HIV-1 subtype diversity trends in a Northern California cohort

Abstract

Between 2000 and 2019, the Stanford Healthcare Clinical Virology Laboratory performed HIV-1 resistance testing for 9199 individuals in Northern California. Nonsubtype B viruses were identified in 3.5%, most often CRF01_AE (1.0%), subtype C (1.0%), CRF02_AG (0.46%), and subtype A (0.45%). Non-B viruses, particularly CRF01_AE and CRF02_AG, increased significantly over time. Although subtype B remained dominant, the rising presence of non-B subtypes reflects growing viral diversity within the U.S. epidemic.

HIV type 1 (HIV-1) subtype B was introduced into the United States from the Caribbean approximately 1970 [1]. The proportion of viruses belonging to non-B subtypes have increased in the United States but only gradually, with prevalence rates remaining below 10% [2,3]. In Europe, higher prevalences of nonsubtype B viruses have been reported with prevalences reaching up to 15–30% in newly diagnosed persons with HIV-1 (PWH) [4,5]. Although HIV-1 subtype B remains predominant in the United States, nonsubtype B infections are increasingly observed. These non-B infections, though still uncommon, they indicate the need for ongoing surveillance for mapping regional HIV-1 transmission patterns. Drawing from 20 years of sequence data in Northern California, we describe the modest but consistent increases in non-B subtypes in a region that was one of the early focal points of the U.S. HIV epidemic.

The Stanford Healthcare Clinical Virology Laboratory performed HIV-1 genotypic resistance testing for routine clinical care for a large Northern California clinic population (Kaiser Permanente Northern California, KPNC) from 1997 to 2019. During this period, nearly all sequences from KPNC clinics were analyzed in our laboratory. After 2019, testing volumes declined sharply when clinicians were able to order tests from multiple other laboratories. We previously reported that between July 1997 and June 2000, 99.4% of 2246 PWH undergoing genotypic resistance testing at Stanford had subtype B viruses [6]. In a subsequent study of 4253 ART-naive individuals from KPNC between 2003 and 2016, 95.3% of PWH had subtype B viruses [7]. To evaluate subsequent trends and to include previously treated as well as ART-naive PWH, we analyzed the prevalence of HIV-1 subtypes in the entire KPNC population from 2000 through 2019. Approval for this study, including a waiver of informed consent, was obtained from the Stanford University and Kaiser Permanente Northern California institutional review boards.

Between 2000 and 2019, a total of 9199 individuals had 13 214 samples submitted for genotypic resistance testing. Overall, 75.4% of individuals had a single sample, 14.7% had two samples, 5.6% had three samples, and 4.3% had four or more samples. The median number of individuals tested per year was 446 (IQR: 434–469; range: 374–730), calculated by assigning each individual to the first year a sample was obtained. Overall, a downward trend was observed, with the three highest annual counts (730, 565, and 486) occurring between 2000 and 2002, and two of the lowest counts (374 and 388) occurring in 2018 and 2019.

The median age at the time of the first sample was 42 years (IQR: 33–50). About 85.8% were men, 9.6% were women, and for 4.6% the sex was not available. Reported race/ethnicity was 46.4% White, 20.7% Black, 18.4% Hispanic, 6.9% Asian, 0.4% Native American, and 7.1% unspecified.

Of the 13 214 samples, 93.9% (12 414) included the protease and reverse transcriptase region; 5.1% (671) included protease, reverse transcriptase, and integrase; and 1.0% (129) included integrase alone. At the time of sequencing, 45.0% of individuals were ART-naive, 32.0% were ART-experienced, and 6.3% had samples obtained both before and after ART initiation. Treatment history was unavailable for 16.7% of individuals undergoing genotypic resistance testing.

Among the 9199 individuals sequenced, 96.5% had subtype B viruses according to the COMET subtyping tool [8]. Non-B subtypes included CRF01_AE (1.0%), subtype C (1.0%), CRF02_AG (0.46%), subtype A (0.45%), subtype D (0.17%), subtype G (0.09%), subtype F1 (0.09%), CRF07_BC (0.07%), as well as seven other circulating recombinant forms, four unique recombinant forms, and subtype F2 (0.17% combined) (Fig. 1). Two cases of superinfection with CRF01_AE were identified in individuals who previously had subtype B viruses. In general, linear logistic regression models with year as a continuous predictor, the proportion of non-B viruses increased significantly over time (P < 0.000001), as did the proportion of CRF01_AE (P < 0.000001) and CRF02_AG (P = 0.0008) viruses. No significant increase was observed for subtypes A or C. Compared to individuals with subtype B, those with non-B viruses were more likely to be Black and female. CRF01_AE infections were concentrated among Asian individuals (58.0% vs. white 27.5%, P < 0.001 Fisher's Exact Test).

Fig. 1.

HIV-1 subtype diversity trends in a Northern California Cohort, 2000–2019.

Numbers and proportions of persons with HIV-1 with nonsubtype B viruses per year between 2000 and 2019. The histograms indicate the number of cases per year. The black line indicates the proportion of cases per year.

In this large, clinic-based Northern California cohort (2000–2019), HIV-1 remained overwhelmingly subtype B, with modest but statistically significant increases in non-B lineages. The overall prevalence of non-B subtypes (3.5%) was slightly lower than in our previous study of ART-naive individuals from the same population (4.7% between 2003 and 2016) [7] likely reflecting that ART-experienced PWH, more often infected earlier in the epidemic, were enriched for subtype B. Our findings align with a San Francisco study reporting 2.8% non-B infections among 7036 cases between 2000 and 2016, primarily subtype C and CRF01_AE [9]. The prevalence we observed was lower than two CDC surveys: 6.7% in seven states between 2006 and 2013 [3] and 4.9% across 28 states between 2014 and 2018 [10]. A national reference laboratory also reported 3.3% non-B infections among 24 386 specimens collected between 2004 and 2011 [11].

Our study is limited by the absence of data on country of birth and by not performing phylogenetic analyses of non-B sequences, which we previously carried out in ART-naïve individuals [7]. However, by extending our analysis to include both ART-naïve and ART-experienced persons over a longer time period (2000–2019), this study updates our two earlier reports: the first, which showed that nearly all infections were subtype B between 1997 and 2000 [6], and the second, which documented a modest rise in non-B subtypes among ART-naïve individuals between 2003 and 2016 [7]. Together, these studies demonstrate the persistence of subtype B as the overwhelmingly predominant lineage in Northern California, while also highlighting a gradual but measurable increase in non-B subtypes.

In conclusion, the persistence of subtype B as the overwhelmingly dominant lineage in Northern California underscores the relative insularity of the U.S. epidemic, yet the gradual emergence of non-B subtypes demonstrates that diversity is increasing. Our analysis provides one of the few regional benchmarks for monitoring HIV-1 subtype diversity in the United States. It is a further demonstration of how data from laboratories performing genotypic resistance can enhance the surveillance of HIV-1 variants [11].

Acknowledgements

R.W.S. conceived of the project. K.T., P.L.T., and R.W.S. analyzed the data. B.A.P., M.K.S. generated the sequence data and contributed to the analysis. C.B.H. contributed to data generation. K.T., B.A.P., C.B.H., and R.W.S. wrote the manuscript.

Of the 13 214 virus sequences described in this study, 9633 (72.9%) were previously submitted to GenBank as a part of previous publications. The remaining 3581 (27.1%) sequences from this study have been submitted to GenBank sequences under the accession numbers PX355021 – PX358602. The complete dataset described in this study is available from the authors upon request.

Conflicts of interest

The authors report no conflicts of interest.