Genomic Surveillance of Emerging and Re Emerging Viral Diseases: Molecular Evolution, Transmission Dynamics, and Antiviral Resistance in Pakistan

Abstract

Pakistan carries an unusual concentration of viral risk. It is one of only two countries where wild poliovirus has never been stopped, its dengue seasons turn over serotype from one year to the next, its Crimean-Congo haemorrhagic fever is endemic and actively reassorting, its hepatitis C burden is the second largest in the world, and its respiratory season now imports globally circulating influenza clades within weeks of their appearance elsewhere. What the country's genomic laboratories have found out about these viruses has never been pulled together in one place. This paper does that, synthesising the published genomic surveillance evidence for Pakistan from 2020 to mid-2026 across six priority viral systems and asking what it shows about molecular evolution, transmission and antiviral resistance. We quantified sequencing coverage from the primary studies, and it varies by two orders of magnitude between pathogens, from 6.3 per cent of confirmed detections in the 2024 national dengue outbreak to 71 per cent in a single well-resourced Crimean-Congo investigation. That range has little to do with which pathogen mattered most and almost everything to do with which outbreak happened to attract a funded study. Three transmission signatures recur across viruses that share nothing else. Importation across borders dominates: wild poliovirus type 1 clusters YB3A and YB3C move within the Pakistan-Afghanistan block, Crimean-Congo strains group with Iranian, Afghan and Indian isolates, and dengue lineages arrived from Southeast Asia. Cryptic local circulation then follows, with time-scaled analyses dating the common ancestor of currently circulating dengue lineages to 2016 and 2018. And environmental sampling repeatedly detects more than clinical reporting does, never more starkly than in 2025, when poliomyelitis cases fell 58 per cent even as wild poliovirus-positive sewage samples climbed to 651. Antiviral resistance is the weakest link of all. Resistance-associated substitutions of clear clinical importance, among them NS5A Y93H and A30K in hepatitis C genotype 3a and neuraminidase E50K and R150H in influenza A, have been documented in Pakistani isolates, yet the national programme runs no routine genotypic resistance testing for any virus. We set out where the surveillance chain loses information and what a proportionate national strategy would fix first.