HIV Genomic Surveillance in Cameroon by Next-Generation Sequencing
CERSI Collaborators: Charles Chiu, MD/PhD; Venice Servellita, BS/CLS
FDA Collaborators: David McGivern, PhD; Jiangqin Zhao, PhD
Project Start Date: August 24, 2020
Regulatory Science Challenge:
The global spread and evolution of HIV (human immunodeficiency virus) provide continual challenges for diagnostics, therapeutic, and the development of efficacious drugs and vaccines. HIV-1 exhibits extensive genetic diversity driven by error-prone replication and recombination, which facilitates the emergence of geographically distinct variants that may adversely impact diagnostic assay performance. Ongoing viral genome surveillance is critical for detecting new strains and for constructing and validating reference panels required for regulatory evaluation of targeted serologic and nucleic acid-based assays. Metagenomic next-generation sequencing (mNGS) provides a comprehensive platform to characterize HIV diversity – particularly in “hotspot” regions such as Cameroon – thereby supporting assay validation and strengthening public health preparedness through broad detection of both known and emerging pathogens.
Project Description and Aims/Goals:
This project sought to characterize the genetic diversity of HIV and circulating bloodborne pathogens in Cameroon to support development of regulatory reference materials and improve diagnostic assay performance. We applied next-generation sequencing methods, including metagenomic sequencing with spiked primer enrichment, to generate full-length HIV genomes from plasma samples of HIV-positive individuals and from previously characterized viral cultures curated at FDA/CBER. These sequence data were used to inform the construction and validation of CBER HIV reference panels for use in the evaluation of serologic antigen/antibody combination and nucleic acid-based diagnostic assays. In parallel, we performed metagenomic sequencing of plasma samples collected by FDA/CBER from blood donors and patients with acute febrile illness in Cameroon to define the human blood virome, identify co-infections, and detect emerging and/or novel pathogens of relevance to public health and pandemic preparedness efforts.
Outcomes/Impact:
The project generated comprehensive genomic data that strengthened FDA regulatory science capacity for HIV and emerging bloodborne pathogens in Cameroon, widely recognized as a global hotspot for viral diversity and transmission. We used metagenomic NGS to analyze 100 high-titer cultured HIV samples and assemble 54 complete or near-complete HIV-1 genotype M genomes representing multiple subgroups (predominantly A, with D, F, G, J, and K), which were then validated by nucleic acid testing and Sanger sequencing and used to inform the strain composition for CBER HIV reference panels. Metagenomic next-generation sequencing (mNGS) of 261 plasma samples from Cameroon identified HIV in 63 (24%) and multiple viral co-infections, including from Epstein-Barr virus (EBV), hepatitis C virus (HCV), herpes simplex virus 1 (HSV-1), cytomegalovirus (CMV), hepatitis B virus (HBV), and hepatitis D virus (HDV), including recovery of 5 full-length, sequence-diverse HDV genomes. Collectively, these findings enhanced characterization of reference materials and validation methods for HIV diagnostic assays, highlighted emerging surveillance approaches for bloodborne pathogens such as mNGS, and yielded two manuscripts—one focused on HIV genomic diversity and reference panel development and one on viral pathogen discovery and HDV diversity, that are currently in peer review.