and codon pair usage will facilitate new approaches to the treatment of AIDS.

Keywords: Codon usage pattern; Human immunodeficiency virus 1; Human immunodeficiency virus 2; Mutational pressure; Natural selection; Relative synonymous codon usage; Simian immunodeficiency virus.

Fig. 1

Phylogenetic trees constructed with nucleotide sequences of lentivirus structural genes. Maximum likelihood trees using nucleotide sequences show evolutionary relationships of primate lentiviruses. Bootstrap values > 70% based on 1000 replications are shown at each node, and branch lengths represent evolutionary distances. [◆] HIV1; [▽] HIV2; [△] SIVagm; [▲] SIVallo; [□] SIVcer; [] SIVcol; [○] SIVcpz_gor; [●] SIVmac; [■]SIVmnd; [▼] SIVpit; [] SIVsmm

Fig. 2

Compositional features of lentiviral gag, pol, and env genes. a Distribution of A, T, C, and G in lentiviral gag genes. b Distribution of A, T, C, and G at the third codon position. c Total GC/AT content and GC/AT content at the third codon position. High AT contents and much higher AT3 contents were observed, indicating the predominant use of A-end codons in primate lentiviral genes

Fig. 3

Mean PR2-bias plot of gag, pol, and env genes of 11 lentivirus groups. AT-bias (A3/(A3 + T3)) and GC-bias (G3/(G3 + C3)) were calculated separately for each four-fold degenerate amino acid (Val, Pro, Thr, Ala, and Gly) and four-codon family of Leu, Ser, and Arg. For all three structural genes of primate lentiviruses, consistent G-end codon avoidance was observed in the amino acids Pro(CC-), Thr(AC-), Ala(GC-), and Ser(TC-), and this CpG dinucleotide avoidance pattern was particularly evident in pol genes

Fig. 4

Neutrality plot for lentiviral gag, pol, and env genes. Different virus groups are represented by different icons, and each icon represents a sequence. If a correlation exists, the linear regression equation is presented; “not fit” indicates that no correlation was present between GC12s and GC3s values. The extent of change in GC12s was very limited compared to that in GC3s, implying that selection pressure plays a major role in shaping codon usage patterns in primate lentiviruses compared to mutational pressure

Fig. 5

RSCU plot of lentiviral gag, pol, and env genes. The degree of variation among the 11 groups was the smallest in the pol gene. Generally, for RSCU values > 1.6, codons were considered over-expressed; for RSCU values < 0.6, codons were considered under-expressed. CCA, ACA, GCA, AGA, AGG, and GGA codons were over-expressed (RSCU > 1.6) in all structural genes of lentiviruses and, based on RSCU values, there was a dominant preference for the A-end codon

Fig. 6

ENC box plot of lentiviral gag, pol, and env genes. Cross: mean ENC value; dots: minimum and maximum ENC values. The HIV1 and SIVcpz_gor groups are highlighted by red boxes and the HIV2 and SIVsmm groups are highlighted by blue boxes. The mean ENC values for gag, pol, and env were 47.8, 43.47, and 49.18, respectively, indicating that the codon diversity was greater in gag and env genes than in the pol gene. HIV1 showed a strong preference for using synonymous codons in all three genes

Fig. 7

ENC-GC3s plot of lentiviral gag, pol, and env genes. The smooth line is the expected value of ENC calculated based on GC3 content. In the gag gene, sequences within the same group are subject to greater differences in selection pressure than in the pol and env genes. Sequences within the same group of the gag gene show a greater difference in selection pressure than those of the pol and env genes. A small portion of HIV1 sequences located on the expected curve within the env ENC-GC3s plot are clones of highly neurovirulent HIV-1 isolates