A unique, naturally occurring single-amino acid mutation in HIV type 1 V3 loop can discriminate between its cytopathicity and replication in vivo and in vitro

Selected amino acid changes in HIV-1 subtype-C gp41 are associated with specific gp120(V3) signatures in the regulation of co-receptor usage

The majority of studies have characterized the tropism of HIV-1 subtype-B isolates, but little is known about the determinants of tropism in other subtypes. So, the goal of the present study was to genetically characterize the envelope of viral proteins in terms of co-receptor usage by analyzing 356 full-length env sequences derived from HIV-1 subtype-C infected individuals. The co-receptor usage of V3 sequences was inferred by using the Geno2Pheno and PSSM algorithms, and also analyzed to the "11/25 rule". All reported env sequences were also analyzed with regard to N-linked glycosylation sites, net charge and hydrophilicity, as well as the binomial correlation phi coefficient to assess covariation among gp120(V3) and gp41 signatures and the average linkage hierarchical agglomerative clustering were also performed. Among env sequences present in Los Alamos Database, 255 and 101 sequences predicted as CCR5 and CXCR4 were selected, respectively. The classical V3 signatures at positions 11 and 25, and other specific V3 and gp41 amino acid changes were found statistically associated with different co-receptor usage. Furthermore, several statistically significant associations between V3 and gp41 signatures were also observed. The dendrogram topology showed a cluster associated with CCR5-usage composed by five gp41 mutated positions, A22V, R133M, E136G, N140L, and N166Q that clustered with T2V(V3) and G24T(V3) (bootstrap=1). Conversely, a heterogeneous cluster with CXCR4-usage, involving S11GR(V3), 13-14insIG/LG(V3), P16RQ(V3), Q18KR(V3), F20ILV(V3), D25KRQ(V3), Q32KR(V3) along with A30T(gp41), S107N(gp41), D148E(gp41), A189S(gp41) was identified (bootstrap=0.86). Our results show that as observed for HIV-1 subtype-B, also in subtype-C specific and different gp41 and gp120V3 amino acid changes are associated individually or together with CXCR4 and/or CCR5 usage. These findings strengthen previous observations that determinants of tropism may also reside in the gp41 protein.

HIV-1 gp120 N-linked glycosylation differs between plasma and leukocyte compartments

Background

N-linked glycosylation is a major mechanism for minimizing virus neutralizing antibody response and is present on the Human Immunodeficiency Virus (HIV) envelope glycoprotein. Although it is known that glycosylation changes can dramatically influence virus recognition by the host antibody, the actual contribution of compartmental differences in N-linked glycosylation patterns remains unclear.

Methodology and Principal Findings

We amplified the env gp120 C2-V5 region and analyzed 305 clones derived from plasma and other compartments from 15 HIV-1 patients. Bioinformatics and Bayesian network analyses were used to examine N-linked glycosylation differences between compartments. We found evidence for cellspecific single amino acid changes particular to monocytes, and significant variation was found in the total number of N-linked glycosylation sites between patients. Further, significant differences in the number of glycosylation sites were observed between plasma and cellular compartments. Bayesian network analyses showed an interdependency between N-linked glycosylation sites found in our study, which may have immense functional relevance.

Conclusion

Our analyses have identified single cell/compartment-specific amino acid changes and differences in N-linked glycosylation patterns between plasma and diverse blood leukocytes. Bayesian network analyses showed associations inferring alternative glycosylation pathways. We believe that these studies will provide crucial insights into the host immune response and its ability in controlling HIV replication in vivo. These findings could also have relevance in shielding and evasion of HIV-1 from neutralizing antibodies.

Molecular and biological interactions between two HIV-1 strains from a coinfected patient reveal the first evidence in favor of viral synergism

An intravenous drug user was found to be dually infected with two genetically and phylogenetically distinct human immunodeficiency virus type 1 (HIV-1) subtype B strains (designated groups I and II). Viral isolation revealed a simultaneous copassaging of two strains in PBMC. The culture of viral strains on monocytes and monocyte-derived macrophages preferentially segregated the two viral strains. The group I strain utilized CXCR4 and group II used CCR5 coreceptor for entry. Sequencing of >100 clones from uncultured PBMC consistently showed the predominance of group II virus in vivo. Importantly, the group II virus alone could not productively infect PBMC, but when used together with group I virus for infection, the group II virus regained its high replication potential and predominance in cultured PBMC. These data are the first to provide direct evidence in favor of molecular and biological interaction between two infecting strains in a coinfected patient and show their differential pathogenic effects, tropism, and modes of entry. In addition, our data provide the first evidence for synergism between these two strains. Cumulatively, these data emphasize that in order to clearly interpret coreceptor usage, biological segregation of viral strains from primary isolates in vitro may be imperative.