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

Cohort Studies HIV Infections HIV-1 Humans Molecular Epidemiology Phylogeny Superinfection / epidemiology Switzerland / epidemiology Vaccines

HIV-1 superinfection molecular epidemiology screening phylogenetics

Journal

The Journal of infectious diseases

ISSN: 1537-6613

Titre abrégé: J Infect Dis

Pays: United States

ID NLM: 0413675

Informations de publication

Date de publication:
28 09 2022

Historique:

received: 10 12 2021

accepted: 27 04 2022

pubmed: 30 4 2022

medline: 1 10 2022

entrez: 29 4 2022

Statut: ppublish

Résumé

Studying human immunodeficiency virus type 1 (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. 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 4575 SHCS participants with longitudinal sequences. A subset of potential superinfections was tested by near-full-length viral genome sequencing (NFVGS) of biobanked plasma samples. Based on phylogenetic and distance criteria, 325 potential HIV-1 superinfections were identified and categorized by their likelihood of being detected as superinfections due to sample misidentification. NFVGS was performed for 128 potential superinfections; of these, 52 were confirmed by NFVGS, 15 were not confirmed, and for 61 sampling did not allow 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 of 67 adequately sampled potential superinfections. 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.

Sections du résumé

BACKGROUND

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 4575 SHCS participants with longitudinal sequences. A subset of potential superinfections was tested by near-full-length viral genome sequencing (NFVGS) of biobanked plasma samples.

RESULTS

Based on phylogenetic and distance criteria, 325 potential HIV-1 superinfections were identified and categorized by their likelihood of being detected as superinfections due to sample misidentification. NFVGS was performed for 128 potential superinfections; of these, 52 were confirmed by NFVGS, 15 were not confirmed, and for 61 sampling did not allow 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 of 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.

Identifiants

DOI: 10.1093/infdis/jiac166 PMID: 35485458

pubmed: 35485458

pii: 6575836

doi: 10.1093/infdis/jiac166

doi:

Substances chimiques

Vaccines 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

Pagination

1256-1266

Subventions

Organisme : Swiss National Science Foundation

ID : 177499

Pays : Switzerland

Investigateurs

K Aebi-Popp (K)

A Anagnostopoulos (A)

M Battegay (M)

E Bernasconi (E)

J Böni (J)

D L Braun (DL)

H C Bucher (HC)

A Calmy (A)

M Cavassini (M)

A Ciuffi (A)

G Dollenmaier (G)

M Egger (M)

L Elzi (L)

J Fehr (J)

J Fellay (J)

H Furrer (H)

C A Fux (CA)

H F Günthard (HF)

D Haerry (D)

B Hasse (B)

H H Hirsch (HH)

M Hoffmann (M)

I Hösli (I)

M Huber (M)

C R Kahlert (CR)

L Kaiser (L)

O Keiser (O)

T Klimkait (T)

R D Kouyos (RD)

H Kovari (H)

B Ledergerber (B)

G Martinetti (G)

B Martinez de Tejada (BM)

C Marzolini (C)

K J Metzner (KJ)

N Müller (N)

D Nicca (D)

P Paioni (P)

G Pantaleo (G)

M Perreau (M)

A Rauch (A)

C Rudin (C)

K Kusejko (K)

P Schmid (P)

R Speck (R)

M Stöckle (M)

P Tarr (P)

A Trkola (A)

P Vernazza (P)

G Wandeler (G)

R Weber (R)

S Yerly (S)

Informations de copyright

Déclaration de conflit d'intérêts

Potential conflicts of interest. The institution of E. B. received fees for E. B. participation in advisory boards and travel grants from Gilead Sciences, MSD, ViiV Healthcare, Pfizer, AbbVie, and Sandoz. K. J. M. has received advisory board honoraria from Gilead Sciences; has received travel grants and honoraria from Gilead Sciences, Roche Diagnostics, GlaxoSmithKline, Merck Sharp & Dohme, Bristol-Myers Squibb, ViiV, and Abbott; the University of Zurich received research grants from Gilead Science, Novartis, Roche, and Merck Sharp & Dohme for studies for which K. J. M. serves as principal investigator. H. F. G. has received unrestricted research grants from Gilead Sciences and Roche; fees for data and safety monitoring board membership from Merck; consulting/advisory board membership fees from Gilead Sciences, Merck, and ViiV Healthcare; and grants from SystemsX, and the National Institutes of Health. The institution of H. F. G. received educational grants from Gilead Sciences, ViiV, MSD, AbbVie, and Sandoz. All other authors report no potential conflicts of interest. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed.