HIV, which causes acquired immune deficiency syndrome, invades the host cell via the CD4 receptor and CCR5 or CXCR4 co-receptors. Interferons induced early in HIV infection induce an antiviral defense mechanism through IFNAR signaling. Our study aimed to examine the relationship between CCR5, CXCR4, and IFNAR1 gene variations as a risk factor in HIV (+) patients and their response to their clinical parameters. Targeted next-generation sequencing (tNGS) was used to perform molecular genotyping analysis of the CCR5, CXCR4 and IFNAR1 genes in genomic DNA from 22 HIV+ patients and 25 healthy individuals as controls. We detected a total of 13 rare mutations in the study, including 3 missense, 1 synonumous, 2 5′UTR, 4 3′UTR, 1 frameshift variations. We also detected 6 common variants in the IFNAR1 and CXCR4 genes. HIV+ patients carrying the wild type TT genotype of IFNAR1 gene rs2856973 T>A variant had higher CD4+ T cell count compared with patients carrying the TA+AA genotypes of rs2856973 variant in naive and 1st month of ART period (p=0.0011 and p=0.0019, respectively). Similarly, participants receiving ART with TT genotype of rs2856973 showed a significantly higher CD4+ T cell count in the third month (p=0.0008). Patients carrying the homozygous wild type genotype of CXCR4 gene rs2680880 A>T SNP had lower CD4+ T cell count compared with subjects carrying the AT+TT mutant genotypes of rs2680880 in naive and first month period (p=0.0152 and P=0.0256, respectively). Our results demonstrate that variations in the IFNAR1 and CXCR4 genes can contribute to modifications in HIV progression.

Convalescent plasma samples that can be collected from individuals after the resolution of infection and vaccination are an invaluable source of neutralization antibodies against the virus. Although plaque reduction assay with replicative virus is the gold standard of analyzing neutralization potency of convalescent plasma, it is a technically demanding procedure requiring high biosafety level (BSL-3/4) laboratory and equipment. The abundance of neutralizing antibodies varies among individuals, therefore fast and reliable methods to identify neutralization potency of plasma samples are needed. In this paper, G-protein deficient vesicular stomatitis virus (VSV-ΔG) carrying a C-terminal 21 amino acid truncated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike protein was generated for pseudovirus neutralization assay. We analyzed SARS-CoV-2 neutralizing potency of vaccinated human convalescent plasma samples (n=13) and plasma samples of healthy people (n=2). Human convalescent plasma samples were examined against the ancestral Wuhan strain and two SARS-CoV-2 variants (B.1.1.7, and B.1.351) using a VSV-ΔG-Sdel21 pseudovirus and Vero E6 cell line. Neutralization values against pseudotyped virus were compared to those of plaque reduction assay against authentic virus. The serum neutralizing titer of convalescent plasma measured by pseudovirus assay has a good correlation with that measured by plaque reduction assay (R 2= 0.7). The pseudovirus assay is safer and timesaving than the replicative virus-based plaque reduction assay, and has several advantages in evaluating a new vaccine, newly emergent variants, and approved vaccine efficacy against variants of concern as well as in viral fusion-focused treatment analysis that can be performed under BSL-2 conditions.