AccuNGS: a sequencing protocol for detection of ultra-rare variants reveals extensive variation in HIV during first days of infection

Gelbart, M.; Harari, S.; Ben-Ari, Y.; Kustin, T.; Meir, M.; Miller, D.; Mor, O.; Stern, A.

doi:10.1101/349498

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bioRxiv · 10.1101/349498

AccuNGS: a sequencing protocol for detection of ultra-rare variants reveals extensive variation in HIV during first days of infection

Gelbart, M.·Harari, S.·Ben-Ari, Y.·Kustin, T.·Meir, M.·Miller, D.·Mor, O.·Stern, A.

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Abstract

Mutations fuel evolution and facilitate adaptation to novel environments. However, characterizing the spectrum of mutations in a population is obscured by high error rates of next generation sequencing. Here, we present AccuNGS, a novel in vivo sequencing approach that detects variants as rare as 1:10,000. Applying it to 46 clinical samples taken from early infections of the human-infecting viruses HIV, RSV and CMV, revealed large differences in within-host genetic diversity among virus populations. Haplotype reconstruction revealed that increased diversity was mostly driven by multiple transmitted/founder viruses in HIV and CMV samples. Conversely, we detected an abundance of defective virus genomes (DVGs) in RSV samples, including hyper-edited genomes, nonsense mutations and single point deletions. Higher proportions of DVGs correlated with increased viral loads, suggesting increased cellular co-infection rates, which enable DVG persistence. AccuNGS establishes a general platform that allows detecting DVGs, and in general, rare variants that drive evolution.

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Gelbart, M., Harari, S., Ben-Ari, Y., Kustin, T., Meir, M., Miller, D., Mor, O., Stern, A.. 2018-06-18. AccuNGS: a sequencing protocol for detection of ultra-rare variants reveals extensive variation in HIV during first days of infection. https://doi.org/10.1101/349498

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