The rate of mother-to-child transmission (vertical) of HIV-1 is about 30% when infected mothers are not treated with antiretroviral drugs during pregnancy [1Ahmad N. Maternal-fetal transmission of human immunodeficiency virus. J Biomed Sci 1996; 3(4): 238-50.
[http://dx.doi.org/10.1007/BF02253703] [PMID: 11725104] -5Mok JQ, Giaquinto C, De Rossi A, Grosch-Wörner I, Ades AE, Peckham CS. Infants born to mothers seropositive for human immunodeficiency virus. Preliminary findings from a multicentre European study. Lancet 1987; 1(8543): 1164-8.
[http://dx.doi.org/10.1016/S0140-6736(87)92142-8] [PMID: 2883489] ]. Vertical transmission primarily takes place at three steps: prepartum through transplacental passage, intrapartum where the infants skin and mucus membrane are exposed to mother’s blood and vaginal secretions, and postpartum through breast milk. HIV-1 vertical transmission is influenced by several factors in the mothers such as high viral load, low CD4 T cell counts, symptomatic HIV disease, immune response, recent infections and heterogeneous HIV-1 population [1Ahmad N. Maternal-fetal transmission of human immunodeficiency virus. J Biomed Sci 1996; 3(4): 238-50.
[http://dx.doi.org/10.1007/BF02253703] [PMID: 11725104] -5Mok JQ, Giaquinto C, De Rossi A, Grosch-Wörner I, Ades AE, Peckham CS. Infants born to mothers seropositive for human immunodeficiency virus. Preliminary findings from a multicentre European study. Lancet 1987; 1(8543): 1164-8.
[http://dx.doi.org/10.1016/S0140-6736(87)92142-8] [PMID: 2883489] ]. However, antiretroviral treatment (ART) during pregnancy has significantly reduced HIV-1 vertical transmission rates [6McGowan JP, Crane M, Wiznia AA, Blum S. Combination antiretroviral therapy in human immunodeficiency virus-infected pregnant women. Obstet Gynecol 1999; 94(5 Pt 1): 641-6.
[http://dx.doi.org/10.1016/S0029-7844(99)00526-8] [PMID: 10546703] ] mainly in the developed countries. More importantly, HIV-1 mother-to-child transmission is still a grave concern in many developing countries where much of HIV infection in children occurs through vertical transmission [7Gumbo FZ, Duri K, Kandawasvika GQ, et al. Risk factors of HIV vertical transmission in a cohort of women under a PMTCT program at three peri-urban clinics in a resource-poor setting. J Perinatol 2010; 30(11): 717-23.
[http://dx.doi.org/10.1038/jp.2010.31] [PMID: 20336078] , 8Forbes JC, Alimenti AM, Singer J, et al. A national review of vertical HIV transmission. AIDS 2012; 26(6): 757-63.
[http://dx.doi.org/10.1097/QAD.0b013e328350995c] [PMID: 22210635] ].

Elucidation of viral determinants and maternal factors involved in HIV-1 vertical transmission has several merits for preventive strategies because more than two-third of the infants born to HIV-1 infected mothers are uninfected without any antiretroviral treatment. Several studies have shown that HIV-1 variants present in mothers that are transmitted to infants were not efficiently neutralized by maternal antibody [9Scarlatti G, Albert J, Rossi P, et al. Mother-to-child transmission of human immunodeficiency virus type 1: Correlation with neutralizing antibodies against primary isolates. J Infect Dis 1993; 168(1): 207-10.
[http://dx.doi.org/10.1093/infdis/168.1.207] [PMID: 8515110] , 10Wu X, Parast AB, Richardson BA, et al. Neutralization escape variants of human immunodeficiency virus type 1 are transmitted from mother to infant. J Virol 2006; 80(2): 835-44.
[http://dx.doi.org/10.1128/JVI.80.2.835-844.2006] [PMID: 16378985] ], including those maternal viral variants that are near the time of transmission [10Wu X, Parast AB, Richardson BA, et al. Neutralization escape variants of human immunodeficiency virus type 1 are transmitted from mother to infant. J Virol 2006; 80(2): 835-44.
[http://dx.doi.org/10.1128/JVI.80.2.835-844.2006] [PMID: 16378985] ]. We and others have characterized the molecular and biological properties of HIV-1 from mothers and their infants after vertical transmission, and demonstrated that a minor maternal HIV-1 variant was transmitted to their infants [11Wolinsky SM, Wike CM, Korber BT, et al. Selective transmission of human immunodeficiency virus type-1 variants from mothers to infants. Science 1992; 255(5048): 1134-7.
[http://dx.doi.org/10.1126/science.1546316] [PMID: 1546316] -16Mulder-Kampinga GA, Simonon A, Kuiken CL, et al. Similarity in env and gag genes between genomic RNAs of human immunodeficiency virus type 1 (HIV-1) from mother and infant is unrelated to time of HIV-1 RNA positivity in the child. J Virol 1995; 69(4): 2285-96.
[PMID: 7884875] ]. Several studies have shown a similar pattern of transmission of HIV-1 from transmitter to recipient during sexual transmission [17Cichutek K, Merget H, Norley S, et al. Development of a quasispecies of human immunodeficiency virus type 1 in vivo. Proc Natl Acad Sci USA 1992; 89(16): 7365-9.
[http://dx.doi.org/10.1073/pnas.89.16.7365] [PMID: 1502146] -19Zhu T, Mo H, Wang N, et al. Genotypic and phenotypic characterization of HIV-1 patients with primary infection. Science 1993; 261(5125): 1179-81.
[http://dx.doi.org/10.1126/science.8356453] [PMID: 8356453] ]. Furthermore, the biological phenotype of HIV-1 involved in both vertical and sexual transmission was shown to be consistently R5 HIV-1 [20vant Wout AB, Kootstra NA, Mulder-Kampinga GA, et al. Macrophage-tropic variants initiate human immunodeficiency virus type 1 infection after sexual, parenteral, and vertical transmission. J Clin Invest 1994; 94(5): 2060-7.
[http://dx.doi.org/10.1172/JCI117560] [PMID: 7962552] -23Philpott S, Burger H, Charbonneau T, et al. CCR5 genotype and resistance to vertical transmission of HIV-1. J Acquir Immune Defic Syndr 1999; 21(3): 189-93.
[http://dx.doi.org/10.1097/00126334-199907010-00002] [PMID: 10421241] ].

In a more comprehensive approach to understand the molecular properties of HIV-1 that are associated with vertical transmission, we showed that there was a high degree of preservation of the functional domains of HIV-1 in the structural genes, including gag p17 [24Hahn T, Matala E, Chappey C, Ahmad N. Characterization of mother-infant HIV type 1 gag p17 sequences associated with perinatal transmission. AIDS Res Hum Retroviruses 1999; 15(10): 875-88.
[http://dx.doi.org/10.1089/088922299310584] [PMID: 10408724] ] and NC [25Wellensiek BP, Sundaravaradan V, Ramakrishnan R, Ahmad N. Molecular characterization of the HIV-1 gag nucleocapsid gene associated with vertical transmission. Retrovirology 2006; 3: 21.
[http://dx.doi.org/10.1186/1742-4690-3-21] [PMID: 16600029] ], pol RT [26Sundaravaradan V, Hahn T, Ahmad N. Conservation of functional domains and limited heterogeneity of HIV-1 reverse transcriptase gene following vertical transmission. Retrovirology 2005; 2: 36.
[http://dx.doi.org/10.1186/1742-4690-2-36] [PMID: 15918905] ], env gp120 [13Ahmad N, Baroudy BM, Baker RC, Chappey C. Genetic analysis of human immunodeficiency virus type 1 envelope V3 region isolates from mothers and infants after perinatal transmission. J Virol 1995; 69(2): 1001-12.
[PMID: 7815476] ] and gp41 [27Ramakrishnan R, Mehta R, Sundaravaradan V, Davis T, Ahmad N. Characterization of HIV-1 envelope gp41 genetic diversity and functional domains following perinatal transmission. Retrovirology 2006; 3: 42.
[http://dx.doi.org/10.1186/1742-4690-3-42] [PMID: 16820061] ], regulatory genes tat [28Husain M, Hahn T, Yedavalli VR, Ahmad N. Characterization of HIV type 1 tat sequences associated with perinatal transmission. AIDS Res Hum Retroviruses 2001; 17(8): 765-73.
[http://dx.doi.org/10.1089/088922201750237040] [PMID: 11429117] ] and rev [29Ramakrishnan R, Hussain M, Holzer A, Mehta R, Sundaravaradan V, Ahmad N. Evaluations of HIV type 1 rev gene diversity and functional domains following perinatal transmission. AIDS Res Hum Retroviruses 2005; 21(12): 1035-45.
[http://dx.doi.org/10.1089/aid.2005.21.1035] [PMID: 16379607] ] and their cis-acting responsive regions, HIV-1 LTR [30Mehta R, Ramakrishnan R, Doktor K, Sundaravaradan V, Ahmad N. Genetic characterization of HIV type 1 long terminal repeat following vertical transmission. AIDS Res Hum Retroviruses 2008; 24(3): 437-45.
[http://dx.doi.org/10.1089/aid.2007.0234] [PMID: 18327987] , 31Mehta R, Sundaravaradan V, Ahmad N. Mutations generated in human immunodeficiency virus type 1 long terminal repeat during vertical transmission correlate with viral gene expression. Virology 2008; 375(1): 170-81.
[http://dx.doi.org/10.1016/j.virol.2008.01.048] [PMID: 18313715] ] and RRE [32Ramakrishnan R, Ahmad N. Derivation of primary sequences and secondary structures of rev responsive element from HIV-1 infected mothers and infants following vertical transmission. Virology 2007; 359(1): 201-11.
[http://dx.doi.org/10.1016/j.virol.2006.09.003] [PMID: 17045321] ] and accessory genes, vif [33Yedavalli VR, Chappey C, Matala E, Ahmad N. Conservation of an intact vif gene of human immunodeficiency virus type 1 during maternal-fetal transmission. J Virol 1998; 72(2): 1092-102.
[PMID: 9445004] ], vpr [34Yedavalli VR, Chappey C, Ahmad N. Maintenance of an intact human immunodeficiency virus type 1 vpr gene following mother-to-infant transmission. J Virol 1998; 72(8): 6937-43.
[PMID: 9658150] ], vpu [35Yedavalli VR, Husain M, Horodner A, Ahmad N. Molecular characterization of HIV type 1 vpu genes from mothers and infants after perinatal transmission. AIDS Res Hum Retroviruses 2001; 17(11): 1089-98.
[http://dx.doi.org/10.1089/088922201300343780] [PMID: 11485627] ] and nef [36Hahn T, Ramakrishnan R, Ahmad N. Evaluation of genetic diversity of human immunodeficiency virus type 1 NEF gene associated with vertical transmission. J Biomed Sci 2003; 10(4): 436-50.
[PMID: 12824703] ] from mother-infant pairs after vertical transmission. While most of these studies focused on elucidating the properties of HIV-1 associated with vertical transmission, limited studies have characterized the properties of HIV-1 that are associated with lack of vertical transmission. Better characterization of viral determinants and host factors associated with lack of vertical transmission could be critical in developing preventive strategies. Our group has performed a comparative analysis of the properties of HIV-1, including genetic variability and functional domains of HIV-1, between non-transmitting mothers (mothers who failed to transmit the virus to their infants in the absence of any antiretroviral therapy) and transmitting mothers (mothers who transmitted the virus to their infants). In this article, we will focus to compile the unique features of HIV-1 that are associated with lack of vertical transmission, especially in two important regions of the HIV-1 genome; the structural regions gag p17 and env V3 and accessory genes, vif and vpr.

HIV-1 structural gene gag p17 matrix plays an important role in HIV-1 replication, viral determinants or motifs in gag p17 may be associated with and/or lack of vertical transmission. Therefore, our previous study analyzed the HIV-1 gag p17 sequences from non-transmitting mothers, including a mother with several births [37Hahn T, Ahmad N. Genetic characterization of HIV type 1 gag p17 matrix genes in isolates from infected mothers lacking perinatal transmission. AIDS Res Hum Retroviruses 2001; 17(17): 1673-80.
[http://dx.doi.org/10.1089/088922201753342095] [PMID: 11779356] ] and compared with our and others published study on transmitting mothers’ sequences [24Hahn T, Matala E, Chappey C, Ahmad N. Characterization of mother-infant HIV type 1 gag p17 sequences associated with perinatal transmission. AIDS Res Hum Retroviruses 1999; 15(10): 875-88.
[http://dx.doi.org/10.1089/088922299310584] [PMID: 10408724] , 38Narwa R, Roques P, Courpotin C, et al. Characterization of human immunodeficiency virus type 1 p17 matrix protein motifs associated with mother-to-child transmission. J Virol 1996; 70(7): 4474-83.
[PMID: 8676472] ]. Our analysis revealed that there were intact Gag p17 matrix open reading frames in most of our non-transmitting [37Hahn T, Ahmad N. Genetic characterization of HIV type 1 gag p17 matrix genes in isolates from infected mothers lacking perinatal transmission. AIDS Res Hum Retroviruses 2001; 17(17): 1673-80.
[http://dx.doi.org/10.1089/088922201753342095] [PMID: 11779356] ] and transmitting mothers’ sequences [24Hahn T, Matala E, Chappey C, Ahmad N. Characterization of mother-infant HIV type 1 gag p17 sequences associated with perinatal transmission. AIDS Res Hum Retroviruses 1999; 15(10): 875-88.
[http://dx.doi.org/10.1089/088922299310584] [PMID: 10408724] ]. We also compared the viral heterogeneity and found that the gag p17 matrix sequences in non-transmitting mothers [37Hahn T, Ahmad N. Genetic characterization of HIV type 1 gag p17 matrix genes in isolates from infected mothers lacking perinatal transmission. AIDS Res Hum Retroviruses 2001; 17(17): 1673-80.
[http://dx.doi.org/10.1089/088922201753342095] [PMID: 11779356] ] were less heterogeneous than transmitting mothers’ sequences [24Hahn T, Matala E, Chappey C, Ahmad N. Characterization of mother-infant HIV type 1 gag p17 sequences associated with perinatal transmission. AIDS Res Hum Retroviruses 1999; 15(10): 875-88.
[http://dx.doi.org/10.1089/088922299310584] [PMID: 10408724] ]. With respect to variability in the nucleotide sequences of p17 matrix, the distance ranged from 0 to 5.6% (0% median values) and amino acid from 0 to 7.7% (0% median values) in non-transmitting mothers [37Hahn T, Ahmad N. Genetic characterization of HIV type 1 gag p17 matrix genes in isolates from infected mothers lacking perinatal transmission. AIDS Res Hum Retroviruses 2001; 17(17): 1673-80.
[http://dx.doi.org/10.1089/088922201753342095] [PMID: 11779356] ] compared transmitting mothers [24Hahn T, Matala E, Chappey C, Ahmad N. Characterization of mother-infant HIV type 1 gag p17 sequences associated with perinatal transmission. AIDS Res Hum Retroviruses 1999; 15(10): 875-88.
[http://dx.doi.org/10.1089/088922299310584] [PMID: 10408724] ] where the nucleotide distances ranged from 0.2 to 6.5% (2.3% median values) and amino acid from 0 to 12.0% (4.5% median values). These findings supported the notion that a low degree of viral heterogeneity in infected mothers is associated with lack of vertical transmission.

Several motifs in Gag p17 matrix sequences, including glutamic acid (E) at position 93, KIEEEQN motif (positions 103-109, the major antibody binding site) were conserved more in transmitting than non-transmitting mothers [24Hahn T, Matala E, Chappey C, Ahmad N. Characterization of mother-infant HIV type 1 gag p17 sequences associated with perinatal transmission. AIDS Res Hum Retroviruses 1999; 15(10): 875-88.
[http://dx.doi.org/10.1089/088922299310584] [PMID: 10408724] , 37Hahn T, Ahmad N. Genetic characterization of HIV type 1 gag p17 matrix genes in isolates from infected mothers lacking perinatal transmission. AIDS Res Hum Retroviruses 2001; 17(17): 1673-80.
[http://dx.doi.org/10.1089/088922201753342095] [PMID: 11779356] , 38Narwa R, Roques P, Courpotin C, et al. Characterization of human immunodeficiency virus type 1 p17 matrix protein motifs associated with mother-to-child transmission. J Virol 1996; 70(7): 4474-83.
[PMID: 8676472] ]. In addition, a valine (V) at position 104 was shown to be present in non-transmitting status compared with transmitting mothers’ sequences [24Hahn T, Matala E, Chappey C, Ahmad N. Characterization of mother-infant HIV type 1 gag p17 sequences associated with perinatal transmission. AIDS Res Hum Retroviruses 1999; 15(10): 875-88.
[http://dx.doi.org/10.1089/088922299310584] [PMID: 10408724] , 38Narwa R, Roques P, Courpotin C, et al. Characterization of human immunodeficiency virus type 1 p17 matrix protein motifs associated with mother-to-child transmission. J Virol 1996; 70(7): 4474-83.
[PMID: 8676472] ]. Several studies found that the C-terminal 6-mer QVSQNY, a lysine (K) or glutamine (Q) at position 15, an alanine (A) at 54, a lysine (K) at 76, a valine (V) at 104 and an aspartic acid (D) at 102 and 121 were associated with non-transmitting status [37Hahn T, Ahmad N. Genetic characterization of HIV type 1 gag p17 matrix genes in isolates from infected mothers lacking perinatal transmission. AIDS Res Hum Retroviruses 2001; 17(17): 1673-80.
[http://dx.doi.org/10.1089/088922201753342095] [PMID: 11779356] , 38Narwa R, Roques P, Courpotin C, et al. Characterization of human immunodeficiency virus type 1 p17 matrix protein motifs associated with mother-to-child transmission. J Virol 1996; 70(7): 4474-83.
[PMID: 8676472] ]. Our study also compared the motifs required for functional activity of Gag p17 matrix protein between non-transmitting and transmitting mothers’ sequences and found that the functions such as targeting of Gag to the plasma membrane, virus assembly and release, envelope glycoprotein incorporation into the virion, and localization of the virus preintegration complex to the nucleus of nondividing cells [39Yuan X, Yu X, Lee T-H, Essex M. Mutations in the N-terminal region of human immunodeficiency virus type 1 matrix protein block intracellular transport of the Gag precursor. J Virol 1993; 67(11): 6387-94.
[PMID: 8411340] -42Von Schwedler U, Kornbluth RS, Trono D. The nuclear localization signal of the matrix protein of human immunodeficiency virus type 1 allows the establishment of infection in macrophages and quiescent T lymphocytes. Proc Natl Acad Sci USA 1994; 91(15): 6992-6.
[http://dx.doi.org/10.1073/pnas.91.15.6992] [PMID: 8041734] ] were largely preserved in non-transmitting [37Hahn T, Ahmad N. Genetic characterization of HIV type 1 gag p17 matrix genes in isolates from infected mothers lacking perinatal transmission. AIDS Res Hum Retroviruses 2001; 17(17): 1673-80.
[http://dx.doi.org/10.1089/088922201753342095] [PMID: 11779356] ] and transmitting mothers’ [24Hahn T, Matala E, Chappey C, Ahmad N. Characterization of mother-infant HIV type 1 gag p17 sequences associated with perinatal transmission. AIDS Res Hum Retroviruses 1999; 15(10): 875-88.
[http://dx.doi.org/10.1089/088922299310584] [PMID: 10408724] ] sequences. Another functional domains of Gag p17 matrix namely the polymerization site located at positions 47 to 59 was less conserved in non-transmitting mothers’ sequences [37Hahn T, Ahmad N. Genetic characterization of HIV type 1 gag p17 matrix genes in isolates from infected mothers lacking perinatal transmission. AIDS Res Hum Retroviruses 2001; 17(17): 1673-80.
[http://dx.doi.org/10.1089/088922201753342095] [PMID: 11779356] ] than transmitting mothers’ sequences [24Hahn T, Matala E, Chappey C, Ahmad N. Characterization of mother-infant HIV type 1 gag p17 sequences associated with perinatal transmission. AIDS Res Hum Retroviruses 1999; 15(10): 875-88.
[http://dx.doi.org/10.1089/088922299310584] [PMID: 10408724] ]. Some of these motifs in gag p17 matrix that differ between transmitting and non-transmitting mothers could be targeted for preventive strategies of HIV vertical transmission.

Comparison of the V3 region of HIV-1 envelope gene, which plays an important role in virus neutralization, cellular tropism, replication and pathogenesis [43Shioda T, Levy JA, Cheng-Mayer C. Macrophage and T cell-line tropisms of HIV-1 are determined by specific regions of the envelope gp120 gene. Nature 1991; 349(6305): 167-9.
[http://dx.doi.org/10.1038/349167a0] [PMID: 1986308] -45Choe H, Farzan M, Sun Y, et al. The beta-chemokine receptors CCR3 and CCR5 facilitate infection by primary HIV-1 isolates. Cell 1996; 85(7): 1135-48.
[http://dx.doi.org/10.1016/S0092-8674(00)81313-6] [PMID: 8674119] ], between non-transmitting and transmitting mothers’ sequences may provide important viral information related to vertical transmission. While the coding potential of the V3 region were highly conserved in non-transmitting [46Matala E, Crandall KA, Baker RC, Ahmad N. Limited heterogeneity of HIV type 1 in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2000; 16(15): 1481-9.
[http://dx.doi.org/10.1089/088922200750006001] [PMID: 11054261] ] and transmitting [13Ahmad N, Baroudy BM, Baker RC, Chappey C. Genetic analysis of human immunodeficiency virus type 1 envelope V3 region isolates from mothers and infants after perinatal transmission. J Virol 1995; 69(2): 1001-12.
[PMID: 7815476] -16Mulder-Kampinga GA, Simonon A, Kuiken CL, et al. Similarity in env and gag genes between genomic RNAs of human immunodeficiency virus type 1 (HIV-1) from mother and infant is unrelated to time of HIV-1 RNA positivity in the child. J Virol 1995; 69(4): 2285-96.
[PMID: 7884875] ] mothers’ sequences, the V3 region sequences of non-transmitting mother’s sequence [46Matala E, Crandall KA, Baker RC, Ahmad N. Limited heterogeneity of HIV type 1 in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2000; 16(15): 1481-9.
[http://dx.doi.org/10.1089/088922200750006001] [PMID: 11054261] ] were significantly less heterogeneous compared with transmitting mothers’ V3 region sequences [13Ahmad N, Baroudy BM, Baker RC, Chappey C. Genetic analysis of human immunodeficiency virus type 1 envelope V3 region isolates from mothers and infants after perinatal transmission. J Virol 1995; 69(2): 1001-12.
[PMID: 7815476] ]. Furthermore, the estimates of genetic diversity of non-transmitting mothers’ V3 region sequences were significantly lower compared with transmitting mothers’ V3 region sequences [46Matala E, Crandall KA, Baker RC, Ahmad N. Limited heterogeneity of HIV type 1 in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2000; 16(15): 1481-9.
[http://dx.doi.org/10.1089/088922200750006001] [PMID: 11054261] ]. The lower level of viral heterogeneity of V3 region sequences in non-transmitting mothers compared with transmitting mothers’ sequences correlated with lack of vertical transmission, as also seen in p17 gag sequences. Another striking feature in support of the correlation of less heterogeneity of HIV with lack of vertical transmission was the decreasing viral heterogeneity and rate of genetic diversity with successive births in non-transmitting mothers [46Matala E, Crandall KA, Baker RC, Ahmad N. Limited heterogeneity of HIV type 1 in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2000; 16(15): 1481-9.
[http://dx.doi.org/10.1089/088922200750006001] [PMID: 11054261] ].

There were several amino acid sequence motifs present in non-transmitting mothers that were specific to each non-transmitting mother when compared to transmitting mothers [46Matala E, Crandall KA, Baker RC, Ahmad N. Limited heterogeneity of HIV type 1 in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2000; 16(15): 1481-9.
[http://dx.doi.org/10.1089/088922200750006001] [PMID: 11054261] ] did not provide any specific pattern related to either associated with or lack of vertical transmission. However, examining the non-transmitting mothers and one non-transmitting mother with multiple deliveries suggested clearly that if HIV stays less heterogeneous, the mother-to-child transmission could be significantly reduced. This conclusion is further supported by the fact that the one non-transmitting mother’s HIV sequences were almost homogeneous at the time of her fifth delivery [46Matala E, Crandall KA, Baker RC, Ahmad N. Limited heterogeneity of HIV type 1 in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2000; 16(15): 1481-9.
[http://dx.doi.org/10.1089/088922200750006001] [PMID: 11054261] ].

Mother-to-child transmission has been shown to be significantly reduced by use of ART, which suggests that suppression of HIV replication is achieved, that also reduces HIV heterogeneity because of suppression of HIV replication. A low level of HIV-1 heterogeneity associated with lack of mother-to-child of transmission [46Matala E, Crandall KA, Baker RC, Ahmad N. Limited heterogeneity of HIV type 1 in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2000; 16(15): 1481-9.
[http://dx.doi.org/10.1089/088922200750006001] [PMID: 11054261] ] provides a logical explanation on the mechanism of reduction in HIV vertical by using ART during pregnancy. The use of ART is known to suppress HIV-1 replication and lowers viral load in infected patients [6McGowan JP, Crane M, Wiznia AA, Blum S. Combination antiretroviral therapy in human immunodeficiency virus-infected pregnant women. Obstet Gynecol 1999; 94(5 Pt 1): 641-6.
[http://dx.doi.org/10.1016/S0029-7844(99)00526-8] [PMID: 10546703] , 47Baba M, Pauwels R, Herdewijn P, De Clercq E, Desmyter J, Vandeputte M. Both 2,3-dideoxythymidine and its 2,3-unsaturated derivative (2,3-dideoxythymidinene) are potent and selective inhibitors of human immunodeficiency virus replication in vitro. Biochem Biophys Res Commun 1987; 142(1): 128-34.
[http://dx.doi.org/10.1016/0006-291X(87)90460-8] [PMID: 3028398] , 48Sheehy N, Desselberger U, Whitwell H, Ball JK. Concurrent evolution of regions of the envelope and polymerase genes of human immunodeficiency virus type 1 during zidovudine (AZT) therapy. J Gen Virol 1996; 77(Pt 5): 1071-81.
[http://dx.doi.org/10.1099/0022-1317-77-5-1071] [PMID: 8609473] ], which also reduces viral heterogeneity because of no active viral replication in the presence of ART [48Sheehy N, Desselberger U, Whitwell H, Ball JK. Concurrent evolution of regions of the envelope and polymerase genes of human immunodeficiency virus type 1 during zidovudine (AZT) therapy. J Gen Virol 1996; 77(Pt 5): 1071-81.
[http://dx.doi.org/10.1099/0022-1317-77-5-1071] [PMID: 8609473] ]. This decrease in HIV-1 heterogeneity due to ART in infected mothers most likely reduced HIV-1 mother-infant transmission. The lower estimates of genetic diversity in non-transmitting mothers’ HIV-1 populations joined with different levels of selection pressure [46Matala E, Crandall KA, Baker RC, Ahmad N. Limited heterogeneity of HIV type 1 in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2000; 16(15): 1481-9.
[http://dx.doi.org/10.1089/088922200750006001] [PMID: 11054261] ] suggest the mothers’ ability to mount a different degree of effective immune response against the viral population and prevent transmission by neutralizing the virus. We saw in our study that HIV-1 sequences in the non-transmitting mothers were homogeneous [46Matala E, Crandall KA, Baker RC, Ahmad N. Limited heterogeneity of HIV type 1 in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2000; 16(15): 1481-9.
[http://dx.doi.org/10.1089/088922200750006001] [PMID: 11054261] ], which provides an indication that the HIV-1 population has attained a state of optimum adaptation as seen in long-term progressors of HIV-1 infection [49Wolinsky SM, Korber BT, Neumann AU, et al. Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infection. Science 1996; 272(5261): 537-42.
[http://dx.doi.org/10.1126/science.272.5261.537] [PMID: 8614801] ] may also apply in the case of non-transmitting mothers. These findings of a more slowly evolving virus population in the V3 region provide a better target for developing strategies for mounting an immune response to control the infection and prevent transmission.

HIV-1 replication is regulated by several regulatory and accessory genes, including vif and vpr that are required for HIV-1 pathogenesis [50Sova P, van Ranst M, Gupta P, et al. Conservation of an intact human immunodeficiency virus type 1 vif gene in vitro and in vivo. J Virol 1995; 69(4): 2557-64.
[PMID: 7884906] -52Sharp PM, Bailes E, Stevenson M, Emerman M, Hahn BH. Gene acquisition in HIV and SIV. Nature 1996; 383(6601): 586-7.
[http://dx.doi.org/10.1038/383586a0] [PMID: 8857532] ] and may also have some role in mother-to-child transmission. Therefore, a comparative analysis of HIV-1 vif and vpr genes from transmitting and non-transmitting mothers should provide useful information that may allow us to correlate the properties of these genes with HIV-1 vertical transmission, as shown in our studies [33Yedavalli VR, Chappey C, Matala E, Ahmad N. Conservation of an intact vif gene of human immunodeficiency virus type 1 during maternal-fetal transmission. J Virol 1998; 72(2): 1092-102.
[PMID: 9445004] , 34Yedavalli VR, Chappey C, Ahmad N. Maintenance of an intact human immunodeficiency virus type 1 vpr gene following mother-to-infant transmission. J Virol 1998; 72(8): 6937-43.
[PMID: 9658150] , 53Yedavalli VR, Ahmad N. Low conservation of functional domains of HIV type 1 vif and vpr genes in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2001; 17(10): 911-23.
[http://dx.doi.org/10.1089/088922201750290032] [PMID: 11461677] ]. In these studies, we have shown that the molecular motifs that are essential for the biological function of vif and vpr in HIV-1 were conserved in HIV-1 isolates from mothers and infants after vertical transmission [33Yedavalli VR, Chappey C, Matala E, Ahmad N. Conservation of an intact vif gene of human immunodeficiency virus type 1 during maternal-fetal transmission. J Virol 1998; 72(2): 1092-102.
[PMID: 9445004] , 34Yedavalli VR, Chappey C, Ahmad N. Maintenance of an intact human immunodeficiency virus type 1 vpr gene following mother-to-infant transmission. J Virol 1998; 72(8): 6937-43.
[PMID: 9658150] ], suggesting that vif and vpr proteins are required for transmission and pathogenesis. In contrast, the functional domain of vif and vpr in non-transmitting mother isolates were less conserved [53Yedavalli VR, Ahmad N. Low conservation of functional domains of HIV type 1 vif and vpr genes in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2001; 17(10): 911-23.
[http://dx.doi.org/10.1089/088922201750290032] [PMID: 11461677] ], providing a first line of evidence that vif and vpr may have a role in HIV-1 vertical transmission. Another important finding was that vif and vpr sequences were less heterogeneous in non-transmitting HIV-1 isolates [53Yedavalli VR, Ahmad N. Low conservation of functional domains of HIV type 1 vif and vpr genes in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2001; 17(10): 911-23.
[http://dx.doi.org/10.1089/088922201750290032] [PMID: 11461677] ] than transmitting mothers [33Yedavalli VR, Chappey C, Matala E, Ahmad N. Conservation of an intact vif gene of human immunodeficiency virus type 1 during maternal-fetal transmission. J Virol 1998; 72(2): 1092-102.
[PMID: 9445004] , 34Yedavalli VR, Chappey C, Ahmad N. Maintenance of an intact human immunodeficiency virus type 1 vpr gene following mother-to-infant transmission. J Virol 1998; 72(8): 6937-43.
[PMID: 9658150] ], which is consistent with a low level of heterogeneity seen in gag p17 [37Hahn T, Ahmad N. Genetic characterization of HIV type 1 gag p17 matrix genes in isolates from infected mothers lacking perinatal transmission. AIDS Res Hum Retroviruses 2001; 17(17): 1673-80.
[http://dx.doi.org/10.1089/088922201753342095] [PMID: 11779356] ] and env V3 region [46Matala E, Crandall KA, Baker RC, Ahmad N. Limited heterogeneity of HIV type 1 in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2000; 16(15): 1481-9.
[http://dx.doi.org/10.1089/088922200750006001] [PMID: 11054261] ].

Some of the in-depth analysis of the deduced amino acid sequences of vif nucleotide sequences from non-transmitting HIV-1 isolates showed that some non-transmitting mothers vif sequences contained stop codons and lacked initiation codons [53Yedavalli VR, Ahmad N. Low conservation of functional domains of HIV type 1 vif and vpr genes in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2001; 17(10): 911-23.
[http://dx.doi.org/10.1089/088922201750290032] [PMID: 11461677] ], indicating that vif was not functional and therefore may have prevented mother-to-child transmission. One of the other important findings was that the vif sequences from some non-transmitting mothers [53Yedavalli VR, Ahmad N. Low conservation of functional domains of HIV type 1 vif and vpr genes in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2001; 17(10): 911-23.
[http://dx.doi.org/10.1089/088922201750290032] [PMID: 11461677] ] carried a substitution of histidine in place of tyrosine at position 30 in a highly conserved motif SL (I/V) X4YX9Y among HIV-1 isolates located between amino acid 23-40 that was preserved in our transmitting mothers [33Yedavalli VR, Chappey C, Matala E, Ahmad N. Conservation of an intact vif gene of human immunodeficiency virus type 1 during maternal-fetal transmission. J Virol 1998; 72(2): 1092-102.
[PMID: 9445004] ]. Some other non-transmitting mothers [53Yedavalli VR, Ahmad N. Low conservation of functional domains of HIV type 1 vif and vpr genes in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2001; 17(10): 911-23.
[http://dx.doi.org/10.1089/088922201750290032] [PMID: 11461677] ] contained substitutions such as asparagine at position 22, lysine at 77 and histidine at 110 [50Sova P, van Ranst M, Gupta P, et al. Conservation of an intact human immunodeficiency virus type 1 vif gene in vitro and in vivo. J Virol 1995; 69(4): 2557-64.
[PMID: 7884906] ]. The substitutions of polar charged lysine to polar uncharged asparagine at position 22 and non-polar tyrosine to polar histidine at 30 and 110 are major changes and may affect vif function. The vif gene is highly conserved in all HIV-1 isolates in HIV-1 infected patients [50Sova P, van Ranst M, Gupta P, et al. Conservation of an intact human immunodeficiency virus type 1 vif gene in vitro and in vivo. J Virol 1995; 69(4): 2557-64.
[PMID: 7884906] ] as well as transmitting mother-infant pairs [33Yedavalli VR, Chappey C, Matala E, Ahmad N. Conservation of an intact vif gene of human immunodeficiency virus type 1 during maternal-fetal transmission. J Virol 1998; 72(2): 1092-102.
[PMID: 9445004] ]. In contrast, the non-transmitting mothers’ vif sequences [53Yedavalli VR, Ahmad N. Low conservation of functional domains of HIV type 1 vif and vpr genes in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2001; 17(10): 911-23.
[http://dx.doi.org/10.1089/088922201750290032] [PMID: 11461677] ] were less functional, suggesting a role in preventing HIV-1 vertical transmission.

Upon examination of the deduced amino acid sequences of vpr in non-transmitting mothers’ HIV-1 isolates [53Yedavalli VR, Ahmad N. Low conservation of functional domains of HIV type 1 vif and vpr genes in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2001; 17(10): 911-23.
[http://dx.doi.org/10.1089/088922201750290032] [PMID: 11461677] ], we found that some non-transmitting mother vpr sequences had stop codons and lacked initiation codons, whereas some non-transmitting mothers’ vpr sequences contained a substitution of serine in place of alanine at position 30, arginine in place of glycine at position 75, and a deletion in the C-terminus necessary for vpr function. Some non-transmitting mother sequences had a substitution of arginine in place of glycine at position 75 of the conserved dipeptide (GC) that is important in virion incorporation and stability of vpr [54Mahalingam S, Ayyavoo V, Patel M, Kieber-Emmons T, Weiner DB. Nuclear import, virion incorporation, and cell cycle arrest/differentiation are mediated by distinct functional domains of human immunodeficiency virus type 1 vpr. J Virol 1997; 71(9): 6339-47.
[PMID: 9261351] ] and cell cycle arrest [55Mahalingam S, Khan SA, Jabbar MA, Monken CE, Collman RG, Srinivasan A. Identification of residues in the N-terminal acidic domain of HIV-1 vpr essential for virion incorporation. Virology 1995; 207(1): 297-302.
[http://dx.doi.org/10.1006/viro.1995.1081] [PMID: 7871742] ] and a serine in place of alanine at position 30 that is required for cell cycle arrests by vpr [55Mahalingam S, Khan SA, Jabbar MA, Monken CE, Collman RG, Srinivasan A. Identification of residues in the N-terminal acidic domain of HIV-1 vpr essential for virion incorporation. Virology 1995; 207(1): 297-302.
[http://dx.doi.org/10.1006/viro.1995.1081] [PMID: 7871742] , 56Di Marzio P, Choe S, Ebright M, Knoblauch R, Landau NR. Mutational analysis of cell cycle arrest, nuclear localization and virion packaging of human immunodeficiency virus type 1 vpr. J Virol 1995; 69(12): 7909-16.
[PMID: 7494303] ]. More importantly, the vpr sequences from a non-transmitting mother from three time points contained an in-frame deletion at the C-terminus [53Yedavalli VR, Ahmad N. Low conservation of functional domains of HIV type 1 vif and vpr genes in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2001; 17(10): 911-23.
[http://dx.doi.org/10.1089/088922201750290032] [PMID: 11461677] ] that has been shown to affect cell cycle arrest property of vpr [55Mahalingam S, Khan SA, Jabbar MA, Monken CE, Collman RG, Srinivasan A. Identification of residues in the N-terminal acidic domain of HIV-1 vpr essential for virion incorporation. Virology 1995; 207(1): 297-302.
[http://dx.doi.org/10.1006/viro.1995.1081] [PMID: 7871742] ], which were also seen in long-term survivors of HIV-1 infection [57Wang B, Ge YC, Palasanthiran P, et al. Gene defects clustered at the C-terminus of the vpr gene of HIV-1 in long-term nonprogressing mother and child pair: in vivo evolution of vpr quasispecies in blood and plasma. Virology 1996; 223(1): 224-32.
[http://dx.doi.org/10.1006/viro.1996.0471] [PMID: 8806556] ]. In summary, the functional domains of vpr in non-transmitting mother were either defective, less functional or contained substitution in important domains that affected vpr function compared with transmitting mothers vpr sequences that had all functional domains intact [53Yedavalli VR, Ahmad N. Low conservation of functional domains of HIV type 1 vif and vpr genes in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2001; 17(10): 911-23.
[http://dx.doi.org/10.1089/088922201750290032] [PMID: 11461677] ]. These data suggested that vif and vpr are important viral determinants of HIV-1 vertical transmission and defect in these genes may be associated with lack of vertical transmission, as found in non-transmitting mothers vif and vpr sequences [53Yedavalli VR, Ahmad N. Low conservation of functional domains of HIV type 1 vif and vpr genes in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2001; 17(10): 911-23.
[http://dx.doi.org/10.1089/088922201750290032] [PMID: 11461677] ].

While HIV-1 mother-to-child (vertical) transmission of HIV-1 is multifactorial in nature, viral determinants may play an important role in either influencing or preventing vertical transmission. Several studies, including our study characterized the molecular and biological properties of HIV-1 associated with vertical transmission and showed that HIV-1 structural, regulatory and accessory genes were highly conserved and functional. We have performed several studies examining HIV-1 structural and accessory genes from infected mothers who failed to transmit the virus to their infants in the absence of any antiretroviral therapy. In this article, we have compiled the findings of our studies that showed that HIV-1 p17 gag matrix, envelope V3 regions, vif and vpr sequences were significantly less heterogeneous in non-transmitting mothers than transmitting mothers. In addition, the vif and vpr from non-transmitting mothers were either defective, less functional or had substitution in important domains affecting function, whereas transmitting mothers vif and vpr were intact and functional. These findings are consistent with the data showing that more than two-third of HIV-infected pregnant women do not transmit HIV to their infants more likely of their HIV-1 sequences being less heterogeneous and vif and vpr less functional. In addition, our findings are also consistent with the use of antiretroviral therapy in preventing HIV-1 vertical transmission because antiretroviral therapy suppresses viral replication and reduces viral heterogeneity. Our non-transmitting mothers harbored a homogenous HIV sequences, whereas transmitting mothers had a heterogeneous HIV sequences, suggesting that less HIV heterogeneity was associated with the lack of vertical transmission. These results provide an explanation for the reduction of vertical transmission by antiretroviral therapy (ART) during pregnancy, as ART is known to suppress virus replication and reduce viral load viral heterogeneity. These findings may have ramifications in combating vertical transmission by developing new therapies.