Does antiretroviral treatment change HIV-1 codon usage patterns in its genes: a preliminary bioinformatics study.

BACKGROUND: Codon usage bias has been described for various organisms and is thought to contribute to the regulation of numerous biological processes including viral infections. HIV-1 codon usage has been previously shown to be different from that of other viruses and man. It is evident that the antiretroviral drugs used to restrict HIV-1 replication also select for resistance variants. We wanted to test whether codon frequencies in HIV-1 sequences from treatment-experienced patients differ from those of treatment-naive individuals due to drug pressure affecting codon usage bias. RESULTS: We developed a JavaScript to determine the codon frequencies of aligned nucleotide sequences. Irrespective of subtypes, using HIV-1 pol sequences from 532 treatment-naive and 52 treatment-experienced individuals, we found that pol sequences from treatment-experienced patients had significantly increased AGA (arginine; p = 0.0002***) and GGU (glycine; p = 0.0001***), and decreased AGG (arginine; p = 0.0001***) codon frequencies. The same pattern was not observed when subtypes B and C sequences were analyzed separately. Additionally, irrespective of subtypes, using HIV-1 gag sequences from 524 treatment-naive and 54 treatment-experienced individuals, gag sequences from treatment-experienced patients had significantly increased CUA (leucine; p < 0.0001***), CAG (glutamine; p = 0.0006***), AUC (isoleucine; p < 0.0001***) and UCU (serine; p = 0.0005***), and decreased AUA (isoleucine; p = 0.0003***) and CAA (glutamine; p = 0.0006***) codon frequencies. CONCLUSION: Using pol and gag genes derived from the same HIV-1 genome, we show that antiretroviral therapy changed certain HIV-1 codon frequencies in a subtype specific way.

Dolutegravir inhibits HIV-1 Env evolution in primary human cells.

OBJECTIVE: In treatment-naive HIV-positive individuals, the integrase strand-transfer inhibitor dolutegravir (DTG) has not been associated with emergent drug-resistance mutations, neither against this drug nor against other antiretroviral drugs that were used in combination with it. This is in contrast to all other antiretroviral drugs tested so far, including the integrase strand-transfer inhibitors raltegravir (RAL) and elvitegravir that can lead to treatment failure with the emergence of drug-resistance mutations. DESIGN: These observations suggest that DTG may provide an additional protection against resistance compared to other drugs by decreasing HIV-1 genetic evolution. METHODS: Here, we tested this hypothesis by measuring the genetic and amino-acid diversity of Env/gp160 from two HIV-1 primary isolates that were grown in the presence of increasing concentrations of DTG or RAL over the course of 38-55 weeks. RESULTS: The results show that treatment with DTG led to less HIV-1 genetic and amino-acid diversification over time, as compared to treatment with RAL or the absence of drug. CONCLUSION: These results may help to explain the absence of emergent resistance mutations in treatment-naive individuals treated with DTG.

[L'usage de papier buvard de type « FTATM Classic ¼ pour la détection et le génotypage du VIH chez des hommes ayant des relations sexuelles avec d'autres hommes à Montréal (Québec, Canada)]. / L'usage de papier buvard de type « FTATM Classic ¼ pour la détection et le génotypage du VIH chez des hommes ayant des relations sexuelles avec d'autres hommes à Montréal (Québec, Canada).

As part of a program for HIV-1 detection in the gay community of Montreal, blood sampling on "FTA Classic" papers (DBS "dried blood spot") has been tested and validated. It turns out to be sensitive (up to 1 000 copies of proviral DNA/mL) and reliable. Thus, this approach should be considered when a blood sampling is subject to various constraints.

Age-related immunoglobulin G seroprevalence of human parvovirus B-19 in Israeli children.

BACKGROUND: Human parvovirus B19 is a global and common infectious pathogen in humans, particularly in children. OBJECTIVES: To assess the immunoglobulin G3 seroprevalence of B19 in children in Israel. METHODS: Overall, 128 previously healthy children (1.5-17 years old) hospitalized for various diseases other than acute human parvovirus B19 infection were assessed for IgG to the virus by enzyme-linked immunosorbent assay. RESULTS: The IgG seroprevalence increased from 22% in children aged 1.5-9 years to 52% in older children (P = 0.001). CONCLUSIONS: Our data suggest that most acute parvovirus B19 infections in Israel occur in the early school years, and that by 18 years of age 50% of Israeli children have been infected by the virus.

Longitudinal quantification of Ehrlichia canis in experimental infection with comparison to natural infection.

Ehrlichia canis is a major tick-borne bacterial pathogen of dogs. Quantitative real-time PCR was evaluated for the detection of E. canis in naturally (NI) and experimentally infected (EI) dogs. DNA was extracted from blood, spleen and conjunctival swabs of experimentally infected dogs pre- and post-infection (PI), and during doxycycline therapy, and from blood and conjunctivas of naturally infected dogs. The primers and probe were designed to amplify a 93bp fragment of the single copy E. canis 16S rRNA gene with the TaqMan system. All EI dogs were positive for E. canis DNA by 7d PI and developed clinical ehrlichiosis by 9-12d PI. A rapid increase in ehrlichial DNA in EI dogs correlated with the appearance of severe clinical signs of disease. The mean spleen and blood DNA copies significantly increased by more than 10-folds from 7d PI to 10 and 12d PI (p<0.05). E. canis DNA was undetectable in the blood by day 9 post-treatment. Although the spleen was more frequently positive than blood (15/15 specimens vs. 13/15), no significant differences were found between the mean ehrlichial DNA copies in the spleen and blood on each day of examination. In 12 naturally infected dogs, the mean blood DNA copies was similar to the number found in EI 7d PI, but significantly lower than the means of 10 and 12d PI (p<0.0001). Although the conjunctivas of all EI dogs were positive by 12d PI, only 3/5 (60%) NI dogs were positive also by conjunctival PCR. In conclusion, the kinetics of E. canis during acute experimental infection with complete pathogen clearance following doxycyline treatment was demonstrated for the first time by real-time PCR. The value of real-time PCR was shown in NI dogs as well as in EI dogs with spleen and blood sampling more sensitive than non-invasive conjunctival PCR.

Acute human parvovirus B-19 infection in hospitalized children: A serologic and molecular survey.

BACKGROUND: The extent and clinical manifestations of acute human parvovirus B19 (B19) infection were assessed in previously healthy hospitalized children admitted with clinical syndromes potentially associated the virus. PATIENTS AND METHODS: The study was prospective and was conducted between October 2002 and August 2004 in the pediatric departments of 3 hospitals in Israel. The survey included previously healthy children who were hospitalized with 1 or more of the following acute diseases: acute nonallergic exanthema, fever for >1 week, aplastic anemia or pancytopenia, acute nonbacterial arthropathy, immune thrombocytopenic purpura (ITP), Henoch-Schönlein purpura (HSP) and aseptic meningitis. A control group of children with a proven, non-B19 infection was also studied. Serum samples obtained from each child on admission were tested for B19 DNA by real-time PCR and B19 IgM by ELISA. Acute B19 infection was defined by the following criteria: positive serum B19-DNA and/or B19 IgM, negative serum B19 IgG, and no other proven infection. RESULTS: Overall, 167 children were included in the study. The mean age was 5.5 +/- 4.6 years (range, 0.5-17), males and females equally divided. Acute B19 infection was demonstrated in 12.6% (n = 21) of the children. Both tests were performed in 19 children and were positive in 10 (53%). In 7 and 2 children, only B19-DNA or B19 IgM, respectively, was positive. Acute B19 infection was documented in 27% (10/39) of children who presented with a variety of acute exanthema diseases; 9% (5/57) of children with acute arthropathy (all 5 had transient synovitis); 10% (2/21) of children with fever >1 week, both presented as mononucleosis syndrome; and in 44% (4/9) of children with transient pancytopenia or aplastic anemia. No acute B19 infection was demonstrated in 15 children with ITP, 9 with HSP, and 6 with aseptic meningitis and among 70 children in the control group. By logistic regression analysis, manifestations significantly associated with acute B19 infection were exanthema (OR 2.9; 95% CI = 1.1-7.5), anemia (OR 6.35; 95% CI = 2.2-18.2) and leucopenia (OR 4.14; 95% CI =1.2-14.2). CONCLUSIONS: Acute B19 infection was documented among 12.6% of children hospitalized with clinical syndrome potentially associated with the virus. Clinical and laboratory features associated with acute B19 infection were exanthema, anemia and leucopenia. Determination of both serum B19-DNA and serum B19 IgM should be performed for the accurate diagnosis of acute B19 infection.