Genotypic resistance tests sequences reveal the role of marginalized populations in HIV-1 transmission in Switzerland. Â Â Scientific Reports
Shilaih et al. aimed to investigate the utility of HIV-1 sequence data from the Swiss HIV Cohort Study (SHCS) and non-cohort sequences to assess the proportion of marginalized/underrepresented populations (e.g., patients facing barriers for enrolment) which might be missed by the SHCS.
A phylogenetic tree was built using 11’127 SHCS and 2’875 Swiss non-SHCS sequences. The non-SHCS sequences were obtained from the database of the ’Bundesamt für Sozialversicherungen’, into which mandatory all genotypic resistance tests in Switzerland have to be entered. Overall, 79% of all patients who ever had a genotypic resistance test performed in Switzerland were enrolled in the SHCS. Non-B subtype (odds-ratio [OR]: 1.9), female gender (OR 1.7), black ethnicity (OR 1.9) and heterosexual transmission group (OR 1.8), were all associated with underrepresentation in the SHCS. There were 344 transmission clusters consisting only of non-SHCS patients. These clusters occurred frequently but were limited in size with a median size of 2 patients and a maximum cluster size of seven patients. Thus, outbreaks outside the SHCS were rather small in numbers. In general, there was a strong overlap between transmission chains among SHCS and non-SHCS populations. 65% of the sequences of the non-SHCS individuals were part of SHCS clusters of > 50 individuals. In addition, the authors were capable to infer based on the sequences the transmission group of considerable numbers of non-SHCS sequences for which no epidemiological data is available, thus allowing to obtain an overall picture of the epidemic also for non-SHCS enrolled HIV infected individuals.
In conclusion, this work highlights the utility of molecular epidemiology in extending and testing the scope of classical epidemiological data. The data suggests that marginalized populations are underrepresented in the SHCS. However, there was no evidence that the SHCS misses larger outbreaks consisting of purely non-cohort patients.