A Systematic Molecular Epidemiology Screen Reveals Numerous Human Immunodeficiency Virus (HIV) Type 1 Superinfections in the Swiss HIV Cohort Study

Abstract

Background Studying HIV-1 superinfection is important to understand virus transmission, disease progression, and vaccine design. But detection remains challenging, with low sampling frequencies, and insufficient longitudinal samples. Methods Using the Swiss HIV Cohort Study(SHCS), we developed a molecular epidemiology screening for superinfections. A phylogeny built from 22,243 HIV-1 partial-polymerase sequences was used to identify potential superinfections among 4,575 SHCS participants with longitudinal sequences. A subset of potential superinfections was tested by near-full-length viral genome sequencing (NFVGS) of bio-banked plasma samples. Results Based on phylogenetic and distance criteria, 325 potential HIV-1 superinfections were identified and categorised by their likelihood of being detected as superinfection due to sample misidentification. NFVGS was performed for 128 potential superinfections: Of these, fifty-two were confirmed by NFVGS, 15 were not confirmed, and for 61 sampling did not allow for confirming or rejecting superinfection because the sequenced samples did not include the relevant time points causing the superinfection signal in the original screen. Thus, NFVGS could support 52/67 adequately sampled potential superinfections. Conclusions This cohort-based molecular approach identified, to our knowledge, the largest population of confirmed superinfections, showing that, while rare with a prevalence of 1-7%, superinfections are not negligible events.

Comparative Evaluation of Bioinformatic Pipelines for Full-Length Viral Genome Assembly

“…We note, however, that in the majority of applications group M samples will be analyzed, and the observed suboptimal performance with divergent samples can be easily improved by using a matched reference sequence, either by implementing automatic selection (as in the shiver pipeline), or by supplying a matching reference sequence for the current pipelines. While it is still common practice to employ the HXB2 sequence as a reference for HIV-1 genome assembly [65][66][67][68][69],…”

“…We note, however, that in the majority of applications group M samples will be analyzed, and the observed suboptimal performance with divergent samples can be easily improved by using a matched reference sequence, either by implementing automatic selection (as in the shiver pipeline), or by supplying a matching reference sequence for the current pipelines. While it is still common practice to employ the HXB2 sequence as a reference for HIV-1 genome assembly [65–69], selecting a more suitable reference sequence is a viable option even without the modification of the genome assembler pipeline. To guide the selection, the predominant viral subtype can be determined by HIV subtyping tools such as REGA [63] or COMET [70], using either Sanger sequencing data (if available from the same sample) or the result of the first round of genome assembly.…”