Drawing from published and gray literature, this manuscript focuses on the following topics: (1) changing patterns of substance use and abuse in Vietnam since the early 1990s; (2) the roles of substance use in the HIV epidemic; (3) the responses of the Vietnamese government and other entities (both domestic and international) to substance use disorders (SUDs) and HIV; and (4) the current research capacity in Vietnam and ways in which furthering research in Vietnam could enrich our knowledge of the linkages between SUDs and HIV and of effective measures to reduce their public health consequences. A growing number of studies during the past two decades show dynamic and still evolving twin epidemics of SUDs and HIV in Vietnam, including a shift from consumption of opium to heroin and amphetamine-type stimulants, the concurrent use of drugs, and the increasing embrace by the government of internationally recognized effective responses (including harm reduction and methadone substitution therapy). And yet, remaining issues, such as the rapid ascendance of amphetamine-type stimulant use among the country's most vulnerable populations, the lack of effective integration of SUD and HIV services for HIV-infected drug users, and the reliance on international resources for maintaining quality services, among others, are posing challenges for building sustainable Vietnamese responses. Therefore, building local research and training capacity is a crucial foundation to meet these challenges.

Next-generation sequencing (NGS) has revolutionized genetics and enabled the accurate identification of many genetic variants across many genomes. However, detection of biologically important low-frequency variants within genetically heterogeneous populations remains challenging, because they are difficult to distinguish from intrinsic NGS sequencing error rates. Approaches to overcome these limitations are essential to detect rare mutations in large cohorts, virus or microbial populations, mitochondria heteroplasmy, and other heterogeneous mixtures such as tumors. Modifications in library preparation can overcome some of these limitations, but are experimentally challenging and restricted to skilled biologists. This paper describes a novel quality filtering and base pruning pipeline, called Complex Heterogeneous Overlapped Paired-End Reads (CHOPER), designed to detect sequence variants in a complex population with high sequence similarity derived from All-Codon-Scanning (ACS) mutagenesis. A novel fast alignment algorithm, designed for the specified application, has O(n) time complexity. CHOPER was applied to a p53 cancer mutant reactivation study derived from ACS mutagenesis. Relative to error filtering based on Phred quality scores, CHOPER improved accuracy by about 13% while discarding only half as many bases. These results are a step toward extending the power of NGS to the analysis of genetically heterogeneous populations.