Phylogeny of partial gag, pol and env genes show predominance of HIV-1G and CRF02_AG with emerging recombinants in south-eastern Nigeria

Abstract

Human Immunodeficiency Virus is characterized by high degree of genetic diversity with marked differences in its geographic distribution even within a country. This study was designed to identify the strains of HIV-1 circulating among infected individuals in southeastern parts of Nigeria. Genomic DNA was extracted from blood samples of 30 HIV-1 infected individuals from Anambra, Delta and Imo states of southeastern Nigeria. Portions of the genome corresponding to entire p24 gag , entire protease and C2–V3 env genes were amplified by nested PCR, sequenced using Sanger's method and phylogenetically analysed. Out of the 30 samples sequenced, 17, 28 and 14 readable sequences were obtained for gag , pol and env regions respectively. The most prevalent subtypes were CRF02_AG (41.2% in gag , 57.1% in pol protease and 50.0% in env ) and G (29.4% in gag , 35.7% in pol protease and 35.7% in env ). Other subtypes identified include A (17.7% in gag , 7.1% in env ) and J (7.1% in env ). Also 2 sequences each in gag (11.8%) and pol protease (7.1%) regions were unclassified but preliminary analysis showed they are recombinants. Furthermore, 71.4% of the isolates with sequences in the 3 regions and 26.7% of those with sequences in 2 genomic regions were recombinant forms. CRF02_AG and subtype G are the predominant HIV-1 strains circulating among infected individuals in southeastern Nigeria. Preliminary analysis results of unclassified sequences suggest that they are new recombinants.

HIV-1 drug resistance and genetic diversity in a cohort of people with HIV-1 in Nigeria

“…This study shows the circulation of HIV-1 subtypes/sub-subtypes A, A3, G, CRF02_AG, D, F2, CRF37_CPX, CRF06_CPX, CRF09_CPX, CRF45_CPX, CRF11_CPX, CRF56_CPX, and CRF05_DF in different proportions among PWH in Nigeria. The predominance of CRF02_AG (22 out of 33 in integrase , 23 out of 33 in protease , 10 out of 17 in reverse transcriptase , seven out of 24 in V1V3 , three out of eight in whole genome sequences) and subtype G (8 out of 33 in integrase , five out of 33 in protease , four out of 17 in reverse transcriptase , two out of 24 in V1V3 , and one out of eight in whole genome sequences) is in line with previous studies carried out in Nigeria [ 14 , 18 , 20 – 21 , 25 , 50 – 56 ]. CRF02_AG and subtype G are the dominant circulating forms of HIV-1 in Nigeria and they are largely driving the epidemic in the country.…”

“…The observation of a wide array of subtypes among a small number of individuals in this study further emphasizes the high genetic diversity of the virus in Nigeria. Previous studies have shown that movement of people from one country to another has contributed largely to the spread of HIV-1 diversity worldwide [ 20 ]. In developing countries, the migration of rural populations because of poverty, famine, civil wars, and so forth have been additional contributing factors to the genetic diversity of the virus [ 59 , 60 ].…”

“…This has a lot of implications for clinical management of patients in the region. It can affect the sensitivity of diagnostic kits and can result in reduction in the susceptibility of patients to antiretroviral drugs [ 20 , 62 , 63 ].…”

“…The epidemic in Nigeria is complex. Several subtypes and other recombinants have been circulating, these include: subtype G, CRF06-cpx, CRF02-AG, sub-subtype A3, and other recombinants [14,18,20,[22][23][24][25][26]. The high diversity of the virus within the country further contributes to the challenge of viral diagnosis, viral load determination, drug resistance testing, and HIV vaccine development.…”

“…Subtype B is the predominant strain of HIV-1 in highincome countries whereas in low-income and middleincome countries (LMICs), especially in the African continent, the non-B subtypes together with several CRFs and URFs currently drive the epidemic. In sub-Saharan Africa, several studies have reported the presence of multiple HIV-1 subtypes along with a number of CRFs, such as CRF01_AE in Central Africa and CRF02_AG in West Africa [9][10][11][12][13][14][15][16][17][18][19][20][21].…”