HIV-1 pol gene diversity and molecular dating of subtype C from Sri Lanka.

BACKGROUND: The first case of HIV infection in Sri Lanka was reported in 1987 and at the end of 2018 there were 3500 people living with HIV. There have been commendable efforts made towards the detection, treatment, and prevention of HIV in the country. Even though the genetic diversity of HIV has been shown to affect the parameters ranging from detection to vaccine development, there is no data available with respect to the molecular epidemiology of HIV-1 in Sri Lanka. METHODS: In this report we have performed the ancillary analysis of pol gene region sequences (n = 85) obtained primarily for the purpose of HIV-1 drug resistance genotyping. Briefly, dried blood spot specimens (DBS) collected from HIV-1 infected individuals between December 2015 and August 2018 were subjected to pol gene amplification and sequencing. These pol gene sequences were used to interpret the drug resistance mutation profiles. Further, sequences were subjected to HIV-1 subtyping using REGA 3.0, COMET, jPHMM and, RIP online subtyping tools. Moreover, Bayesian phylogenetic analysis was employed to estimate the evolutionary history of HIV-1 subtype C in Sri Lanka. RESULTS: Our analysis revealed that the majority (51.8%) of pol gene sequences were subtype C. Other than subtype C, there were sequences categorized as subtypes A1, B, D and G. In addition to pure subtypes there were sequences which were observed to be circulating recombinant forms (CRFs) and a few of the recombinants were identified as potential unique recombinants (URFs). We also observed the presence of drug resistance mutations in 56 (65.9%) out of 85 sequences. Estimates of the Bayesian evolutionary analysis suggested that the HIV-1 subtype C was introduced to Sri Lanka during the early 1970s (1972.8). CONCLUSION: The findings presented here indicate the presence of multiple HIV-1 subtypes and the prevalence of drug resistance mutations in Sri Lanka. The majority of the sequences were subtype C, having their most recent common ancestor traced back to the early 1970s. Continuous molecular surveillance of HIV-1 molecular epidemiology will be crucial to keep track of drug resistance, genetic diversity, and evolutionary history of HIV-1 in Sri Lanka.

Completeness of consent forms in research proposals submitted to an ethics review committee.

This was a descriptive cross-sectional study which analysed the consent forms submitted to the ethics review committee at the faculty of medicine of the University of Kelaniya, Sri Lanka, between January 2007 and December 2008. Of the 145 consent forms reviewed, 94.5% (137) explained the purpose of the study, 77% (111) included a statement that participation was voluntary, 44% (64) stated that refusal of participation did not affect care, 65.5% (95) mentioned the ability to withdraw consent at any time, 79% (115) that confidentiality of records would be maintained and 45.5% (66) that further clarifications were possible. Thirty nine (75%) of 52 eligible consent forms described the potential benefits and 19% (18) of 93 consent forms explained that there were no benefits to the participants. Twenty eight (59%) of 47 eligible consent forms described possible risks or discomfort to patients and 30% (29) of 98 consent forms explained that there were no risks to the participants. In conclusion, essential elements of the consent forms were missing in this study. It is recommended that a checklist of compulsory elements to include on forms be used before proposals are submitted to an ethics review committee.