Spatio-Temporal History of HIV-1 CRF35_AD in Afghanistan and Iran

Frequency of Fusion Inhibitor Resistance Mutations Among Therapy-Naïve HIV Patients

Glycoprotein 41 (gp41) of the human immunodeficiency virus type 1 (HIV-1) protein plays a critical role in membrane fusion. Gp41 binds to proteins in the plasma membrane of CD4+ T cells, particularly the T-cell antigen receptor (TCR). These findings indicate that gp41 is involved in the assembly of HIV-1 at the plasma membrane of T cells and affects the stimulation of the TCR. To control HIV-1, new inhibitors were introduced to target the gp41 protein. However, mutations in this region might reduce their efficacy. The Gp41 region was amplified from the sera of 30 patients using nested polymerase chain reaction. The sequences were analyzed by bioinformatics tools to identify mutations and gp41 structural features. Subtyping and the interaction between fusion inhibitors and gp41 proteins were also examined. As the first report from Iran, docking analysis between fusion inhibitors and Iranian gp41 proteins showed that mutations in gp41 could not reduce the efficacy of the fusion inhibitors. Most of the patients were infected with CRF35-AD. Several post-modification positions, including glycosylation and phosphorylation sites, were identified in the gp41 protein. Our findings revealed no known multinational drug resistance to gp41 inhibitors; thus, fusion inhibitors can effectively inhibit HIV in Iranian patients. In addition, the present study introduced a new gp41 region (36-44 aa), which considerably influences the interactions between gp41 inhibitors and the gp41 protein. This region may play a pivotal role in suppressing gp41 inhibitors in CFR35-AD. Furthermore, gp41 can be considered a good target for subtyping analysis via the phylogenetic method.

The daunting task of fighting HIV in Afghanistan: Current evidence and future recommendations

The human immunodeficiency virus (HIV), like any other disease, has created great worry in Afghanistan. The country's slew of issues has paved the way for HIV to spread and go unchecked. International groups have banded together to stop the virus's spread since the first case was confirmed in Afghanistan. The cumulative effects of international collaboration have aided in the reduction of cases and improved awareness. Because of their injection use, a large portion of the country's population has been classified as a vulnerable category for HIV infection. Awareness campaigns and international collaboration should be implemented to further limit the spread of HIV.

HIV in Iran: onset, responses, and future directions

Iran, a country in the Middle East and North Africa (MENA) region, has been actively involved in the fight against HIV/AIDS over the past three decades. The unique features of the HIV epidemic in Iran are reflected by the modes of transmission and its recent changes to improve management and prevention programs. In this review, we recount the initial onset and subsequent spread of HIV infection in Iran, beginning with the first case diagnosed to the ongoing responses and most recent achievements in controlling this epidemic. Although in the MENA region, Iran is one of the pioneers in implementing pertinent policies including harm reduction services to decrease HIV incidence, drug injection still continues to be the major risk of infection. In line with other nations, the programs in Iran aim at the UNAIDS 90-90-90 targets (UNAIDS 90-90-90 global targets to end the AIDS epidemic by 2020: by 2020, 90% of all people living with HIV will know their HIV status; 90% of all people with diagnosed HIV infection will receive sustained antiretroviral therapy; and 90% of all people receiving antiretroviral therapy will have viral suppression) and to eliminate mother-to-child HIV transmission. In this article, we discuss the strengths and shortcomings of the current HIV programs and offer suggestions to provide a better perspective to track and respond to the HIV epidemic. More generally, our account of the national religious and cultural circumstances as well as obstacles to the approaches chosen can provide insights for decision-makers in other countries and institutions with comparable settings and infrastructures.

Epidemiology of West Nile Virus in the Eastern Mediterranean region: A systematic review

Background

West Nile Virus (WNV), a member of the genus Flavivirus, is one of the most widely distributed arboviruses in the world. Despite some evidence for circulation of WNV in countries summarized by the World Health Organization as the Eastern Mediterrian Regional Office (EMRO), comprehensive knowledge about its epidemiology remains largely unknown. This study aims to provide a concise review of the published literature on WNV infections in the Eastern Mediterranean Regional Office of WHO (EMRO).

Methodology/principal findings

A systematic review of WNV prevalence studies on humans, animals and vectors in the EMRO region was performed by searching: Web of Science, Science Direct, Scopus, PubMed, Embase and Google Scholar. Finally, 77 citations were included, comprising 35 seroprevalence studies on general population (24460 individuals), 15 prevalence studies among patients (3439 individuals), 22 seroprevalence studies among animals (10309 animals), and 9 studies on vectors (184242 vector species). Of the 22 countries in this region, five had no data on WNV infection among different populations. These countries include Kuwait, Bahrain, Oman, Syria and Somalia. On the other hand, among countries with available data, WNV-specific antibodies were detected in the general population of all investigated countries including Djibouti (0.3–60%), Egypt (1–61%), Iran (0–30%), Iraq (11.6–15.1%), Jordan (8%), Lebanon (0.5–1%), Libya (2.3%), Morocco (0–18.8%), Pakistan (0.6–65.0%), Sudan (2.2–47%), and Tunisia (4.3–31.1%). WNV RNA were also detected in patient populations of Iran (1.2%), Pakistan (33.3%), and Tunisia (5.3% –15.9%). WNV-specific antibodies were also detected in a wide range of animal species. The highest seropositivity rate was observed among equids (100% in Morocco) and dogs (96% in Morocco). The highest seroprevalence among birds was seen in Tunisia (23%). In addition, WNV infection was detected in mosquitoes (Culex, and Aedes) and ticks (Argas reflexus hermanni). The primary vector of WNV (Culex pipiens s.l.) was detected in Djibouti, Egypt, Iran and Tunisia, and in mosquitoes of all these countries, WNV was demonstrated.

Conclusions

This first systematic regional assessment of WNV prevalence provides evidence to support the circulation of WNV in the EMRO region as nearly all studies showed evidence of WNV infection in human as well as animal/vector populations. These findings highlight the need for continued prevention and control strategies and the collection of epidemiologic data for WNV epidemic status, especially in countries that lack reliable surveillance systems.

West Nile Virus (WNV) is a mosquito-borne Flavivirus belonging to the Flaviviridae family, which is endemic in a vast geographical area, including the EMRO region. However, the epidemiology of WNV in the EMRO region remains poorly understood. To address this gap, we performed a systematic review on WNV prevalence studies conducted on human populations, animals and vectors across Eastern Mediterranean countries. Our review indicated the infection of most investigated human, animal and vector populations with WNV; however, the paucity of epidemiological data underline the need for integrated surveillance programs as well as continued deployment of prevention and control strategies.

Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequences

Accurate classification of HIV-1 group M lineages, henceforth referred to as subtyping, is essential for understanding global HIV-1 molecular epidemiology. Because most HIV-1 sequencing is done for genotypic resistance testing pol gene, we sought to develop a set of geographically-stratified pol sequences that represent HIV-1 group M sequence diversity. Representative pol sequences differ from representative complete genome sequences because not all CRFs have pol recombination points and because complete genome sequences may not faithfully reflect HIV-1 pol diversity. We developed a software pipeline that compiled 6,034 one-per-person complete HIV-1 pol sequences annotated by country and year belonging to 11 pure subtypes and 70 CRFs and selected a set of sequences whose average distance to the remaining sequences is minimized for each subtype/CRF and country to generate a Geographically-Stratified set of 716 Pol Subtype/CRF (GSPS) reference sequences. We provide extensive data on pol diversity within each subtype/CRF and country combination. The GSPS reference set will also be useful for HIV-1 pol subtyping.

Molecular epidemiology of infectious diseases

Molecular epidemiology (ME) is a branch of epidemiology developed by merging molecular biology into epidemiological studies. In this paper, the authors try to discuss the ways that molecular epidemiology studies identify infectious diseases' causation and pathogenesis, and unravel infectious agents' sources, reservoirs, circulation pattern, transmission pattern, transmission probability, and transmission order. They bring real-world examples of research works in each area to make each study design more understandable. They also address some research areas and study design aspects that need further attention in future. They close with some thoughts about future directions in this field and emphasize on the need for training competent molecular epidemiology specialists that are capable of dealing with rapid advances in the field.

Genetic characterization of human immunodeficiency virus type 1 transmission in the Middle East and North Africa

BACKGROUND

The HIV-1 spread in the Middle East and North Africa (MENA) has not been previously characterised using the phylogenetic approach. The aim of the current study was to investigate the genetic diversity and domestic transmission of HIV-1 in the MENA.

METHODS

A total of 2036 HIV-1 sequences available in Genbank and collected in the MENA during 1988-2016 were used together with 715 HIV-1 reference sequences that were retrieved from Genbank based on genetic similarity with the MENA sequences. The REGA and COMET tools were used to determine HIV-1 subtypes and circulating recombinant forms. Maximum Likelihood and Bayesian phylogenetic analyses were used to identify and date HIV-1 transmission clusters.

RESULTS

At least 21 HIV-1 subtypes and recombinant forms were prevalent in the MENA. Subtype B was the most common variant (39%), followed by CRF35_AD (19%) and CRF02_AG (14%). The most common genetic region was pol, and 675 partial pol sequences (average of 1005 bp) were eligible for detailed phylogenetic analysis. Fifty-four percent of the MENA sequences formed HIV-1 transmission clusters. Whereas numerous clusters were country-specific, some clusters indicated transmission links between countries for subtypes B, C and CRF02_AG. This was more common in North Africa compared with the Middle East (p < 0.001). Recombinant forms had a larger proportion of clustering compared to pure subtypes (p < 0.001). The largest MENA clusters dated back to 1991 (an Algerian CRF06_cpx cluster of 43 sequences) and 2002 (a Tunisian CRF02_AG cluster of 48 sequences).

CONCLUSIONS

We found an extensive HIV-1 diversity in the MENA and a high proportion of sequences in transmission clusters. This study highlights the need for preventive measures in the MENA to limit HIV-1 spread in this region.

Prevalence of HIV-1 transmitted drug resistance in recently infected, treatment-naïve persons in the Southwest of Iran, 2014-2015

The emergence and transmission of drug resistant HIV mutants is a major concern, especially in resource-limited countries with expanding antiretroviral therapy. Studies have recently reported the prevalence of HIV-1 transmitted drug resistance (TDR) mutations in certain Iranian cities; however, no information is currently available about the level of TDR, as well as the nature of the circulating HIV-1 subtypes, in the Southwestern bordering province of Iran, Khuzestan. Herein, we used a WHO-recommended TDR survey method to classify the prevalence of TDR in indigenous people of Khuzestan province. For this purpose, between March 2014 and February 2015, blood samples were collected from 52 newly diagnosed, antiretroviral treatment-naïve, HIV-1 infected persons aged from 18 to 30 years. TDR mutations were determined by sequencing the protease (PR) and reverse transcriptase (RT) genes and interpreted using the WHO drug resistance mutations surveillance list. HIV-1 subtypes were characterized by sequencing the PR-RT, C2-V5, and p17 regions of the pol, env and gag genes, respectively. Two participants had non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance mutations, specifically K103N in one individual and K101EK/K103KN/G190AG in the other. No nucleoside reverse transcriptase inhibitor (NRTI) or major protease inhibitor (PI) mutations were identified. HIV-1 subtyping revealed that all participants were infected with HIV-1 CRF35_AD. According to the WHO sequential sampling method, the prevalence of HIV-1 TDR in the sampling area (Khuzestan province) was classified as moderate for NNRTIs and low for NRTIs and PIs. This is the first HIV-1 drug resistance threshold survey in the Khuzestan province of Iran and shows a predominance of NNRTI TDR mutations in this area.