Use of Dried Blood Spots to Elucidate Full-Length Transmitted/Founder HIV-1 Genomes

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Jesus F. Salazar-Gonzalez
Maria G. Salazar
Damien C. Tully
Colin B. Ogilvie
Gerald H. Learn
Todd M. Allen
Sonya L. Heath
Paul Goepfert
Katharine J. Bar


Background: Identification of HIV-1 genomes responsible for establishing clinical infection in newly infected individuals is fundamental to prevention and pathogenesis research. Processing, storage, and transportation of the clinical samples required to perform these virologic assays in resource-limited settings requires challenging venipuncture and cold chain logistics. Here, we validate the use of dried-blood spots (DBS) as a simple and convenient alternative to collecting and storing frozen plasma.

Methods: We performed parallel nucleic acid extraction, single genome amplification (SGA), next generation sequencing (NGS), and phylogenetic analyses on plasma and DBS.

Results: We demonstrated the capacity to extract viral RNA from DBS and perform SGA to infer the complete nucleotide sequence of the transmitted/founder (TF) HIV-1 envelope gene and full-length genome in two acutely infected individuals. Using both SGA and NGS methodologies, we showed that sequences generated from DBS and plasma display comparable phylogenetic patterns in both acute and chronic infection. SGA was successful on samples with a range of plasma viremia, including samples as low as 1,700 copies/ml and an estimated ~50 viral copies per blood spot. Further, we demonstrated reproducible efficiency in gp160 env sequencing in DBS stored at ambient temperature for up to three weeks or at -20ºC for up to five months.

Conclusions: These findings support the use of DBS as a practical and cost-effective alternative to frozen plasma for clinical trials and translational research conducted in resource-limited settings.


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Salazar-Gonzalez JF, Salazar MG, Tully DC, Ogilvie CB, Learn GH, Allen TM, et al. Use of Dried Blood Spots to Elucidate Full-Length Transmitted/Founder HIV-1 Genomes. PAI [Internet]. 2016 Jul. 20 [cited 2023 Sep. 30];1(1):129-53. Available from:
Author Biography

Katharine J. Bar, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA

Assistant Professor of Medicine, Division of Infectious Diseases


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