Killer cell immunoglobulin-like receptor three domains long cytoplasmic tail 1 gene *007 may modulate disease progression of human immunodeficiency virus-1 infection in the Japanese population.

One of the KIR allele, KIR3DL1*007, was associated with the progression to acquired immunodeficiency syndrome and not with the susceptibility to HIV-1 infection in the Japanese and Indian populations, implying that KIR3DL1*007-positive NK cells might eliminate HIV-infected cells less effectively than NK cells bearing the other KIR3DL1 alleles or KIR3DS1 alleles.

Insights in tuberculosis immunology: Role of NKT and T regulatory cells.

Background: Tuberculosis (TB) control is challenging due to poor drug compliance and emerging resistance. The need of the hour is to determine the prediction of disease cure and relapse. Patients' immune response is crucial to the disease outcome. This study was designed to study the immune profile of TB patients during treatment and cure. Methods: The cross-sectional study included newly diagnosed pulmonary TB patients and healthy controls. Levels of serum cytokines/chemokines (Th1/Th2/Th17) were measured by BD cytometric bead array. The cell surface markers assessed in the study were CD3, CD4, CD8, CD16, CD56, and BD human regulatory T cell cocktail (CD4/CD25/CD127). Results: Data analysis observed statistically significant differences in CD3dim/CD56 + natural killer T (NKT) among TB patients with significantly low levels in healthy controls and after treatment completion (P < 0.0001). The analysis also revealed a high percentage of CD3dim/CD56 + NKT in fast responders. The percentage of T regulatory was found to be high in patients when compared with healthy controls; the values were statistically significant (0.0002). Interleukin-6 was significantly associated with the disease (P < 0.0485). Discussion: A comprehensive understanding of role of CD3dim/CD56+ NKT in antimycobacterial immunity may enable new possibilities for NK cell-based prophylactic and/or therapeutic strategies against TB.

Cytokine gene polymorphisms among North Indians: Implications for genetic predisposition?

Variations in the production and activity of cytokines influence the susceptibility and/or resistance to various infectious agents, autoimmune diseases, as well as the post-transplant engraftment/ rejection. Differences in the production of cytokines between individuals have been correlated to single nucleotide polymorphisms (SNPs) in the promoter, coding or non-coding regions of cytokine genes. The present study aimed at understanding distribution of cytokine gene variants among HIV seropositive subjects including HIV + TB+ subjects of Indian origin. Our findings indicate significant association of pro-inflammatory (IL2, IFN-γ, TNF-α) and anti-inflammatory cytokine gene variants (IL4, IL10) with the risk to acquire the HIV infection and development of AIDS related illness in Indian population. Since distribution of genetic polymorphisms varies significantly across different populations, different genotypes might exhibit different disease-modifying effects. An understanding of the immunogenetic factors or AIDS restriction genes is important not only for elucidating the mechanisms of disease pathogenesis but also for vaccine design and its application.

Comparative Proliferation Capacity of Gag-C-Specific Naive and Memory CD4+ and CD8+ T Lymphocytes in Rapid, Viremic Slow, and Slow Progressors During Human Immunodeficiency Virus Infection.

The exact cause of altered dynamics in T cells compartment during HIV infection remains elusive to date. In this longitudinal study, the proliferation frequency of different T cell subsets was investigated in untreated HIV-1-infected Indian individuals stratified as rapid (R), viremic slow (VS), slow (S) progressors, and healthy controls. Ten healthy and 20 treatment-naive HIV-1-infected individuals were enrolled. Expression of Ki67 nuclear antigen was examined on HIV-specific T cell subsets in peripheral blood lymphocytes. Upon stimulation with HIV-1 Gag-C peptide pools, effector memory (EM) CD4 T cells (R vs. S, EM CD4, p < 0.05) of R progressors proliferated significantly compared with those of S progressors at baseline. However, central memory (CM) CD8 T cell subsets proliferated significantly in VS and S progressors compared with those in R progressors, wherein highest proliferation frequency of EM CD8 T cells was observed. At follow-up visit, the proliferation frequency of naive CD8 T cells was significantly higher in R progressors than S progressors (R vs. S naive CD8, p < 0.05). The findings suggest altered dynamics of different CD4+ and CD8+ T cell subsets in R, VS, and S progressors. The increase in CM T cell proliferation in VS and S progressors could be attributed to slower progression of the HIV infection. Hence, treatment strategies must be focused on restoring the homeostatic balance to restore T cell functionality.

Impact of HIV infection and highly active antiretroviral therapy (HAART) on B cell subpopulations in children.

B-cells play an important role in defending children against various infections. In view of scare data, we undertook this prospective cohort study to describe B cell compartment in HIV infected children (<5 years of age) and the effect of HAART on B cell subpopulations. HIV infected children (<5 years) from Pediatric HIV services of the Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, were recruited (April 2012-December 2015). The enrolled HIV-1 infected children (n = 59) were followed up regularly for 12 months; healthy controls (n = 51) included HIV uninfected children with no major illness. Flow cytometry was performed on fresh EDTA-treated blood samples to characterize B cell subpopulations. In HIV-infected children, marked depletion of naive (P = 0.003), non-switched memory (P = 0.02), mature (P = 0.0005), resting memory (P < 0.0001) B cells, and expansion of double negative memory (P < 0.0001), activated memory (P < 0.0001) and tissue like memory (P < 0.0001) B cells were observed as compared to healthy controls. In children started on HAART, at the end of 12 months of therapy, frequencies of non-switched memory (P = 0.04), switched memory (P = 0.01), and resting memory (P = 0.003) B cells were lower; activated memory (P = 0.04), and tissue-like memory (P = 0.0001) B cells were still higher than healthy controls. HIV infection resulted in reduced memory B cells in HIV infected children. Following HAART, there was normalization of some B cell subpopulations. The study emphasizes the need of re-vaccination in HIV infected children to maintain the memory B cell pool and adequate humoral immune response against infections.

Comparative evaluation of microbial translocation products (LPS, sCD14, IgM Endocab) in HIV-1 infected Indian individuals.

BACKGROUND: Microbial translocation of lipopolysaccharides (LPS), soluble CD14 (sCD14) and IgM Endocab levels have been reported to be associated with disease progression in HIV-1 infection. In this longitudinal study, plasma levels of different microbially translocated products (LPS, sCD14, Endocab) was investigated in HIV-1 infected Indian Individuals stratified as Rapid (R), Viremic slow (VS), Slow progressors (S) and healthy controls. METHOD: Ten healthy and twenty HIV-1 infected individuals were enrolled. Plasma levels of LPS, sCD14, Endocab was examined using commercially available Limulus Amebocyte assay and enzyme-linked immunosorbent assay (ELISA) enzyme linked immunosorbant assay. RESULTS: Elevated levels of sCD14, IgM EndoCab and LPS were observed during HIV-1 infection compared to healthy controls. Rapid progressors had higher levels of sCD14, IgM EndoCab, LPS (median% 1553, 3596, 202.2) compared to viremic slow, slow progressors and healthy controls both at baseline and follow up visits. At baseline, LPS correlated positively with IgM Endocab and negatively with sCD14 levels while at follow-up, significant positive correlation was observed between IgM Endocab and sCD14 (IgM EndoCab r = 0.490, p = 0.05; sCD14 r = 0.051, p = 0.830). Plasma levels of sCD14 correlated positively with viral load in rapid, viremic slow and slow progressors while CD + T cell count correlated positively with sCD14 and IgM EndoCab levels in viremic slow and slow progressors. CONCLUSION: Our findings indicate that elevated levels of sCD14, IgM EndoCab and LPS in HIV-1 infected individuals are strong predictors of disease progression and could be considered as candidate biomarkers for disease monitoring.

Cross-neutralizing anti-HIV-1 human single chain variable fragments(scFvs) against CD4 binding site and N332 glycan identified from a recombinant phage library.

More than 50% of HIV-1 infection globally is caused by subtype_C viruses. Majority of the broadly neutralizing antibodies (bnAbs) targeting HIV-1 have been isolated from non-subtype_C infected donors. Mapping the epitope specificities of bnAbs provides useful information for vaccine design. Recombinant antibody technology enables generation of a large repertoire of monoclonals with diverse specificities. We constructed a phage recombinant single chain variable fragment (scFv) library with a diversity of 7.8 × 108 clones, using a novel strategy of pooling peripheral blood mononuclear cells (PBMCs) of six select HIV-1 chronically infected Indian donors whose plasma antibodies exhibited potent cross neutralization efficiency. The library was panned and screened by phage ELISA using trimeric recombinant proteins to identify viral envelope specific clones. Three scFv monoclonals D11, C11 and 1F6 selected from the library cross neutralized subtypes A, B and C viruses at concentrations ranging from 0.09 µg/mL to 100 µg/mL. The D11 and 1F6 scFvs competed with mAbs b12 and VRC01 demonstrating CD4bs specificity, while C11 demonstrated N332 specificity. This is the first study to identify cross neutralizing scFv monoclonals with CD4bs and N332 glycan specificities from India. Cross neutralizing anti-HIV-1 human scFv monoclonals can be potential candidates for passive immunotherapy and for guiding immunogen design.

Cross-Reactive Potential of HIV-1 Subtype C-Infected Indian Individuals Against Multiple HIV-1 Potential T Cell Epitope Gag Variants.

Vaccine immunogen with expanded T cell coverage for protection against HIV-1 diversity is the need of the hour. This study was undertaken to examine the ability of T cells to respond to a broad spectrum of potential T cell epitope (PTE) peptides containing variable as well as conserved sequences that would most accurately reflect immune responses to different circulating strains. Set of 320 PTE peptides were pooled in a matrix format that included 40 pools of 32 peptides per pool. These pools were used in interferon-γ enzyme-linked immunospot assay for screening and confirmation of HIV-1 PTE Gag-specific T cell immune responses in 34 HIV-1 seropositive Indian individuals. "Deconvolute This" software was used for result analysis. The dominant target in terms of magnitude and breadth of responses was observed to be the p24 subunit of Gag protein. Of the 34 study subjects, 26 (77%) showed a response to p24 PTE Gag peptides, 17 (50%) to p17, and 17 (50%) responded to p15 PTE peptides. The total breadth and magnitude of immune response ranged from 0.75 to 14.50 and 95.02 to 1,103 spot-forming cells/106 cells, respectively. Seventy-six peptides located in p24 Gag were targeted by 77% of the study subjects followed by 51 peptides in p17 Gag and 46 peptides in p15 Gag with multiple variants being recognized. Maximum study participants recognized PTE peptide sequence Gag271→285NKIVRMYSPVSILDI located in p24 Gag subunit. T cells from HIV-1-infected individuals can recognize multiple PTE peptide variants, although the magnitude of the responses can vary greatly across these variants.

APOBEC3H polymorphisms and susceptibility to HIV-1 infection in an Indian population.

Human APOBEC3H (A3H) is a member of APOBEC cytidine deaminase family intensively constraining the HIV-1 replication. A3H is known to be polymorphic with different protein stability and anti-HIV-1 activity in vitro. We recently reported that A3H haplotypes composed of two functional polymorphisms, rs139292 (N15del) and rs139297 (G105R), were associated with the susceptibility to HIV-1 infection in Japanese. To confirm the association of A3H and HIV-1 infection in another ethnic group, a total of 241 HIV-1-infected Indian individuals and ethnic-matched 286 healthy controls were analyzed for the A3H polymorphisms. The frequency of 15del allele was high in the HIV-1-infected subjects as compared with the controls (0.477 vs 0.402, odds ratio (OR)=1.36, P=0.014). Haplotype analysis showed that the frequencies of 15del-105R was high (0.475 vs 0.400, OR=1.36, permutation P=0.037) in the HIV-1-infected subjects, confirming the association of A3H polymorphisms with the susceptibility to HIV-1 infection.

Identification of CD4-Binding Site Dependent Plasma Neutralizing Antibodies in an HIV-1 Infected Indian Individual.

Dissecting antibody specificities in the plasma of HIV-1 infected individuals that develop broadly neutralizing antibodies (bNAbs) is likely to provide useful information for refining target epitopes for vaccine design. Several studies have reported CD4-binding site (CD4bs) antibodies as neutralization determinants in the plasma of subtype B-infected individuals; however there is little information on the prevalence of CD4bs specificities in HIV-infected individuals in India. Here, we report on the presence of CD4bs antibodies and their contribution to virus neutralization in the plasma from a cohort of HIV-1 infected Indian individuals. Plasma from 11 of the 140 HIV-1 infected individuals (7.9%) studied here exhibited cross-neutralization activity against a panel of subtype B and C viruses. Analyses of these 11 plasma samples for the presence of CD4bs antibodies using two CD4bs-selective probes (antigenically resurfaced HXB2gp120 core protein RSC3 and hyperglycosylated JRFLgp120 mutant ΔN2mCHO) revealed that five (AIIMS 617, 619, 627, 642, 660) contained RSC3-reactive plasma antibodies and only one (AIIMS 660) contained ΔN2mCHO-reactive antibodies. Plasma antibody depletion and competition experiments confirmed that the neutralizing activity in the AIIMS 660 plasma was dependent on CD4bs antibodies. To the best of our knowledge, this is the first study to report specifically on the presence of CD4bs antibodies in the plasma of a cohort of HIV-1 infected Indian donors. The identification of CD4bs dependent neutralizing antibodies in an HIV-1 infected Indian donor is a salient finding of this study and is supportive of ongoing efforts to induce similar antibodies by immunization.

Outcome of highly active antiretroviral therapy in HIV-infected Indian children.

BACKGROUND: With the advent of highly active antiretroviral therapy (HAART), HIV infection has become a chronic condition in children with improved survival and quality of life. Reports on long term effectiveness of non-nucleoside reverse transcriptase inhibitor based HAART in HIV-infected children in developing countries are limited. METHODS: A chart review was conducted and children who received at least six months of HAART between 2004-2011 at All India Institute of Medical Sciences (AIIMS), Delhi were included. The clinical, immunological and virological responses to HAART were documented. Factors predicting non-adherence and non-response to treatment were described. RESULTS: One seventy five children (boys: 74.9%) were included in the study, with a median follow up of 43 (IQR: 17, 68) months. The median age at diagnosis was 119 (IQR: 75, 156) months. The median CD4 count at start of HAART was 340 cells/µL (IQR: 185,704), which increased to 924 cells/µL (IQR: 591,1278) at 48 months after HAART and plateaued at 749 (IQR: 542,1056) cells/ µL after 90 months of therapy. The weight for age (WAZ) and height for age (HAZ) z score both showed improvement with time after HAART initiation [baseline: WAZ -2.8 (IQR: -4,-1.6), HAZ -2.1 (IQR: -3.4,-0.69); at 42 months of therapy: WAZ -1.2 (IQR: -2.1, 0.01), HAZ -0.75(IQR: -1.6,-0.37)]. Adverse events were reported in 21 (12%) children. Non-adherence to therapy, treatment failure and death were noted in 35 (20%), 9 (5.1%) and 6 (3.4%) children respectively. CONCLUSIONS: Our experience shows that HAART in HIV-infected children is effective, safe and is associated with good immunological and virological response as well as improvement in growth parameters.

Immunologic effect of zinc supplementation in HIV-infected children receiving highly active antiretroviral therapy: a randomized, double-blind, placebo-controlled trial.

BACKGROUND: We conducted this study to assess the immunologic effect of daily 20 mg zinc supplementation for 24 weeks in HIV-infected children older than 6 months receiving highly active antiretroviral therapy (ART). METHODS: Fifty-two HIV-infected children older than 6 months in whom ART was initiated were randomized to receive either 20 mg of zinc or placebo for a period of 24 weeks. Children underwent clinical examination, anthropometry, and laboratory evaluations: CD4% and count, viral load, and serum zinc level at baseline, 12 weeks, and 24 weeks. The primary outcome evaluated was CD4% value at the end of 12 and 24 weeks of study intervention in the enrolled children. RESULTS: Of 52 children enrolled, 49 completed the study. The median CD4% value rose from 10% to 23% at 12 weeks and to 24.5% at 24 weeks in the zinc group, whereas in the placebo group, the value rose from 11% to 20% at 12 weeks and to 22% at 24 weeks (P = 0.188 for comparison between the zinc and the placebo group at 12 wk and P = 0.3 for comparison at 24 wk). The median (interquartile range) log reductions in the viral load at 12 weeks in the 2 arms were similar at 12 (P = 0.84) and 24 weeks (P = 0.43). CONCLUSIONS: Supplementation of 20 mg zinc daily for 24 weeks did not have any statistically significant effect on the increase in CD4%, decrease in viral load, anthropometric indices, and morbidity profile in HIV-infected children started on ART.

Comparative evaluation of a reverse transcriptase based assay for HIV-1 viral load quantitation in resource limited settings.

Molecular viral load assays are routinely used in high income countries for monitoring the copy number of human immunodeficiency virus (HIV) RNA. However, they require sophisticated facilities and expensive reagents and instruments. Hence, their routine use for patients belonging to resource limited settings is difficult and a low cost alternative is the need of the hour. This was a cross sectional study that analyzed and compared a reverse transcriptase enzyme based assay (Cavidi ExaVir Load version 3) with a real time polymerase chain reaction (PCR) assay (Roche COBAS TaqMan) in resource limited settings with subtype C predominance. The study included 75 HIV-1 positive treatment naïve patients whose CD4+ T lymphocytes count was estimated using BD FACS system and viral loads were quantified using both Cavidi ExaVir Load assay version 3 and Roche COBAS TaqMan Real Time PCR assay. The statistical analysis was performed using the Graph Pad Prism 5 software. The difference in the mean log10 viral load values was found to be 0.2log10copies/ml. The Bland Altman plot showed a clustering of viral load values toward the lower copy range. 78% of the samples had an agreement of ≤0.5 log10 copies/ml and 90.74% of the samples had an agreement of ≤1 log10 copies/ml. Both the assays showed a trend of negative correlation with the CD4+ T cell counts. The study found that ExaVir Load assay can be used as an alternative to the existing molecular assays in resource limited settings for the purpose of routine viral load measurement and monitoring treatment response.

Cellular interplay among Th17, Th1, and Treg cells in HIV-1 subtype "C" infection.

CD4 T cell depletion is central to HIV pathogenesis and disease progression. Different subsets of CD4 T cells cooperate to combat an infection. Therefore, the immune balance among Th17, Th1, and Treg cells may be critical in HIV immunopathogenesis which is not adequately defined yet. The impact of HIV-1 infection on the interplay of Th17/Th1/Treg cells in HIV-1 infected Indian individuals was examined in the present study and report that HIV-1 Gag specific peripheral blood Th17 cells were significantly depleted in late infected subjects, compared to early infected subjects and slow progressors. Although, the gradual loss of Th1 cells was also reported during HIV-1 disease progression but relative to Th17 cells, Th1 cells were found to be more resistant to HIV-1 infection. Additionally, a significant and progressive gain in Treg cellular frequency was observed as disease progress from early to late stage of HIV-1 infection. This study also indicate that slow progressors might have an intrinsic capacity to develop strong HIV-1 specific Th17 and Th1 cell responses contrasted with a faint Treg cellular performance signifies the importance of these cellular subsets in progressive versus nonprogressive HIV-1 infection. A significant gradual loss of Th17/Treg ratio was found to be associated with disease state, plasma viral load and immune activation.

Loss of RORγt DNA binding activity inhibits IL-17 expression in HIV-1 infected Indian individuals.

Abstract IL-17 producing CD4 T cells have recently been shown to play an important role in mucosal immunity in HIV infection. But its role in peripheral immunity and the molecular mechanism underlying its regulation during HIV-1 infection are ill defined. In this study, we report a significant negative correlation between IL-17 production in peripheral blood and HIV-1 plasma viral load (pVL). On further investigation, we observe a marked reduction in retinoid-related orphan nuclear receptor (RORγt; Th17 lineage specific transcription factor) binding at IL-17 promoter in HIV patients with high viremia (pVL>10,000 copies/mL) in contrast to relatively low viremic patients which indicate the magnitude of viral copy number on RORγt binding at IL-17 promoter. Additionally, our study highlights that FoxP3 influences IL-17 production by binding to and acting together with RORγt, consequently inhibiting RORγt binding to IL-17 promoter with growing viremia in HIV infection. Collectively, our data suggest that FoxP3 interacts with RORγt transcription factor in a viral load-dependent fashion and brings about negative impact on IL-17 production in HIV-1 infection.

Status of TIM-1 exon 4 haplotypes and CD4+T cell counts in HIV-1 seroprevalent North Indians.

The TIM (T cell/transmembrane, immunoglobulin and mucin) proteins are crucial regulators of Th1/Th2 immune responses and have been implicated in several diseases including HIV-1/AIDS. The TIM1 exon 4 that codes for mucin domain is highly diverse, with sequence variants associated with varying phenotypes. In this study, TIM1 exon 4 was sequenced among 227 HIV-1 seroprevalent and 288 healthy non infected individuals from North Indian population and haplotypes established. A novel but rare haplotype D1(∗) was identified among the healthy and differed from D1 by a synonymous substitution G>T at Thr208Thr. The TIM1 haplotype diversity showed no association with susceptibility to HIV-1 infection. The seroprevalent individuals carrying D3A had relatively higher median CD4+T cell counts (368/µl) than those without (313/µl; p=0.02). A comparison of CD4+T counts between D3-A individuals on ART or ART naïve did not show any significant difference plausibly due to confounding nature of ART and other factors.

Genomic architecture of HIV-1 infection: current status & challenges.

Studies on host genomics have revealed the existence of identifiable HIV-1 specific protective factors among infected individuals who remain naturally resistant viraemia controllers with little or no evidence of virus replication. These factors are broadly grouped into those that are immune associated (MHC, chemokines, cytokines, CTLs and others), linked to viral entry (chemokine co-receptors and ligands), act as post-entry restriction elements (TRIM5a, APOBEC3) and those associated with viral replication (cytokines and others). These features have been identified through multiple experimental approaches ranging from candidate gene approaches, genome wide association studies (GWAS), expression analysis in conjunction with functional assays in humans to primate based models. Several studies have highlighted the individual and population level gross differences both in the viral clade sequences as well as host determined genetic associations. This review collates current information on studies involving major histocompatibility complex (MHC) as well as non MHC genes in the context of HIV-1 infection and AIDS involving varied ethnic groups. Special focus of the review is on the genetic studies carried out on the Indian population. Further challenges with regard to therapeutic interventions based on current knowledge have been discussed along with discussion on documented cases of stem cell therapy and very early highly active antiretroviral therapy (HAART) interventions.

The enduring tale of T cells in HIV immunopathogenesis.

HIV continues to be a major health problem worldwide even today. Owing to the intricate nature of its interactions with the immune system, HIV has remained an enigma that cleverly utilizes the host machinery to survive. Its ability to evade the host immune system, at both levels, innate and adaptive, allows the pathogen to replicate and transmit from one host to another. It has been shown that HIV has multipronged effects especially on the adaptive immunity, with CD4+ T cells being the worst affected T cell populations. Various analyses have revealed that the exposure to HIV results in clonal expansion and excessive activation of the immune system. Also, an abnormal process of differentiation has been observed suggestive of an alteration and blocks in the maturation of various T cell subsets. Additionally, HIV has shown to accelerate immunosenescence and exhaustion of the overtly activated T cells. Apart from causing phenotypic changes, HIV has adverse effects on the functional aspect of the immune system, with evidences implicating it in the loss of the capacity of T cells to secrete various antiviral cytokines and chemokines. However, there continues to be many aspects of the immunopathogenesis of HIV that are still unknown and thus require further research to convert the malaise of HIV into a manageable epidemic.

Multiple NF-κB sites in HIV-1 subtype C long terminal repeat confer superior magnitude of transcription and thereby the enhanced viral predominance.

We demonstrate that at least three different promoter variant strains of HIV-1 subtype C have been gradually expanding and replacing the standard subtype C viruses in India, and possibly in South Africa and other global regions, over the past decade. The new viral strains contain an additional NF-κB, NF-κB-like, or RBEIII site in the viral promoter. Although the acquisition of an additional RBEIII site is a property shared by all the HIV-1 subtypes, acquiring an additional NF-κB site remains an exclusive property of subtype C. The acquired κB site is genetically distinct, binds the p50-p65 heterodimer, and strengthens the viral promoter at the levels of transcription initiation and elongation. The 4-κB viruses dominate the 3-κB "isogenic" viral strains in pairwise competition assays in T-cell lines, primary cells, and the ecotropic human immunodeficiency virus mouse model. The dominance of the 4-κB viral strains is also evident in the natural context when the subjects are coinfected with κB-variant viral strains. The mean plasma viral loads, but not CD4 counts, are significantly different in 4-κB infection suggesting that these newly emerging strains are probably more infectious. It is possible that higher plasma viral loads underlie selective transmission of the 4-κB viral strains. Several publications previously reported duplication or deletion of diverse transcription factor-binding sites in the viral promoter. Unlike previous reports, our study provides experimental evidence that the new viral strains gained a potential selective advantage as a consequence of the acquired transcription factor-binding sites and importantly that these strains have been expanding at the population level.