GENOMIC SURVEILLANCE: ITS BACKGROUND AND IMPLEMENTATION IN HIV SURVEILLANCE IN PAKISTAN

Abstract

Genomic Surveillance is a powerful technique to understand disease outbreaks. Pathogen sequencing has become more accessible and cost-effective than previously, offering a valuable complement to epidemiological approaches. In this review, we describe the advanced techniques employed in sequencing and phylogenetic analysis to trace transmission, and evolutionary patterns of the pathogen. Furthermore, this study also provides an overview of various genomic surveillance studies conducted in Pakistan to explore the genetic diversity, distribution of subtypes, drug resistance patterns, and molecular epidemiology of HIV-1 strains. These studies provide insights into the complexity of HIV subtypes circulating in the country and their distinct genetic characteristics. Key findings include diverse HIV subtypes in Punjab, an outbreak investigation in Larkana revealing CRF02_AG and subtype A1, multiple subtypes in Lahore with drug resistance mutations, genetic links between Pakistan and China, distinct clusters in a Karachi HIV-1 subtype A1 outbreak, a prevalent A1 subtype with resistance mutations in Pakistan, and the discovery of unclassified recombinant forms in children. They emphasized the importance of continuous surveillance, understanding risk factors, and developing targeted prevention and treatment strategies to combat HIV and its potential epidemics in various populations.