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The Merck Adenovirus-5 Gag/Pol/Nef HIV-1 subtype-B vaccine evaluated in predominately subtype B epidemic regions (Step Study), while not preventing infection, exerted vaccine-induced immune pressure on HIV-1 breakthrough infections. Here we investigated if the same vaccine exerted immune pressure when tested in the Phambili Phase 2b study in a subtype C epidemic. A sieve analysis, which compares breakthrough viruses from placebo and vaccine arms, was performed on 277 near full-length genomes generated from 23 vaccine and 20 placebo recipients. Vaccine coverage was estimated by computing the percentage of 9-mers that were exact matches to the vaccine insert. There was significantly greater protein distances from the vaccine immunogen sequence in Gag (p=0.045) and Nef (p=0.021) in viruses infecting vaccine recipients compared to placebo recipients. Twenty-seven putative sites of vaccine-induced pressure were identified (p<0.05) in Gag (n=10), Pol (n=7) and Nef (n=10), although they did not remain significant after adjustment for multiple comparisons. We found the epitope sieve effect in Step was driven by HLA A∗02:01; an allele which was found in low frequency in Phambili participants compared to Step participants. Furthermore, the coverage of the vaccine against subtype C Phambili viruses was 31%, 46% and 14% for Gag, Pol and Nef, respectively, compared to subtype B Step virus coverage of 56%, 61% and 26%, respectively. This study presents evidence of sieve effects in Gag and Nef; however could not confirm effects on specific amino acid sites. We propose that this weaker signal of vaccine immune pressure detected in the Phambili study compared to the Step study may have been influenced by differences in host genetics (HLA allele frequency) and reduced impact of vaccine-induced immune responses due to mismatch between the viral subtype in the vaccine and infecting subtypes.

Background: The Antibody Mediated Prevention (AMP) trial evaluated if VRC01, a CD4 binding site broadly neutralizing antibody, could prevent HIV-1 acquisition. To inform our understanding of how prevention efficacy depended on viral env gene charateristics, viral quasis-pecies and neutralization sensitivity of HIV-1 breakthrough infections were analyzed. Methods: The trial evaluated VRC01 in women from sub-Saharan Africa (703/081); and men and transgender persons who have sex with men (704/085), from the Americas. Control samples from Thailand, Kenya and South Africa are being used for calibrating infection timing using sequence data. Rev-env-nef (REN) sequences were generated using Sanger and PacBio Single Molecule Real-Time (SMRT) sequencing platforms. To improve PacBio accuracy and enable quantitation, each viral RNA molecule was labelled with a unique molecular identifier (SMRT-UMI). Rev-env genes from imputed founder viruses were synthesized for pseudovirus production and in vitro sensitivity to VRC01 determined using the TZM-bl assay. Results: Approximately 84 000 unique REN sequences were generated from the first HIV-1 positive visit from 218 infected individuals in both trials, and two to four weeks later from a subset of individuals, providing a median of 174 unique env sequences per participant per time point. In approximately 2/3 of individuals, viral diversity was low, consistent with infection with a single founder virus. Of the 1/3 of individuals with higher viral diversity, consistent with infection with multiple founders, a third had low frequency variants (<5% of sequences). We synthesized 1 to 4 Env-pseudoviruses per person, and identified some individuals infected with variants with different neutralization phenotype, including infection with both sensitive (IC.sub.80]<1 [micro]g/mL) and resistant ([IC.sub.80]>3 [micro]g/mL) viruses. In some individuals, the unique VRC01 resistance mutations were associated with distinct viral lineages, suggestive of infection with resistant viruses. However, we also found evidence of low frequency resistant mutations, that were likely derived from resistance acquired after infection. Conclusions: SMRT-UMI sequencing allowed a very detailed evaluation of viral populations following infection, including identification of minor founders not detected using conventional approaches. We found evidence of infection with viruses of mixed neutralization phenotypes, and in some cases, low frequency resistance mutations that were likely to be due VRC01 pressure. The study is not yet unblinded.

To understand how broad recognition of HIV-1 variants may be achieved we examined T-cell reactivity in newly infected persons as well as vaccine recipients to a broad spectrum of potential T-cell epitope (PTE) variants containing conservative, semi-conservative and non-conservative amino acid substitutions. Among early infected persons T-cells recognized epitope variants with one substitution at a significantly higher frequency versus those with two (P=0.0098) and three (P=0.0125) substitutions. Furthermore T-cells recognized variants containing conservative substitutions at a higher frequency versus those containing semi-conservative (P=0.0029) and non-conservative (P<0.0001) substitutions. Similar effects were observed on recognition of variants by vaccine-induced T-cells. Moreover even when variants were recognized, the IFN-γ and granzyme B responses as well as T-cell proliferation were of lower magnitude. Finally, we show that epitope distribution is strongly influenced by both processing preferences and amino acid entropy. We conclude that induction of broad immunity is likely to require immunogen sequences that encompass multiple variants. However, cost-effective design of peptide and sequence based vaccine immunogens that provide maximal coverage of circulating sequences may be achieved through emphasis on virus domains likely to be T-cell targets.

Suppressive therapy for herpes simplex virus 2 (HSV-2) has also been shown to reduce the levels of human immunodeficiency virus type 1 (HIV-1). However, in this placebo-controlled trial involving 3408 African couples who were discordant in serologic status for these two viruses, daily treatment with acyclovir did not reduce the frequency of HIV-1 transmission, despite a reduction in HIV-1 RNA levels and a 73% reduction in the occurrence of HSV-2–positive genital ulcers. In African couples who were discordant in serologic status for HIV-1 and HSV-2, daily treatment with acyclovir did not reduce the frequency of HIV-1 transmission, despite a reduction in HIV-1 RNA levels and a 73% reduction in the occurrence of HSV-2–positive genital ulcers. The seroprevalence of herpes simplex virus type 2 (HSV-2), the most common cause of genital ulcer disease worldwide, is 60 to 90% in populations with human immunodeficiency virus type 1 (HIV-1). 1 Clinical manifestations of HSV-2 range from unrecognized or mild genital symptoms in most persons with HIV-1 infection to severe genital ulcer disease in persons with advanced HIV-1 disease. 2 , 3 Genital shedding of the herpes simplex virus occurs on up to 30% of days in persons infected with HIV-1, often when they have no symptoms or observable lesions. 4 , 5 Laboratory and epidemiologic studies suggest that HSV-2 may increase the infectiousness . . .

A replication-defective variant of feline leukemia virus was molecularly cloned directly from infected tissue and found to induce a rapid and fatal immunodeficiency syndrome in cats. Studies with cloned viruses also showed that subtle mutational changes would convert a minimally pathogenic virus into one that would induce an acute form of immunodeficiency. The data suggest that acutely pathogenic viruses may be selected against by current methods for isolation of the human and simian immunodeficiency viruses.

Feline leukemia viruses (FeLVs) belonging to the C subgroup induce aplastic anemia in domestic cats and have the ability, unique among FeLV strains, to proliferate in guinea pig fibroblasts in tissue culture. Previous studies have shown that the pathogenic and host range specificity of a prototype molecular clone of FeLV-C [FeLV-Sarma-C (FSC)] colocalize to a region encoding the 3' 73 amino acids of the pol gene product and the N-terminal 241 amino acids of the envelope surface glycoprotein named SU. Here, we amplified, via PCR, cloned, and sequenced the SU coding sequence from three additional anemia-inducing subgroup C FeLV isolates. Chimeric viruses were constructed by replacement of fragments of FeLV-C envelope genes into the FeLV-A prototype virus 61E. Using a modified vesicular stomatitis virus-FeLV pseudotype assay, we demonstrated that the subgroup C receptor specificity for each virus was determined by changes within the N-terminal 87-92 amino acids of SU, in which most changes occurred within the 15- to 20-amino-acid first variable region (V1). Determinants for growth in guinea pig cells colocalized to this region. Despite the consistent localization of biological determinants, the only consistent features that distinguished the deduced FeLV-A and FeLV-C proteins was one lysine-to-arginine change and a structural prediction of an alpha-helix in FeLV-A proteins versus random coil in FeLV-C proteins within V1. However, arginine in equilibrium with lysine substitutions were not sufficient to convert the subgroup A virus to the subgroup C phenotype or vice versa. Thus, certain distinct structural changes within the N-terminal region of FeLV SU can result in convergent viral phenotypes

Feline leukemia virus (FeLV) C-Sarma (or FSC) is a prototype of subgroup C FeLVs, which induce fatal aplastic anemia in outbred specific-pathogen-free (SPF) cats. FeLV C isolates also possess an extended host range in vitro, including an ability, unique among FeLVs, to replicate in guinea pig cells. To identify the viral determinants responsible for the pathogenicity and host range of FSC we constructed a series of proviral DNAs by exchanging gene fragments between FSC and FeLV-61E (or F6A), the latter of which is minimally pathogenic and whose host range in vitro is restricted to feline cells. Transfer of an 886-base-pair (bp) fragment of FSC, encompassing the codons for 73 amino acids at the 3′ end of pol (the integrase/endonuclease gene) and the codons for 241 amino acids of the N-terminal portion of env [the extracellular glycoprotein (gp70) gene], into the F6A genome was sufficient to confer onto chimeric viruses the ability to induce fatal aplastic anemia in SPF cats. In contrast, no chimera lacking this sequence induced disease. When assayed in vitro, all chimeric viruses containing the 886-bp fragment of FSC acquired the ability to replicate in heterologous cells, including dog and guinea pig cells. Thus, the pathogenic and the host range determinants of the feline aplastic anemia retrovirus colocalize to a 3′ pol-5′ env region of the FSC genome and likely reside within a region encoding 241 amino acid residues of the N terminus of the extracellular glycoprotein.

The presence and location of DNA sequences related to the U3 and U5 portions of the infectious exogenous feline leukemia virus (FeLV) long terminal repeat (LTR) in various cat DNAs have been determined by hybridization experiments. In uninfected cat DNAs, the U5 LTR segment from the Gardner-Arnstein strain B virus is present at approximately 150 copies per cell. This level is approximately 10-fold greater than that of endogenous internal FeLV sequences. The U5 sequences differ in copy number and, to some extent, in location from one animal to another. For any one animal, the sequence organization of the U5 segments is the same among different tissues, showing that the pattern is inherited through the germ line. Most importantly, the viral U3 LTR probe hybridizes only very weakly with uninfected cat DNAs. Both the U3 and the U5 regions of the LTR from the Gardner-Arnstein strain of virus cross-hybridize with DNA derived from four other infectious FeLVs representing A, B, and C subtypes. Thus, the U3 region may be used as a probe for studying the number and location of exogenously acquired FeLV proviruses in infected cat tissues. In some cases exogenously acquired proviruses are present in unique sites in the genome of virus-positive cat lymphosarcomas, indicating a monoclonal origin for the tumor. In other tumors, the proviral sequences are randomly distributed over many sites. Lymphosarcomas of virus-negative cats have no exogenous U3 sequences despite epidemiological evidence of an association of virus-negative leukemia with exposure to FeLV.