Background: Human immunodeficiency virus type 1 (HIV-1) is characterized by high genetic diversity due to its high mutation and recombination rates. Although, there is an increasing prevalence of Circulating Recombinant Forms (CRFs) worldwide, subtype B is still recognized as the predominant subtype in the Middle East and North Africa (MENA) region. There is a limited sampling of HIV in this region due to its low prevalence. The main purpose of this study is to provide a summary of the current status of the resident HIV subtypes and their distribution among Egyptian patients.

Methodology: Forty-five HIV-1 patients were included in this study. Partial pol gene covering the protease (PR) and Reverse Transcriptase (RT) was successfully amplified in 21 HIV patients using nested PCR of cDNA of the viral genomic RNA, then sequenced. The sequence data were used for viral HIV-1 subtyping by 5 online subtyping tools: NCBI viral genotyping tool, Stanford University HIV database (HIVDB) subtyping program, REGA tool, Context-Based Modeling for Expeditious Typing (COMET) tool, and Recombinant Identification Program (RIP) tool. The final subtype assignment was based on molecular phylogenetic analysis.

Results: Unexpectedly, non-B subtypes are dominating, with the most common circulating one is CRF02_AG (57.1%) followed by subtype B (14.3%), subtype BG recombinant (9.5%), CRF35_ AD (9.5%), subtype A1 and CRF06_cpx (4.8% each).

Conclusion: To the best of our knowledge, this is the first study to tackle HIV-1 subtyping among the group of HIV-1 patients in Egypt. CRF02_AG is the most prevalent subtype in Egypt.

背景：人类免疫缺陷病毒 1 型 (HIV-1) 因其高突变率和重组率而具有高遗传多样性的特点。尽管全球循环重组形式 (CRF) 的流行率越来越高，但 B 亚型仍被认为是中东和北非 (MENA) 地区的主要亚型。由于艾滋病毒流行率低，该地区的艾滋病毒样本有限。本研究的主要目的是总结埃及居民 HIV 亚型的现状及其在埃及患者中的分布情况。

方法：本研究纳入了 45 名 HIV-1 患者。使用病毒基因组 RNA 的 cDNA 的巢式 PCR，在 21 名 HIV 患者中成功扩增了覆盖蛋白酶 (PR) 和逆转录酶 (RT) 的部分 pol 基因，然后对其进行了测序。序列数据通过 5 个在线子分型工具用于病毒 HIV-1 分型：NCBI 病毒基因分型工具、斯坦福大学 HIV 数据库 (HIVDB) 分型程序、REGA 工具、基于上下文的快速分型建模 (COMET) 工具和重组识别程序 (RIP) 工具。最终的亚型分配基于分子系统发育分析。

结果：出乎意料的是，非B亚型占主导地位，最常见的循环亚型是CRF02_AG（57.1%），其次是B亚型（14.3%）、BG重组亚型（9.5%）、CRF35_AD（9.5%）、A1亚型和CRF06_cpx（各 4.8%）。

结论：据我们所知，这是第一项在埃及 HIV-1 患者群体中解决 HIV-1 亚型的研究。CRF02_AG 是埃及最普遍的亚型。