Increasing proportions of HIV-1 non-B subtypes and of NNRTI resistance between 2013 and 2016 in Germany: Results from the national molecular surveillance of new HIV-diagnoses

Abstract

Background: Molecular surveillance of newly diagnosed HIV-infections is important for tracking trends in circulating HIV-variants, including those with transmitted drug resistances (TDR) to sustain ART efficacy.

Methods: Dried serum spots (DSS) are received together with the statutory notification of a new diagnosis. 'Recent infections' (<155 days) classified by a 'recent infection test algorithm' (BED-CEIA and clinical data) are genotyped in HIV-protease (PR), reverse transcriptase (RT) and integrase (INT) to determine the HIV-1 subtype, to calculate prevalence and trends of TDR, to predict baseline susceptibility and to identify potential transmission clusters for resistant variants.

Results: Between January 2013 and December 2016, 1,885 recent infections were analysed regarding the PR/RT genomic region, with 43.5% of these also being subjected to the analysis of INT. The proportion of HIV-1 non-B viruses (31.3%; 591/1,885) increased from 21.6% to 36.0%, particularly the subtypes A (5.0% to 8.3%) and C (3.2% to 7.7%; all ptrends < 0.01). The subtype A increment is mainly due to transmissions within men who have sex with men (MSM) while subtype C transmissions are associated with heterosexuals and people who inject drugs. The prevalence of TDR was stable at 11.0% (208/1,885) over the study period. Resistances to nucleotide RT inhibitors (NRTI) and PR inhibitors (PI) were 4.5% and 3.2%, respectively, without identifiable trends. In contrast, resistances to non-NRTIs (NNRTI, 4.7%) doubled between 2014 and 2016 from 3.2% to 6.4% (ptrend = 0.02) mainly due to the K103N mutation (from 1.7% to 4.1%; ptrend = 0.03) predominantly detected in recently infected German MSM not linked to transmission clusters. Transmitted INSTI mutations were present in only one case (T66I) and resistance to dolutegravir was not identified at all. Reduced susceptibility to recommended first-line therapies was low with 1.0% for PIs, 1.3% for NRTIs and 0.7% for INSTIs, but high for the NNRTIs efavirence (4.9%) and rilpivirine (6.0%) due to the K103N mutation and the polymorphic mutation E138A. These trends in therapy-naïve individuals impact current first-line regimens and require awareness and vigilant surveillance.

Fig 1

Analysis of HIV-1 subtypes. (A) Proportion of HIV-1 subtypes in the study population. (B) Trend analysis for major subtypes that show a significant increase or decrease (p < 0.05) between 2013 and 2016. Trend lines and p-values are indicated for the total proportions of subtypes. MSM: men who have sex with men; HET: persons with heterosexual mode of transmission, PWID: people who inject drugs, GER: German.

Fig 2. Trends of transmitted drug resistance among newly diagnosed HIV cases with recent HIV infections in total and according to drug classes.

The confidence interval for NNRTI resistance is indicated.

Fig 3. Prevalence of predicted resistance to approved HIV therapeutics according to the Stanford HIVdb.

(A) Resistance (low/intermediate/high level) stratified according to the year of diagnosis. (B) Resistance level; # calculated from 820 cases;* drugs included in recommended and alternative first-line treatment option according to EACS 9.0 guidelines; EFV efavirenz, ETR etravirine, NVP nevirapine, RPV rilpivirine, 3TC lamivudine, ABC abacavir, AZT zidovudine, D4T stavudine, DDI didanosine, FTC emtricitabine, TDF tenofovir, ATV atazanavir, DRV darunavir, FPV fosamprenavir, IDV indinavir, LPV lopinavir, NFV nelfinavir, SQV saquinavir, TPV tipranavir, EVG elvitegravir, RAL raltegravir, DTG dolutegravir.

Fig 4. Trends for the K103N mutation between 2013 and 2016 in total and in subgroups.

(A) in MSM, persons with German Origin or subtype B infection (B) in persons with heterosexual transmission route, with non-German origin and with subtype non-B infection. Trend line and p-value are indicated for proportions of total K103N. MSM: men who have sex with men.

Fig 5. Phylogenetic analysis of 251 HIV-1 sequences carrying drug resistance mutations.

Three large clusters with M46I, V82L or T215S mutations are shown with blue branches and all sequences carrying the K103N mutation are depicted with dots at the tips.

Fig 6. Proportion of not-clusters-linked sequences with K103N mutation according to sub-groups of HIV-infected individuals in 2013/2014 compared to 2015/2016.

K103N sequences are grouped according to gender, transmission route, origin and HIV-subtype of the infected person. The proportion is calculated from the total number of sequences of two respective 2-year periods (2013/2014: 744 sequences; 2015/2016: 1140 sequences). Between the two year periods a significant increase of the K103N mutation in males who are not linked to transmission clusters is evident. MSM: men who have sex with men; HET: persons with heterosexual mode of transmission, GER: German, not rep. transm.: not reported transmission, * p < 0.05, **p < 0.01.