The study reports the presence of mutations in ARV-naive patients and genetic diversity of HIV-1 variants that circulate in Benin. Globally, the prevalence of transmitted drug resistance was 10.89% after 17 years of ARV circulation in the country, that is consistent with results from other African countries [10, 19–21]. But, studies from some other Sub-Saharan countries have reported rates lower than 10%, by using the same WHO standard protocol and the WHO list of resistance mutations for epidemiological surveys [22, 23]. HIV-1 drug resistance mutations were known to be one of the major factors limiting the effectiveness of ARVs. In our study, the mutations encountered were those associated with the ARVs used in first-line treatment since the start IBAARV in 2002.
This first-line treatment used two NRTIs (zidovudine/stavudine (AZT/D4T) + lamivudine (3TC)) plus an NNRTI (nevirapine/efivarenz (NVP/EFV)), NNRTI as well as non-boosted protease inhibitor (indinavir) regimens . At that time, virologic monitoring was not available and patients were followed based on clinical signs and CD4 counts. Moreover, those who were in therapeutic failure stayed long periods with ineffective treatment, leading to an accumulation of resistance mutations . This accumulation of resistance mutations may compromise the effectiveness of second-line drugs  and increases the risk of transmission of drug-resistant strains to naïve patients . Among naïve patients in our study, 27 already harbored at least one drug resistance mutations and the NNRTIs represent 10% while the NRTIs and PIs represent 6% and 1% respectively.
NRTIs resistance-associated mutations were present in sixteen patients. M184V was the predominant NRTI encountered which confers resistance to 3TC. The K65R confers resistance to abacavir (ABC) and tenofovir (TDF). Thymidine-associated mutations (TAMs) were found but only one patient in our study harbored at least two TAMs conferring intermediate resistance to zidovudine (AZT). TAMs M41L, T215S has been described in Togo [10, 21] and also in Burkina Faso with D67N and K219Q . K70R was observed in one case in our study was also found in Guinea-Conakry . For non-adherence reasons to treatment, M184IV is quickly selected in patients under 3TC which explains its presence in high proportion in studies of transmitted resistance [22, 23]. The high predominance of M184V could also mean that these individuals are not naive due to the infrequent transmission of this mutation, which is due to its high fitness. Lamivudine is also given to HBV infected individuals or individuals co-infected by HIV and HBV. Since the study was conducted after the time of TDF use (replacing D4T as recommended by WHO), the presence of K65R in patients could easily be explained.
The major mutations associated to NNRTIs were K103N (33%) encountered in fourteen patients which compromise the effectiveness of NNRTIs first generation (NVP and EFV) and G190A (7%) identified in three patients which compromise NVP, EFV and etravirine . The high prevalence of the K103N mutation could be explained by its transmission capacity similar to that of wild-type viruses and may be present for years in infected individuals [29–31]. This mutation is also the most common in women who receive a single dose of NVP for the prevention of mother-to-child transmission [32, 33]. In fact, approximately 64.1% of study participants were women and some of them could be part of PMTCT programs. These mutations associated with high-level resistance have been described in one and four patients in Togo and Conakry [10, 23] respectively in naïve patients. The others mutations excepting Y181C and Y188L detected in two cases were V106A, P225H, and V106M, each detected in one case.
Two people exhibited each one mutations associated to PIs (I85V, n = 1) and (L90M, n = 1). In our study, no patient harboured both mutations which conferred intermediate resistance to atazanavir.
Globally, the presence of these mutations could be explained by the wide use of Triomune at the start of IBAARV in Benin.
Phylogenetic analysis evidenced eight recent and three probable older transmission chains (6.5–8.9% of the study patients), reflecting active ongoing transmission. Interestingly, eight patients reported as being MSM and from them, two were involved into the same transmission chain, in which one patient came from Togo and the second one was from Benin. This situation was described in Dakar where the subtype C predominating in the MSM group is increasing in the general population [34, 35], confirming the existence of a dual epidemic in the country. In our study we did not find any transmission chain involving both population groups individual, however, the number of MSM patients is too low to conclude. Further studies are needed in key groups to assess whether HIV-1 strains from MSM intermix with those from the general population in Benin or with those from other countries.
CRF02_AG predominated with 66.5% rate confirming the stability of genetic diversity in 2011 and 2012. Overall, the genetic diversity in Benin matches with results found in a neighboring country, Togo . The other strains (CRF06_cpx, subtype G and sub-subtype A3) have been also reported in other neighbouring African countries [9, 22, 36]. Regarding the unique recombinants (URFs), their proportion among different regions have changed over time . The rate observed in our study (15.7%, 39/248) is fully concordant with the proportion from West Africa  and is not significantly different from that was observed in Togo (22.9%, 19/83) (p = 0.27). These URFs being composed of predominant or co-circulating strains, demonstrate the existence of frequent dual infections with at least two strains of HIV-1 in the country.
The study documents the moderate prevalence of transmitted drug resistance of HIV-1 in Benin, and active ongoing transmission of HIV-1 strains circulating usually in West Africa.