BackgroundGenetic analysis of a viral infection helps in following its spread in a given population, in tracking the routes of infection and, where applicable, in vaccine design. Additionally, sequence analysis of the viral genome provides information about patterns of genetic divergence that may have occurred during viral evolution.ObjectiveIn this study we have analyzed the subtypes of Human Immunodeficiency Virus -1 (HIV-1) circulating in a diverse sample population of Nairobi, Kenya.Methodology69 blood samples were collected from a diverse subject population attending the Aga Khan University Hospital in Nairobi, Kenya. Total DNA was extracted from peripheral blood mononuclear cells (PBMCs), and used in a Polymerase Chain Reaction (PCR) to amplify the HIV gag gene. The PCR amplimers were partially sequenced, and alignment and phylogenetic analysis of these sequences was performed using the Los Alamos HIV Database.ResultsBlood samples from 69 HIV-1 infected subjects from varying ethnic backgrounds were analyzed. Sequence alignment and phylogenetic analysis showed 39 isolates to be subtype A, 13 subtype D, 7 subtype C, 3 subtype AD and CRF01_AE, 2 subtype G and 1 subtype AC and 1 AG. Deeper phylogenetic analysis revealed HIV subtype A sequences to be highly divergent as compared to subtypes D and C.ConclusionOur analysis indicates that HIV-1 subtypes in the Nairobi province of Kenya are dominated by a genetically diverse clade A. Additionally, the prevalence of highly divergent, complex subtypes, intersubtypes, and the recombinant forms indicates viral mixing in Kenyan population, possibly as a result of dual infections.

BackgroundWe have previously reported a HIV-1 subtype A infection in a community of injection drug users (IDUs) in Karachi, Pakistan. We now show that this infection among the IDUs may have originated from a single source.MethodsPhylogenetic analysis was performed of partial gag sequences, generated using PCR, from 26 HIV-positive IDU samples.ResultsOur results showed formation of a tight monophyletic group with an intra-sequence identity of < 98% indicating a "founder effect". Our data indicate that the HIV-1 epidemic in this community of IDUs may have been transmitted by an HIV positive overseas contract worker who admitted to having contact with commercial sex workers during stay abroad.ConclusionSpecific measures need to implemented to control transmission of HIV infection in Pakistan through infected migrant workers.

There are confusions in the definition of brain death, end-of-life recognition and indications and processes of withdrawal of life support. There are discrepancies between physicians' and nurses' perceptions and attitudes. Clearly, teaching programmes will need to incorporate cultural and religious differences in their ethics curricula.

Aim: Cancer of the oral cavity is extremely prevalent in Pakistan. Human papillomavirus (HPV) has been shown to play a role in the development of oral squamous cell carcinoma (OSCC) and may even improve overall and disease-free survival. The purpose of this study was to determine prevalence and types of HPV in a high risk population and its correlation with overall and disease-free survival, chewing habits and histologic variables. Material and methods:  A total of 140 patients of OSCC, having a long-term follow-up, were included in this study. HPV-general and type-specific 16 and 18 infection were investigated by means of polymerase chain reaction. Results: Out of 140 patients, HPV was detected in 95 (68%) patients, out of whom, 85 (90%) contained HPV16. HPV positive patients had comparatively prolonged overall survival when compared with HPV-negative patients, but this difference was not statistically significant (P = 0.97). HPV presence was also not found to correlate significantly with disease-free survival (P = 0.58). The male were significantly correlated [odds ratio (OR) = 2.34; 95% confidence interval (CI) = 1.13–4.84] with the HPV infection. Betel quid chewer were comparatively more prone to HPV positivity (OR = 2; 95% CI = 1.1–4.31). Conclusion: Our study found a high prevalence of HPV16 in OSCC of Pakistani patients with male sex showing significant correlation with HPV infection. However, we did not find a statistically significant favourable association between HPV, survival and histologic variables. Borderline significance of HPV positivity was also seen with betel quid chewing (P = 0.049

Many studies have proposed an important role of viruses in the pathogenesis of oral cancer. The present study aimed to find out the prevalence of Epstein‐Barr virus (EBV), cytomegalovirus (CMV), and human papillomavirus (HPV) among patients with oral squamous cell carcinoma (OSCC) in a Pakistani cohort. We investigated tissue samples obtained from 58 patients with OSCC using the polymerase chain reaction assay. No sample was positive for HPV. EBV was identified in 15 patients (25.86%), and CMV in three patients (5.17%). Coinfection with one or more viruses was detected in two cases and was coinfection with EBV and CMV. These results suggest a low prevalence of these viruses in OSCC patients in the Pakistani population compared to most other countries where the prevalence of these viruses has been reported in the past. Nevertheless, further studies are necessary to determine the potential role of EBV and the possible importance of CMV as an infection cofactor in oral cancer.