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Background The HIV-1 subtype B epidemic amongst men who have sex with men (MSM) is resurgent in many countries despite the widespread use of effective combination antiretroviral therapy (cART). In this combined mathematical and phylogenetic study of observational data, we aimed to find out the extent to which the resurgent epidemic is the result of newly introduced strains or of growth of already circulating strains. Methods and Findings As of November 2011, the ATHENA observational HIV cohort of all patients in care in the Netherlands since 1996 included HIV-1 subtype B polymerase sequences from 5,852 patients. Patients who were diagnosed between 1981 and 1995 were included in the cohort if they were still alive in 1996. The ten most similar sequences to each ATHENA sequence were selected from the Los Alamos HIV Sequence Database, and a phylogenetic tree was created of a total of 8,320 sequences. Large transmission clusters that included ≥10 ATHENA sequences were selected, with a local support value ≥ 0.9 and median pairwise patristic distance below the fifth percentile of distances in the whole tree. Time-varying reproduction numbers of the large MSM-majority clusters were estimated through mathematical modeling. We identified 106 large transmission clusters, including 3,061 (52%) ATHENA and 652 Los Alamos sequences. Half of the HIV sequences from MSM registered in the cohort in the Netherlands (2,128 of 4,288) were included in 91 large MSM-majority clusters. Strikingly, at least 54 (59%) of these 91 MSM-majority clusters were already circulating before 1996, when cART was introduced, and have persisted to the present. Overall, 1,226 (35%) of the 3,460 diagnoses among MSM since 1996 were found in these 54 long-standing clusters. The reproduction numbers of all large MSM-majority clusters were around the epidemic threshold value of one over the whole study period. A tendency towards higher numbers was visible in recent years, especially in the more recently introduced clusters. The mean age of MSM at diagnosis increased by 0.45 years/year within clusters, but new clusters appeared with lower mean age. Major strengths of this study are the high proportion of HIV-positive MSM with a sequence in this study and the combined application of phylogenetic and modeling approaches. Main limitations are the assumption that the sampled population is representative of the overall HIV-positive population and the assumption that the diagnosis interval distribution is similar between clusters. Conclusions The resurgent HIV epidemic amongst MSM in the Netherlands is driven by several large, persistent, self-sustaining, and, in many cases, growing sub-epidemics shifting towards new generations of MSM. Many of the sub-epidemics have been present since the early epidemic, to which new sub-epidemics are being added., Daniela Bezemer and colleagues investigate the extent to which the resurgent HIV epidemic in the Netherlands is the result of newly introduced strains, or of growth of already circulating strains., Editors' Summary Background Since the first recorded case of AIDS in 1981, the number of people infected with HIV, the virus that causes AIDS, has risen steadily. Now, three and a half decades later, about 35 million people (more than half of whom are women) are infected with HIV, the virus that causes AIDS. HIV is most often spread by having unprotected sex with an infected partner, and, globally, most sexual transmission of HIV occurs during heterosexual sex. Nevertheless, many new HIV infections still occur in men who have sex with men (MSM; homosexual, bisexual, and transgender men, and heterosexual men who sometimes have sex with men), and, in some countries, HIV/AIDS still predominantly affects the MSM community. In the US, for example, 78% of new HIV infections occurred among MSM in 2010 although MSM represent only 4% of the total population, and, in 2011, 54% of all people living with HIV were MSM. Indeed, despite HIV-positive individuals being diagnosed earlier these days and having access to effective combination antiretroviral therapy (cART), which both halts disease progression and reduces the risk of HIV transmission, the HIV epidemic among MSM is resurgent (growing again) in many Western countries. Why Was This Study Done? To control this resurgent epidemic, it is important to know as much as possible about HIV transmission among MSM so that effective prevention strategies can be designed. Here, the researchers use phylogenetic analysis and mathematical modeling to ask whether the introduction of new strains or the spread of already circulating strains is responsible for the resurgent HIV-1 subtype B epidemic occurring among MSM in the Netherlands. Viral phylogenetic analysis infers evolutionary relationships between viral strains by examining their genetic relatedness and can be used to identify HIV transmission clusters. HIV-1 viruses are classified into subtypes based on their genetic sequence and geographical distribution. HIV-1 subtype B is a common subtype that is found in west and central Europe, the Americas, and several other regions. What Did the Researchers Do and Find? The researchers built a phylogenetic tree for the HIV epidemic in MSM in the Netherlands by analyzing HIV-1 subtype B polymerase gene sequences found in 5,852 participants (73% of whom were MSM) in the ATHENA cohort, an observational cohort of all HIV-1-infected patients in care in the Netherlands since 1996 (when cART became available). Examination of this tree identified 106 large transmission clusters (groups of ten or more closely related subtype B HIV-1 strains). Half of the HIV-1 polymerase sequences from HIV-1-positive MSM registered in the ATHENA cohort in the Netherlands were included in 91 MSM-majority clusters: large transmission clusters in which more than half the related sequences originated from MSM. At least 54 of the MSM-majority clusters were circulating before 1996 and have persisted until the present day. Moreover, about a third of new HIV infections diagnosed among MSM since 1996 involve viruses included in these long-lived clusters. The researchers then used mathematical modeling to estimate that the effective reproduction number (the number of secondary infections per primary infection) for all the MSM-majority clusters was around one for the whole study period. Thus, these clusters were self-sustaining and not contracting. Notably, MSM-majority clusters (particularly the newer clusters) tended to have higher reproduction numbers in recent years. Moreover, although the average age at diagnosis within each of the MSM-majority clusters increased over the study period at a rate of 0.45 years/year, the average age at diagnosis was lower at initiation of new clusters and only increased by 0.28 years/year. What Do These Findings Mean? These findings suggest that several large, persistent, and self-sustaining sub-epidemics, many of which have been present since early in the AIDS epidemic, are driving the resurgent HIV epidemic among MSM in the Netherlands, despite the widespread availability of treatment, increasing rates of diagnosis, and earlier treatment initiation. Importantly, however, these findings also suggest that some sub-epidemics have emerged more recently and that some sub-epidemics, particularly the newer ones, are growing and may be preferentially affecting younger MSM. The accuracy of these findings may be limited by some aspects of the study. For example, the reproduction number estimates assume that the time from diagnosis of a case to the diagnoses of secondary cases is similar across clusters. Nevertheless, the new insights provided by this study should help guide the development of strategies to curb the resurgent HIV epidemic that is currently affecting MSM in the Netherlands and elsewhere. Additional Information This list of resources contains links that can be accessed when viewing the PDF on a device or via the online version of the article at http://dx.doi.org/10.1371/journal.pmed.1001898. The US Centers for Disease Control and Prevention provides information on all aspects of HIV/AIDS, including information on HIV/AIDS among MSM (in English and Spanish) NAM/aidsmap provides basic information about HIV/AIDS and summaries of recent research findings, including information on HIV and MSM and personal stories from MSM living with HIV Information is available from Avert, an international AIDS charity on many aspects of HIV/AIDS, including MSM and HIV; Avert also provides personal stories about living with HIV/AIDS The World Health Organization provides information on all aspects of HIV/AIDS, including HIV/AIDS and MSM (in several languages) The UNAIDS Fast-Track Strategy to End the AIDS Epidemic by 2030 provides up-to-date information about the AIDS epidemic and efforts to halt it A 2011 World Bank Report The Global HIV Epidemics among Men Who Have Sex with Men is available A PLOS Computational Biology Topic Page (a review article that is a published copy of record of a dynamic version of an article in Wikipedia) about viral phylodynamics is available