Transmission patterns of HIV-subtypes A/AE versus B: inferring risk-behavior trends and treatment-efficacy limitations from viral genotypic data obtained prior to and during antiretroviral therapy.

BACKGROUND: HIV subtypes A and CRF01_AE (A/AE) became prevalent in Israel, first through immigration of infected people, mostly intravenous-drug users (IVDU), from Former Soviet-Union (FSU) countries and then also by local spreading. We retrospectively studied virus-transmission patterns of these subtypes in comparison to the longer-established subtype B, evaluating in particular risk-group related differences. We also examined to what extent distinct drug-resistance patterns in subtypes A/AE versus B reflected differences in patient behavior and drug-treatment history. METHODS: Reverse-transcriptase (RT) and protease sequences were retrospectively analyzed along with clinical and epidemiological data. MEGA, ClusalX, and Beast programs were used in a phylogenetic analysis to identify transmission networks. RESULTS: 318 drug-naive individuals with A/AE or patients failing combination antiretroviral therapy (cART) were identified. 61% were IVDU. Compared to infected homosexuals, IVDU transmitted HIV infrequently and, typically, only to a single partner. 6.8% of drug-naive patients had drug resistance. Treatment-failing, regimen-stratified subtype-A/AE- and B-patients differed from each other significantly in the frequencies of the major resistance-conferring mutations T215FY, K219QE and several secondary mutations. Notably, failing boosted protease-inhibitors (PI) treatment was not significantly associated with protease or RT mutations in either subtype. CONCLUSIONS: While sizable transmission networks occur in infected homosexuals, continued HIV transmission among IVDU in Israel is largely sporadic and the rate is relatively modest, as is that of drug-resistance transmission. Deviation of drug-naive A/AE sequences from subtype-B consensus sequence, documented here, may subtly affect drug-resistance pathways. Conspicuous differences in overall drug-resistance that are manifest before regimen stratification can be largely explained in terms of treatment history, by the different efficacy/adherence limitations of older versus newer regimens. The phenomenon of treatment failure in boosted-PI-including regimens in the apparent absence of drug-resistance to any of the drugs, and its relation to adherence, require further investigation

The DNA sequence of the RK strain of human herpesvirus 7

The complete DNA sequence of human herpesvirus-7 (HHV-7) strain RK was determined following direct cloning of virion DNA fragments into a sequencing vector. The sequence was compared with the previously published complete sequences of HHV-7 strain JI and human herpesvirus-6 (HHV-6) strain U1102. Despite a very close relationship between the two HHV-7 strains, differences are apparent in regions containing tandem reiterations, particularly in the “telomeric” reiterations located near the termini of the large direct repeat at the genome ends, and in a total of 179 additional positions distributed throughout the genome (i.e., about one nucleotide difference per kbp). This extent of divergence implies that the two strains arose from an ancestral virus several thousands of years ago. Differences that affect coding potential do not cluster in particular protein-coding regions, indicating that specific HHV-7 genes have not been measurably subject to unusual evolutionary pressures since divergence. Reassessments of genetic content indicated that the HHV-7 genome contains 84 different genes, whereas the HHV-6 genome contains 85. All HHV-7 genes but 1 have direct HHV-6 counterparts, and all but 2 HHV-6 genes have HHV-7 homologues. Sequence comparisons between HHV-7 and HHV-6 provided evidence that the protein-coding regions of 11 genes are expressed by splicing

Resistance Mutations in the reverse transcriptase of drug-naive and drug-treated individuals.

<p>250 samples from 234 drug-naive patients and 115 samples from 78 treated A/AE patients were genotyped. 31 patients were sampled both prior to treatment and after treatment failure. RT mutations found in all A/AE naive patients were compared to those found in A/AE drug-treated ones and to samples from 254 drug naive and 60 drug treated B individuals diagnosed since 2001. The first available sample from each drug-naive individual was used for analysis. For mutation-frequency analysis of drug-treated patients each mutation was counted once. Only mutations showing statistically significant differences between drug-naive and drug-treated patients and/or between A/AE and B frequencies are included.</p><p>Major NRTI related mutations included TAMs: M41L, D67N, K70R, L210W, T216Y/F and K219Q/E, as well as A62V, K65R, L74V/I, L77F, F116Y, Q151M and M184V/I. Major NNRTI mutations included A98G, L100I, K101E/P, K103N/S, V106A/M, V108I, Y181C, Y188C/H/I, G190A/S, P225H and K238T.</p><p>NNRTIs – Non-nucleosides reverse transcriptase inhibitors; NS – Not significant; NRTIs – Nucleosides reverse transcriptase inhibitors;</p>a<p>Subtyping was performed using the Stanford Database Rapid Subtyping Tool <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057789#pone.0057789-Rhee1" target="_blank">[23]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057789#pone.0057789-Rhee2" target="_blank">[24]</a>. According to that classification 192 patients had virus containing protease of subtype A and RT most similar to CRF01_AE; for 70 both the protease and the RT were CRF01_AE; 52 were of subtype A; and four had protease classified as CRF01_AE and RT classified as A. Other subtyping tools such as Geno2Pheno (<a href="http://www.geno2pheno.org/" target="_blank">http://www.geno2pheno.org/</a>) or the Rega Subtyping Tool (<a href="http://jose.med.kuleuven.be/subtypetool/html/" target="_blank">http://jose.med.kuleuven.be/subtypetool/html/</a>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057789#pone.0057789-deOliveira1" target="_blank">[57]</a> vary to some extent in the classification of variants.</p

First-administrated and actual drug regimens while failing treatment.

a<p>All except 5 received NRTIs as part of the first regimen. A few received mono- or duo-therapy or combinations of PIs and NNRTIs.</p>b<p>All 78 treatment-failing patients received NRTI backbone. Thirty-four received also PI and 39 NNRTI as additional drug.</p><p>3TC – lamivudine; EFV – efavirenz; FTC – emtricitabine; LPV/r – lopinavir/r; NNRTI – Non-Nucleoside Reverse Trancriptase Inhibitor; NRTI – Nucleoside Reverse Trancriptase Inhibitor; NVP – nevirapine; PI – Protease inhibitor; r – ritonavir; TDF – tenofovir; ZDV – zidovudine.</p