Challenges in Elucidating HIV Genetic Diversity in the Middle East and North Africa: A Review Based on a Systematic Search

1. Introduction

The human immunodeficiency viruses (HIV) are rapidly evolving viruses characterized by extensive genetic diversity [1,2,3]. The extensive diversity of these retroviruses is reflected in its classification into two types: HIV-1 and HIV-2; and four major groups for HIV-1: M, N, O, and P [4]. Group M (major) of is responsible for the vast majority of HIV-1 infections globally and it is further divided into several subtypes (A, B, C, D, F, G, H, J, K), numerous circulating recombinant forms (CRFs), and a countless number of unique recombinant forms (URFs) [5,6,7,8,9].

The global distribution of HIV-1 group M subtypes/CRFs is shaped by historical factors and contemporary transmission dynamics, region-specific distribution of HIV genetic variants [3,4,10,11]. For example, subtype C of HIV-1, which accounts for over half of the global HIV-1 infections, predominates in sub-Saharan Africa (SSA) and India, whereas subtype B is more common in Europe, North America, and certain regions of South America [3,6,12,13]. In Southeast Asia, CRF01_AE is widespread with evidence indicating the role of sex tourism in its global spread [14,15]. In Russia and former Soviet Union countries, subtype A predominates [3,16], while in West and Central Africa, a mixture of HIV-1 and HIV-2 subtypes circulate with predominance of CRF02_AG [3,17,18].

The genetic diversity of HIV-1 is the result of its high evolutionary rate driven by high substitution rate and frequent occurrence of recombination [1,19,20]. The implications of extensive HIV-1 genetic diversity are profound since it contributes to virus virulence, disease progression, and the development of antiretroviral (ARV) drug resistance [19,21,22,23,24,25]. Specifically, variability in the viral envelope (env) gene that encode the HIV surface glycoproteins gp120 and gp41, is a major factor in evasion of humoral immune response [26,27]. Additionally, the swift evolution in the reverse transcriptase, protease, and integrase proteins —the primary targets of ARV drugs— can lead to ARV drug resistance, which would complicate successful management of HIV/AIDS [25,28].

The Middle East and North Africa (MENA) is a region with a complex HIV-1 epidemic [29]. The HIV-1 epidemic in the MENA is characterized by diverse transmission patterns and complex diversity of HIV-1 variants driven by unique socio-cultural factors in the regions [29,30,31,32]. However, accurate mapping of the MENA HIV-1 epidemic is complicated by limited epidemiological and virus sequence data [29,30,31,32,33,34]. Historically, the MENA has been considered as a region with a relatively low prevalence of HIV/AIDS [34,35]. Current estimates suggest that the overall adult HIV prevalence remains below 0.1% in the MENA region; however, certain countries and sub-populations exhibit much higher HIV prevalence rates [36,37,38,39]. Notably, the UNAIDS reported an increase in new HIV infections in the MENA by 116% between 2010 and 2023 [40]. Additionally, recent evidence suggested an accompanying rising trend in HIV prevalence in certain sub-populations [41]. In particular, this trend has been reported among most-at-risk groups such as men who have sex with men (MSM), injection drug users (IDUs), and female sex workers (FSWs) [42].

Regarding the genetic diversity of HIV-1 in the MENA region, a heterogeneous pattern of distribution of HIV-1 genetic variants in the MENA was reported based on the limited sequence data from the region [31,32]. This complex pattern of circulation of diverse range of HIV-1 genetic variants in the MENA likely reflects the region’s geographical location at the crossroads of Asia, Africa, and Europe with frequent population movement [12,32,43]. Therefore, a comprehensive understanding of the genetic diversity of HIV-1 in the MENA region is an important aspect of the regional response to tailor intervention and management measures [32,44,45].

Genetic characterization of HIV-1 through phylogeny-based studies provides valuable insights into the origins and spread of HIV-1, allowing the identification of networks of HIV-1 transmission and enable the tracking of cross-border transmissions [32,46,47,48]. Thus, phylogenetic inference methods can elucidate the role of travel and migration in shaping local HIV-1 epidemics [49,50,51,52]. In the MENA region, phylogenetic analysis revealed a considerable proportion of domestic spread of HIV-1 contrary to the previous notions [32]. The utility of genetic data analysis results in understanding HIV-1 transmission dynamics extends to involve the informing of targeted interventions [53]. However, the lack of systematic and comprehensive HIV-1 genetic surveillance across the MENA countries hinder the ability to map the region-specific HIV-1 dynamics comprehensively [54].

In addition to HIV transmission dynamics studies, genetic characterization of HIV-1 is important to address the challenges of ARV drug resistance [55,56,57,58]. The emergence of drug-resistant mutations poses a significant threat to the success of ARV therapy, particularly in regions with limited access to second-line treatment options [59,60]. In the MENA region, preliminary studies showed a range of resistance-associated mutations (RASs), albeit with varying prevalence across countries [61,62,63,64,65,66]. The variability in ARV drugs’ resistance patterns in the MENA highlights the continuous need for region-specific genetic HIV-1 data to guide the selection of first- and second-line ARV drugs regimens for successful management of the patients in the MENA [67].

Regarding the epidemiology of HIV-1 in the MENA, previous studies revealed country-specific patterns, with high-income countries of the Gulf Cooperation Council (GCC), such as Saudi Arabia and the United Arab Emirates, HIV cases have historically been lower, largely due to strict regulations and religious/cultural norms that traditionally discouraged or legally penalized high-risk behaviors [38,68]. By comparison, North African countries, such as Morocco, Libya, Tunisa, and Egypt, characterized concentrated epidemics among at-risk groups [29,69,70,71,72]. In Sudan, perinatal HIV transmission, especially in conflict-affected areas with limited access to healthcare has been reported [73].

Despite the increasing insights through cumulative HIV research in the MENA, the overall picture of HIV-1 genetic diversity in the MENA region remains fragmented. Challenges to accurate depiction of HIV-1 genetic diversity in the MENA is multifactorial and include limited number of sequence data, variable clinical and epidemiological data quality, and poor regional coordination in surveillance efforts [29,32,33,68,74].

On a related note, the efforts to map the genetic diversity of HIV-1 in the MENA region is hindered by additional challenges, including political instability, limited resources, and social stigma associated with HIV infection [29,75,76]. These factors contribute to the deficiency in robust HIV surveillance, with subsequent gaps in knowledge regarding the true scale of HIV-1 epidemic in the MENA region including its genetic diversity. Additionally, the MENA region is characterized by substantial heterogeneity in terms of health infrastructure and response capacity, ranging from high-income countries with advanced health systems to conflict-affected areas where healthcare access is severely limited [77,78,79,80].

The challenges that may negatively impact the elucidation of HIV-1 genetic diversity in the MENA region necessitate deeper understanding through a focused review of literature. Thus, the current review aimed to identify and describe the specific obstacles that could hinder HIV-1 genetic characterization efforts in the MENA. This description can help to propose actionable strategies to overcome these barriers. By identification of these barriers, we aimed to advance the level of understanding of HIV-1 challenges in the MENA, enhance regional and global public health responses, and contribute to the global efforts to reduce the burden of HIV/AIDS.

2. Materials and Methods

2.1. Review Design

This review was designed to comprehensively analyze the challenges in elucidating HIV-1 genetic diversity within the MENA region. To achieve this, we conducted a systematic search of PubMed/MEDLINE and Google Scholar for records published in English which focused on HIV-1 genetic diversity across 18 MENA countries, including the United Arab Emirates (UAE), Qatar, Bahrain, Oman, Saudi Arabia, Kuwait, Iraq, Syria, Lebanon, Palestine, Jordan, Egypt, Sudan, Libya, Tunisia, Algeria, and Morocco.

The 18 countries were selected based on their geographic and cultural inclusion in the MENA region, as well as their shared epidemiological characteristics, which justify a collective assessment. Conversely, we excluded Türkiye, Iran, Israel, Pakistan, Afghanistan, Djibouti, Somalia, South Sudan, and Mauritania, as previous studies have demonstrated distinct epidemic patterns in these countries that differ significantly from the broader MENA region and would therefore fall outside the scope of this review [81,82,83,84,85,86,87,88,89,90,91,92].

2.2. Search Strategy

The literature search was conducted by the first author (Malik Sallam) on 1 October 2024. The inclusion criteria included: (1) Published records; (2) Language of publication is English; and (3) Any type of publication (original article, review, sequence note, short communication, book, book chapter).

The exact PubMed/MEDLINE search strategy was ((HIV) AND ("Middle East" OR "North Africa" OR "MENA" OR "Arab" OR "United Arab Emirates" OR "UAE" OR "Saudi Arabia" OR "Qatar" OR "Bahrain" OR "Oman" OR "Yemen" OR "Kuwait" OR "Iraq" OR "Syria" OR "Palestine" OR "Jordan" OR "Egypt" OR "Sudan" OR "Libya" OR "Algeria" OR "Tunisia" OR "Morocco")) AND ("genetic diversity" OR "molecular epidemiology").

The Google Scholar search was conducted in Publish or Perish (Version 8) [93]. The exact search strategy was based on the keywords function with 10 hits: HIV molecular epidemiology “Country Name” and HIV genetic diversity “Country Name”.

2.3. Themes to be Extracted from Included Records

To identify the key challenges associated with HIV-1 genetic diversity research in the MENA region, a structured approach was used to establish a priori themes to be extracted from the included records. These themes were developed through a combination of literature review followed by a consensus between the first and senior authors based on these cited publications [94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114]. The process was further informed by barriers previously identified in the first author’s PhD thesis, "Phylogenetic Inference in the Epidemiologic and Evolutionary Investigation of HIV-1, HCV, and HBV," which included analysis of MENA HIV-1 sequences from the Los Alamos HIV Sequence Database [115,116].

Four common themes were identified which are summarized in (Figure 1).

The first theme identified was limited sampling and gaps in clinical and epidemiology data. This included insufficient sampling, poor representation of HIV-1 sequences, low HIV-1 sequencing density, and reliance on non-representative cross-sectional studies. Additionally, this theme included the gaps in clinical and epidemiologic data such as the sex of the patients, age, risk factors for HIV-1 acquisition, viral load, etc. These issues were deemed deficiencies in the genetic analysis approach to delineate HIV-1 genetic diversity.

The second theme identified was limited resources and infrastructure constraints. This issue highlights the reliance on older HIV-1 genetic sequencing methods, such as Sanger sequencing, and the limited use of advanced tools like next-generation sequencing (NGS). Restricted research funding and technical capacity were also included in this theme since these issue were considered as hindrances to progress in HIV-1 genetic diversity research.

The third identified theme was HIV-specific factors, which addressed the genetic complexity of HIV-1 due to high rates of mutation and recombination. A lack of full-genome sequencing and robust HIV-1 isolates’ recombination analysis can limited accurate subtyping and the characterization of CRFs/URFs and thus were deemed as a barrier to HIV-1 genetic characterization.

Finally, the fourth theme identified was the socio-cultural, religious issues, and legal barriers. Stigma, cultural taboos, and punitive laws can hinder access to HIV testing and care for key populations, such as MSM and IDUs. These barriers can cause underreporting and significant data gaps in the investigation of HIV-1 genetic diversity.

3. Results

3.1. Description of the Included Records

A total of 38 records were deemed eligible for inclusion in this review as shown in (Figure 2).

These records were mostly original articles 21/38 (55.3%), followed by reviews including systematic reviews 8/38 (21.1%), and sequence notes/dispatches 4/38 (10.5%). The most common source location for the included records was Libya 6/38 (15.8%), followed by Morocco 5/38 (13.2%), Saudi Arabia and MENA as a whole 4/38 (10.5%) for both, Egypt and Kuwait 3/38 (7.9%) for both (Figure 3 and Table 1).

3.2. Challenge of Limited Sampling and Limited Data

A summary of the included records with HIV-1 sequence and data availability is included in (Table 2).

For the studies where original HIV-1 sequences were originated (n = 23), the average number of sequences included was 62±50 (median: 46, IQR: 25 – 65, range: 6–193). Number of sequences per year is shown in Figure 4, which highlighted gaps in sequencing for HIV-1 in the MENA over two stretches of years (2002–2004) and (2009–2011).

Partial clinical data were available for 14 records (60.9%), and clinical data were totally absent in 5 records (21.7%), while full clinical data were present only in four records (17.4%).

In the included records, the following limitations in terms of limited sampling and limited data were identified: In Morocco, a systematic review by Kouyoumjian et al., reported insufficient data on MSM and IDUs, with reliance on convenience sampling and limited behavioral data often affected by self-report biases [128]. Modes of transmission mathematical model predictions in Morocco exhibited considerable uncertainty due to inadequate input data [129].

In the sole study which investigated domestic HIV-1 transmission in the MENA region as a single unit using the phylogenetic maximum likelihood and Bayesian approaches, eight of the 21 MENA countries lacked HIV-1 sequences, and among the 13 countries with available sequences, only seven countries had more than 50 unique sequences [32]. Many HIV-1 MENA sequences were derived from non-representative cross-sectional studies with low sampling density (<1%) [32].

In Libya, discrepancies were noted between government-reported infection rates and independent estimates as reported by Hamidi et al. [139]. In Saudi Arabia, data quality improved since 2011, but MSM populations remained underrepresented as reported by Al-Mozaini et al. [68]. In Jordan, available data were limited to individuals in HIV care who were willing to participate in research [141].

3.3. Challenge of Limited Resources

The results indicated that HIV surveillance in the MENA region remains limited, with only a small number of cases subtyped, primarily using Sanger sequencing rather than NGS for detecting minor variants as reported by Mumtaz et al. [30]. Only a single record reported using NGS for HIV-1 typing and resistance testing [141].

Challenge of accurate depiction of HIV genetic diversity in the MENA linked to limited resources were identified in Libya by Hamidi et al. [139]. In Libya, monitoring relies on mandatory screenings for certificates and hospital-reported cases, resulting in variable accuracy. In Jordan, limited access to HIV testing and care has been identified as a major factor contributing to late diagnoses, with subsequent increases in healthcare costs [141]. Additionally, in Jordan, contributory factors to late HIV diagnosis include limited access to HIV testing and care with subsequent higher healthcare costs.

On the positive side, Morocco made significant progress in addressing the HIV-1 epidemic and is likely the Arab country with the most advanced HIV-1 surveillance system, research capacity, and response framework as reported by Mumtaz et al. [129]. In Saudi Arabia, despite the progress made, Al-Mozaini et al. highlighted the need for establishing innovative testing services, improving medicine delivery systems which could enhance the understanding of HIV genetic diversity [68].

3.4. Challenge Posed by HIV-Specific Factors

In the majority of included records, HIV-1 subtyping results varied based on the methods employed, particularly for short sequences, which often lacked the resolution necessary for definitive subtype/CRF/URF assignment [32].

The scarcity of full-genome HIV sequences further complicated these challenges, as short sequences are less reliable for subtyping particularly to identify recombinant forms. Only a single record reported sequencing full HIV-1 genomes [126]. Several records relied on subtyping tools that may not account for the complexities of recombination, leading to potential misclassification or incomplete characterization of HIV-1 strains as highlighted in the study which analyzed HIV-1 sequences in the MENA region as a whole [32]. Based on these challenges mutation and recombination present significant obstacles to surveillance efforts.

3.5. Socio-Cultural and legal Issues

Socio-cultural and legal barriers can significantly hinder efforts to characterize HIV-1 genetic diversity in the MENA region, as reported in several included records and in the process shown in (Figure 5).

The groups of MSM was reported in a few records as a stigmatized and hidden HIV risk group, and these records reported that MSM face substantial obstacles to status disclosure and care [36,72]. Despite increasing epidemiological evidence on HIV-1 and risk behaviors among MSM, stigma and cultural norms in the MENA likely result in underreporting of male same-sex transmission in official case notifications [72]. Other high-risk groups, such as truck drivers and prisoners, remain underrepresented in research [33,36,42]. In Palestine, socio-cultural and religious barriers limit the identification of vulnerabilities among high-risk groups, with information gaps persisting on the role of transactional sex in HIV transmission [137]. In Libya, historical policies suppressed accurate HIV data which were considered as part of "national security," dismissing scientific evidence and attributing HIV-1 transmission solely to homosexuality [139]. Conspiratorial beliefs, including claims of clandestine HIV vaccine trials by foreign medical staff, have also been reported [125]. High levels of stigma associating HIV/AIDS with immoral behavior leads many individuals to avoid testing to protect personal and family reputations. In the included records, HIV infected individuals in the MENA were reported to experience severe social consequences, including family rejection, societal isolation, and restricted access to healthcare, education, and employment [137,139]. Women living with HIV were particularly reported to be vulnerable to violence, humiliation, and invasive practices such as virginity testing [139]. These socio-cultural and legal challenges can impede research efforts to delineate HIV-1 genetic diversity in the MENA through underreporting and subsequent gaps in data available for analysis.

4. Discussion

Identification and investigation of possible challenges that could negatively impact the accurate depiction of HIV-1 genetic diversity in the MENA is highly important. HIV-1 is characterized by swift evolutionary rate with subsequent extensive genetic diversity [145,146]. This rapid rate of HIV-1 evolution would in turn complicate HIV/AIDS management and prevention through compromised monitoring of ARV drug resistance and negative effects on vaccine design [147,148]. In the MENA region, the HIV-1 epidemic is characterized by distinct features that result from an interplay of unique socio-cultural, legal, and resource-related aspects [30,33,34,36,42]. Thus, it is important to understand the specific barriers and challenges that would compromise accurate depiction of HIV-1 genetic diversity in the region which in turn would help to develop effective region-specific responses to address the HIV epidemic in the region.

This review identified four key themes that represent barriers to accurate characterization of HIV-1 genetic diversity in the MENA region. These four themes were limited sampling and data gaps, resource and infrastructure constraints, HIV-specific factors, and socio-cultural and legal issues.

The first challenge of limited sampling and insufficient data can profoundly impact efforts to characterize HIV-1 genetic diversity in the MENA region. The molecular epidemiology of an epidemic including HIV-1 epidemics is operating at the population level of pathogens [149]. An important issue to be considered upon conducting genetic diversity investigation is the sampling approach since biased or non-representative sampling will give misleading results [150]. One of the challenging aspects to reconstruct the network of HIV-1 transmission is to obtain a complete sampling density for the population under study given the fraction of undiagnosed HIV-1 infections and the ongoing transmissions [107]. In addition, sampling density will affect the subsequent proportion of HIV-1 phylogenetic clustering indicative of domestic spread of the virus [108,109].

In this review, and across 23 records with HIV-1 sequences, the median number of sequences per record was only 46, with significant gaps in sequencing during two periods, 2002–2004 and 2009–2011. Additionally, as reported in an included record from Morocco, the mathematical models predicting modes of HIV transmission among MSM and IDUs were hampered by insufficient input data and reliance on convenience sampling [129]. Such gaps in data and samples often fail to represent hidden populations, subsequwntly compromising the reliability of transmission estimates [151]. In this review, a record from Libya identified discrepancies between government-reported and independent HIV prevalence rates, which further highlighted the MENA region data limitations aspects [139]. In Jordan, a recent study reported that data were restricted to individuals in HIV care willing to participate in research, creating additional selection bias which might be related to stigma as well [141,152].

The second barrier identified in this review was the challenge of limited resources. This barrier continues to impede HIV-1 genetic diversity research in the MENA region. HIV/AIDS surveillance efforts could also be constrained by traditional methods, with most sequence-based records included in this review relying on Sanger sequencing, which lacks the sensitivity to detect minor variants and recombinants [60,153]. Only one study from Jordan reported the use of NGS, an advanced tool used for robust genetic characterization [141]. Unsurprisingly, the study from Jordan, conducted in collaboration with the Center for Infectious Diseases Research at the Walter Reed Army Institute of Research, emphasize the critical role of international collaboration in addressing resource and capacity constraints faced by the MENA countries to address the topic of HIV-1 genetic diversity [141].

The consequences of health constraints identified in this review can be exemplified in Libya, where monitoring systems relied heavily on mandatory screenings for health certificates and hospital-reported cases [139]. In Jordan, the included study reported that limited access to HIV testing and care contributes to late diagnoses, further complicating health care costs and worsening patient outcomes [141]. These issues resonate with the broader global challenge of healthcare inequity, where underserved populations disproportionately suffer from preventable late-stage complications [154,155,156]. On the other hand, a few MENA countries such as Saudi Arabia and Morocco developed the region’s most advanced HIV surveillance system, demonstrating that resource constraints can be overcome with sustained investment and policy prioritization [68,129]. Saudi Arabia, though making progress, still requires innovative testing services and improved medicine delivery systems to address its unique challenges as reported by an included record in this review by Al-Mozaini et al. [68].

In this review, the third identified challenge was the HIV-specific factors, particularly the genetic complexity of the virus, which pose notable challenges to accurate subtyping and characterization of HIV-1 variants in the MENA region. For example, in HIV-1 molecular epidemiology studies, the choice of the genomic regions to be analyzed are of prime importance with conserved regions unable to resolve the true links compared to phylogenetic noise in hypervariable regions with random links [110,111,112]. Additionally, recombination in HIV is an evident biological phenomenon and can be viewed as means for production of new progeny with higher survival through sharp reduction of deleterious mutations or accumulation of advantageous mutations at a higher rate compared to their occurrence through nucleotide substitution by mutation [157,158]. Additionally, recombination can have adverse effect on molecular clock analysis comprising the validity of estimates of the most recent common ancestor for variant introduction into a region or country [159,160]. Furthermore, construction of phylogenetic trees can be complicated if parts of the nucleotide sequences undergoing analysis were the results of recombination events which implies that the sequences were generated by two viruses, each of which have a distinct evolutionary history [161]. Analysing HIV-1 sequences without excluding recombination will results in misleading findings of phylogenetic analysis [160].

The high mutation and recombination rates in HIV-1 demand advanced methodologies to capture its diversity, yet the majority of studies in the MENA region which were included in this study relied on short sequences that lack the resolution necessary for accurate subtype or recombinant form (CRF/URF) assignment [32,62,64,70,131,133]. Only one study reported sequencing full HIV-1 genomes, underscoring a critical gap in regional research capacity [126]. Additionally, reliance on subtyping tools other than the gold standard phylogenetic based approach with reference full-genome HIV-1 sequences often fail to account for the complexities of recombination, leading to potential misclassification and incomplete characterization of strains [162].

Finally, the socio-cultural and legal barriers remain among the most profound obstacles to understanding HIV-1 genetic diversity in the MENA region. Stigma, deeply rooted in cultural and religious norms in the region, casts a long shadow over public health efforts, particularly for marginalized groups such as MSM [45,163,164,165]. Despite growing epidemiological evidence on HIV-1 and risk behaviors among MSM, the MENA region societal attitudes may result in underreporting of MSM transmission, obscuring the true epidemiological picture of HIV-1 in the MENA [72]. This mirrors the global experience during the early years of the HIV epidemic in the United States, where stigma against MSM delayed effective responses and perpetuated transmission [166]. High-risk populations such as IDUs, FSWs, truck drivers and prisoners are similarly neglected in HIV research in the MENA, creating significant data gaps [29]. The consequences of these barriers are profound since HIV-infected individuals in the MENA region face family rejection, societal isolation, and restricted access to essential services [167]. Women, in particular, are subjected to violence, humiliation, and invasive practices such as virginity testing [139]. Addressing these challenges requires courageous policy reforms, culturally sensitive public health strategies, and a commitment to address stigma to foster transparency and equitable HIV/AIDS research efforts.

4.1. Recommendations

Based on the review findings, several recommendations can be proposed to address the identified barriers that may hinder the investigation of HIV-1 genetic diversity in the MENA. First, investment in infrastructure and research capacity is essential in the MENA region. This includes scaling up the use of advanced sequencing technologies such as NGS and increasing funding for HIV-1 molecular epidemiology studies.

Second, targeted policy reforms are needed to address the socio-cultural and legal barriers that impede access to HIV/AIDS testing and care, particularly among marginalized groups such as MSM, IDUs, and FSWs. Public health campaigns that aim to reduce stigma and promote inclusive policies can play a critical role in overcoming these challenges.

Third, regional and international collaborations should be strengthened to facilitate data sharing and capacity building. A unified regional database for HIV-1 sequences could improve the availability of comprehensive data and enhance cross-border efforts to monitor HIV-1 genetic diversity.

Fourth, increasing the representation of under-researched populations in HIV-1 studies is crucial. This includes prioritizing studies on high-risk groups, such as MSM, FSWs, IDUs, truck drivers, and prisoners, and addressing the gaps in behavioral data that hinder the development of effective interventions.

Finally, integrating socio-cultural considerations into research design and public health strategies is important. Engaging community leaders and stakeholders can help foster acceptance and support for HIV-1 research and interventions, while culturally sensitive approaches can improve participation and data quality. By addressing these challenges, the MENA region can advance its understanding of HIV-1 genetic diversity, ultimately contributing to more effective public health strategies, improved drug resistance monitoring, and tailored treatment protocols in the region.

4.2. Limitations

This review has several limitations that must be acknowledged. First, the geographic and language constraints enforced in the search strategy may have inadvertently excluded relevant records. The focus on English-language publications inherently excludes studies published in Arabic or French, which are widely used in the MENA region especially in the Maghreb region.

Second, the exclusion of specific countries based on distinct epidemic patterns limits the generalizability of the findings. While these exclusions were justified by the review scope, this approach may have resulted in omitting valuable insights into regional HIV-1 genetic diversity. Similarly, the reliance on pre-defined country lists might exclude cross-border insights critical to understanding genetic diversity of HIV-1 in the MENA region characterized by significant population movement.

Third, the literature search relied on PubMed and Google Scholar, which may not fully capture gray literature or unpublished datasets of HIV-1 sequences. This may have lead to potential exclusion of valuable data, since relevant findings might exist in non-traditional repositories or institutional reports.

Fourth, the themes extracted for analysis were derived through consensus among authors and informed by the first author’s prior research. While this approach provides a structured framework, it introduces potential bias, as the thematic focus may overlook emerging challenges not previously documented or emphasized.

5. Conclusions

This review highlighted four key barriers that should be addressed for thorough investigation of HIV-1 genetic diversity in the MENA region. These challenges were limited sampling and data gaps, resource and infrastructure constraints, HIV-specific factors, and socio-cultural issues. Insufficient sampling, reliance on outdated sequencing methods, and a lack of comprehensive recombination analysis hinder accurate depiction of HIV-1 genetic diversity. Additionally, stigma, cultural taboos, and restrictive policies exacerbate HIV-1 underreporting, particularly among at-risk groups such as MSM and IDUs, leaving significant gaps in HIV-1 surveillance data. To overcome these challenges, it is essential to invest in health infrastructure, use advanced technologies, such as NSG, introduce policy reforms to reduce stigma and legal barriers, expand regional and international collaboration and data sharing. Addressing the barriers identified in this review can help in the efforts aiming to accurately map HIV-1 genetic diversity in the MENA region, which is crucial for effective public health strategies. Improved HIV/AIDS surveillance in the MENA would aid in monitoring ARV drug resistance, tailoring treatment protocols, and inform vaccine development efforts.