Characterization Of HIV-1 Subtype Research Articles

Characterization of HIV-1 subtypes and drug resistance mutations in Slovakia: update 2017-2018.

This study aimed to provide an overview on the HIV-1 subtypes circulating in Slovakia between 2017 and 2018 and to evaluate the risk of transmission of HIV‑resistant strains. The HIV epidemic in Slovakia is characterised by low incidence of new and pre-existing infections and aslightly elevated level of strain heterogeneity. Partial HIV pol gene sequences of 110 individuals newly diagnosed with HIV between 2017 and 2018 were analysed. The genotypic analysis revealed sporadic occurrence of mutations linked to HIV resistance to antiretroviral therapy (ART). The HIV-1 Bsubtype has been found as predominant (84.55%) and primarily linked to men who have sex with men (MSM). Atotal of eighteen individuals (15.45%) were found to be infected with HIV-1 non-B subtypes. The data suggest aminimal risk of aresistant HIV strain transmission and amarginal rise of HIV-1 subtypes´ diversity. The HIV-1 Bsubtype remains the most prevalent in the period 2017-2018 in Slovakia (Tab. 2, Fig. 2, Ref. 37).

Diversity and characterization of HIV-1 subtypes in the United States, 2008–2016

PurposeThis article describes subtype diversity among diagnosed HIV-1 infections in the United States during 2008–2016 by demographic or risk group and over time. MethodsHIV-1 polymerase sequences reported to the National HIV Surveillance System for persons in 17 U.S. states with HIV infection diagnosed during 2008–2016 were subtyped using COMET, an automated subtyping tool, and National HIV Surveillance System demographic data were analyzed. ResultsSubtype B was identified in 93.6% of 121,793 reported sequences. The most common non-B subtypes and circulating recombinant forms (CRFs) were C, CRF02_AG, A, CRF01_AE, and G. Elevated percentages of non-B subtypes or CRFs were found in persons who were female, aged less than 13 years at diagnosis, Asian, or had transmission attributable to heterosexual contact (females only) or perinatal exposure. Foreign-born persons had a higher percentage of non-B subtypes. The prevalence of non-B subtypes and CRFs increased from 5.0% in 2008 to 8.5% in 2016; among specific subtypes and CRFs, subtype G and CRF01_AE increased. ConclusionsSubtype B remains the predominant strain in the United States. Non-B subtypes and CRFs were not widespread, but diversity and numbers increased from 2008 through 2016, which could have consequences for clinical management, diagnostic testing, and vaccine development.

Characterization of HIV-1 subtypes and transmitted drug resistance among treatment-naive HIV-infected individuals in Zhejiang, China, 2014-2017.

In recent years, transmitted drug resistance (TDR) has adversely impacted upon first-line therapy for HIV-infected individuals. To understand the current subtype distribution and TDR level in Zhejiang, China we performed phylogenetic analysis and genotypic drug resistance testing of treatment-naive HIV-infected individuals. A total of 153 HIV-1 Pol genes were successfully amplified. The distribution of HIV-1 genotypes was as follows: CRF01_AE (43.8%); CRF07_BC (37.9%); subtype B/B' (7.2%); CRF08_BC (5.2%); and others (5.9%). Drug resistance analysis demonstrated that 11.1% of isolates contained at least one NRTI or NNRTI resistance-associated mutations while 2.0% were identified to be resistant to PIs. These findings enhance our understanding of the genetic diversity of HIV-1 strains circulating in Zhejiang and provide some guidelines for HIV initial treatment therapy.

The First Characterization of HIV-1 Subtypes and Drug Resistance Mutations among Antiretrovirally Treated Patients in Kermanshah, Iran

Background: Insufficient therapy during HIV-1 replication can promote the emergence of drug-resistant strains, reduce the effectiveness of antiretroviral treatment (ART), and increase the likelihood of the onward transmission of drug-resistant viruses. We characterized, for the first time, the prevalence of HIV-1 subtypes and drug resistance mutations in a western region of Iran. Methods: This study was conducted among 122 patients on ART at a major referral center in Kermanshah, Iran. Nested PCR was performed using RT gene-specific primers from the pol gene. Sequencing was followed by amplification and purification of the desired sequence. Subtypes and mutations were determined using the Stanford HIV Drug Resistance Database. Results: Most patients (92.6%) had subtype CRF 35-AD; 7.4% had subtype B. In total, 36.1% of the patients had at least 1 mutation associated with resistance RT inhibitors. The greatest rates of high-level resistance were observed for nevirapine (21.3%) and efavirenz (19.7%). Conclusions: Our results showed a high prevalence of drug resistance mutations in strains isolated from patients on treatment. At our center, we therefore recommend that genotyping be performed. This would allow the physician to prescribe appropriate drugs, reduce treatment costs, and increase the longevity and quality of life of patients.

Characterization of HIV-1 subtypes in a Portuguese cohort.

IntroductionDistribution of HIV-1 subtypes is variable around the world, with the most common subtype in western Europe being subtype B. The aim our study was to describe the prevalence of different HIV-1 subtypes in newly diagnosed patients and identify demographic and epidemiological characteristics related with different subtypes.Materials and MethodsRetrospective single-centre study of patients newly diagnosed with HIV-1 infection between 2006 and 2012. Epidemiological data was gathered and genotyping was performed in each patient identified. Demographic and epidemiological characteristics were compared between patients with subtype B and other subtypes. Continuous variables were summarized by mean and standard deviation whereas categorical variables were presented as proportions. Comparison of groups was performed using the Chi square, Fisher exact test and Student T test. Statistical significance was assumed when p<0.05.ResultsIn the period of the study, 624 patients newly diagnosed with HIV-1 infection were submitted to genotypic testing but information about subtype was available only for 592 patients. General characteristics of the patients are summarized in Table 1. The distribution of the identified subtypes was the following: 286 (48.3%) patients had subtype B, 157 (26.5%) had subtype G, 54 (9.1%) had subtype C, 36 (6.1%) had subtype A, 32 (5.4%) had subtype F and 25 (4.2%) had CRF's. Patients with subtype B were more commonly male (p=0.001) and younger (p<0.0001) than those with subtypes other than B. Subtype B was more common in MSM patients, while non-B subtypes were more common in heterosexual patients and in injecting drug users (p=0.001). CD4-cell count, viral load and AIDS at presentation were not significantly different between subtypes. Resistance associated mutations were significantly more common in patients with non-B subtypes (15.4% vs 9.8%; p=0.048).ConclusionsThe most commonly identified subtype was B in accordance with previous reports from other western European countries. However, in our cohort the proportion of non-B subtypes is higher than that reported for other European countries, probably reflecting the influence of strong bonds with Portuguese speaking African countries. Knowledge about HIV subtypes distribution may help understanding transmission dynamics and can be an important tool in the design of preventive measures.

Genetic Characterization of HIV-1 Subtype D Near-Full-Length Proviral Genomes by Illumina Massively Parallel Sequencing Technology.

This study describes the near-full-length genome deep sequencing of two HIV-1 subtype D strains identified in blood donors in Rio de Janeiro, Brazil, in what seems to have been a small restricted subtype D epidemic in the country.

Genetic characterization of HIV-1 subtype G envelope sequences by single genome analysis

Background Subtype G is the sixth most prevalent subtype of HIV-1 and is responsible for an estimated 1,500,000 infections worldwide. Although systematic analyses of a wide range of HIV-1 envelope sequences and neutralization have been performed, subtype G viruses are severely underrepresented in these studies. There is thus an important need to study subtype G envelope sequences and their neutralization capacities.

Characterization of HIV-1 subtypes and viral antiretroviral drug resistance in men who have sex with men in Beijing, China

To characterize the HIV subtypes prevalent among men who have sex with men (MSM) in Beijing and to perform baseline genotypic analysis of anti-HIV drug resistance in this population. In 2005, half of new HIV-1 infections occurred through unprotected sex in China. MSM have become the second most vulnerable group to HIV infection. HIV-1-prevalent subtypes among this population as well as their genetic and biological characteristics have not been well defined. A cohort consisting of 54 HIV-seropositive MSM were recruited with written informed consent. Samples of plasma and whole blood were collected to characterize prevalent HIV-1 subtypes with overlapped polymerase chain reaction followed by sequencing and phylogenic analysis. The genotypes of anti-HIV drug resistance were analysed. Among the amplified gag sequences, HIV-1 subtype B accounted for 71.1% (32/45), followed by CRF01_AE for 24.4% (11/45) and CRF07_BC for 4.4% (2/45). A similar trend was observed among the amplified env sequences. Six antiretroviral therapy (ART)-naive participants (15%) carried drug-resistant mutations, with intermediate to high-level resistance both to drugs used in China including zidovudine, didanosine, nevirapine, stavudine, and lamivudine, and drugs not used in China such as delavirdine, efavirenz, tenofovir, emtricitabine and abacavir. We also have concerns over nelfinavir and atazanavir regarding their future use in China because low-level resistance was also seen against those drugs. The HIV-1 strains prevalent among Beijing MSM include complex subtypes derived from recombination. High rates of HIV drug-resistant mutations in ART-naive patients represent a serious challenge for HIV prevention and treatment programmes in China.

Characterization of HIV-1 subtype C envelope glycoproteins from perinatally infected children with different courses of disease.

BackgroundThe causal mechanisms of differential disease progression in HIV-1 infected children remain poorly defined, and much of the accumulated knowledge comes from studies of subtype B infected individuals. The applicability of such findings to other subtypes, such as subtype C, remains to be substantiated. In this study, we longitudinally characterized the evolution of the Env V1–V5 region from seven subtype C HIV-1 perinatally infected children with different clinical outcomes. We investigated the possible influence of viral genotype and humoral immune response on disease progression in infants.ResultsGenetic analyses revealed that rapid progressors (infants that died in the first year of life) received and maintained a genetically homogeneous viral population throughout the disease course. In contrast, slow progressors (infants that remained clinically asymptomatic for up to four years) also exhibited low levels variation initially, but attained higher levels of diversity over time. Genetic assessment of variation, as indicated by dN/dS, showed that particular regions of Env undergo selective changes. Nevertheless, the magnitude and distribution of these changes did not segregate slow and rapid progressors. Longitudinal trends in Env V1–V5 length and the number of potential N-glycosylation sites varied among patients but also failed to discriminate between fast and slow progressors. Viral isolates from rapid progressors and slow progressors displayed no significant growth properties differences in vitro. The neutralizing activity in maternal and infant baseline plasma also varied in its effectiveness against the initial virus from the infants but did not differentiate rapid from slow progressors. Quantification of the neutralization susceptibility of the initial infant viral isolates to maternal baseline plasma indicated that both sensitive and resistant viruses were transmitted, irrespective of disease course. We showed that humoral immunity, whether passively acquired or developed de novo in the infected children, varied but was not predictive of disease progression.ConclusionOur data suggest that neither genetic variation in env, or initial maternal neutralizing activity, or the level of passively acquired neutralizing antibody, or the level of the de novo neutralization response appear to be linked to differences in disease progression in subtype C HIV-1 infected children.

Biological, serological, and genetic characterization of HIV-1 subtype E isolates from northern Thailand.

Twenty-three HIV-1 isolates were recovered from PBMCs from 26 HIV-1-seropositive individuals in northern Thailand. The viruses grew readily in human PBMCs but only 7 of 17 (41.2%) and 5 of 17 (29.4%) replicated and only at a low level in primary macrophages and in established T cell lines, respectively. By immunoblot assays, sera from Thai subjects were strongly reactive with gp120 from a Thailand isolate, moderately reactive with a Rwandan isolate, and weakly reactive with a North American strain. These three viruses represent, respectively, examples of subtypes E, A, and B as classified by the sequences of the envelope region. Serological assays indicated that broadly reactive rather than type-specific neutralizing activity was detected among these northern Thai sera. The majority of the sera (approximately 75%) neutralized a representative Thailand isolate and the Rwanda isolate but only 55% neutralized the North American strain. However, the difference was not statistically significant. The genetic analyses indicated that nearly all the Thai isolates were highly homogeneous and distinct from the North American/European consensus sequence (subtype B); they belong to subtype E. This is the first report providing biological, serological, and genetic characterization of HIV-1 strains from Thailand. The findings suggest these viruses were recently introduced into the country and that serological evaluation of viral strains needs to be considered along with genetic subtyping when developing an HIV-1 vaccine.