Prediction of B Cell Epitopes Among Hantavirus Strains Causing Hemorragic Fever With Renal Syndrome.

Hantavirus infections are now recognized to be a global problem. The hantaviruses include several genotypic variants of the virus with different distributions in varying geographical regions. The virus genotypes seem to segregate in association with certain manifestations specific for each syndrome. They primarily include HFRS, HCPS, febrile illness with or without mild involvement of renal diseases. In the course of our study on hantavirus etiology of febrile illnesses, we recovered a hantavirus strain identified by nPCR. This has been sequenced to be Hantaan-like virus (partial S segment). The current manuscript is focused on understanding the N protein coded by S segment in terms of variation of amino acid sequences of the virus genotypes associated with HFRS. The diagnosis of this infection is achieved by PCR testing of serum/plasma or demonstration of IgM/IgG in serum. The limitations of PCR are temporal often not positive after 7 days of onset of infection. IgM detection is possible around this period and up to 21 days. IgG detection is less definitive in acute infections. Here, we report characterization of the sequence diversity of HFRS strains, 3D structure of Hantaan N protein, and B-cell epitopes on this molecule. We predicted a 20 amino acid sequence length peptide by using BepiPred online server in IEDB analysis resource program. We suggest this peptide may be used for development of geographic region-specific immunoassays like EIAs for antibody detection, monoclonal antibody development, and immunoblots (line immunoassay). J. Cell. Biochem. 118: 1182-1188, 2017. © 2016 Wiley Periodicals, Inc.

Comparison of Three Different Hepatitis C Virus Genotyping Methods: 5'NCR PCR-RFLP, Core Type-Specific PCR, and NS5b Sequencing in a Tertiary Care Hospital in South India.

BACKGROUND: Based on genetic heterogeneity, hepatitis C virus (HCV) is classified into seven major genotypes and 64 subtypes. In spite of the sequence heterogeneity, all genotypes share an identical complement of colinear genes within the large open reading frame. The genetic interrelationships between these genes are consistent among genotypes. Due to this property, complete sequencing of the HCV genome is not required. HCV genotypes along with subtypes are critical for planning antiviral therapy. Certain genotypes are also associated with higher progression to liver cirrhosis. METHODS: In this study, 100 blood samples were collected from individuals who came for routine HCV genotype identification. These samples were used for the comparison of two different genotyping methods (5'NCR PCR-RFLP and HCV core type-specific PCR) with NS5b sequencing. RESULTS: Of the 100 samples genotyped using 5'NCR PCR-RFLP and HCV core type-specific PCR, 90% (κ = 0.913, P < 0.00) and 96% (κ = 0.794, P < 0.00) correlated with NS5b sequencing, respectively. Sixty percent and 75% of discordant samples by 5'NCR PCR-RFLP and HCV core type-specific PCR, respectively, belonged to genotype 6. All the HCV genotype 1 subtypes were classified accurately by both the methods. CONCLUSION: This study shows that the 5'NCR-based PCR-RFLP and the HCV core type-specific PCR-based assays correctly identified HCV genotypes except genotype 6 from this region. Direct sequencing of the HCV core region was able to identify all the genotype 6 from this region and serves as an alternative to NS5b sequencing.

Investigation of apoptotic markers among human immunodeficiency virus (HIV-1) infected individuals.

BACKGROUND & OBJECTIVES: Apoptosis causes a decline in the counts of uninfected bystander CD4+ T cells in HIV infection. The rate of disease progression of HIV infection is considered to be faster in the developing countries. The present study was carried out to investigate certain markers for apoptosis in immunopathogensis of disease in HIV infected south Indian population. METHODS: Soluble Fas (sFas) antigen and Fas ligand levels in plasma samples from 39 antiretroviral treatment naïve patients was estimated and compared with T cell subsets and HIV-1 viral load. RESULTS: The mean sFas antigen levels among controls and the CDC A, B and C clinical stages were 2.77, 3.08, 3.26 and 3.28 ng /ml respectively, higher though not significantly among HIV-1 infected individuals compared to controls. The mean sFas ligand levels in CDC A, B and C stages were 0.138, 0.125 and 0.117 ng/ml respectively were higher (P<0.001) than controls (0.073 ng/ml) and positively correlated with total lymphocyte % (r=0.43, P =0.007). sFas antigen levels were negatively correlated with total WBC count (r=-0.34, P=0.04), CD4% (r=-0.4, P=0.01) and CD4:CD8 ratio (r=-0.37, P=0.02). There was an increase in plasma levels of sFas antigen and Fas ligand over time in asymptomatics. INTERPRETATION & CONCLUSION: The high levels of sFas antigen and Fas ligand seen in HIV infected individuals suggest increased activation and apoptosis of T cells, due to constant stimulation of the immune system by inter-current infections of HIV infected individuals in south India.

Characterization of soluble FAS, FAS ligand and tumour necrosis factor-alpha in patients with chronic HCV infection.

BACKGROUND: There are limited reports on the role of the cell surface receptor Fas and its ligand molecule in mediating apoptosis during infection with the hepatitis C virus (HCV). OBJECTIVES: The aims of this study were (1) to assess the susceptibility of the Fas antigen expressed on peripheral blood mononuclear cells to Fas ligand-induced-death in patients with chronic HCV infection and (2) to investigate the correlation between the plasma levels of soluble Fas (sFas), soluble Fas ligand (sFasL), tumour necrosis factor-alpha (TNF-alpha), alanine amino transferase (ALT), and HCV viral load. STUDY DESIGN: The susceptibility of peripheral blood mononuclear cells from 17 subjects with chronic HCV infection to Fas ligand induced cell death was assessed using a water soluble tetrazolium assay. The plasma levels of associated markers such as sFas, sFasL, and TNF-alpha were quantified using immunoassays. ALT values were obtained from hospital records. Viral loads were quantified using a commercially available quantitative assay--the Amplicor Monitor (version 2.0). Controls for comparison included a group of healthy individuals and individuals infected with the human immunodeficiency virus 1. RESULTS: The percentage of cell death induced in hepatitis C virus infected individuals was lower than that seen in the healthy control group. Patients infected with HCV had higher average values of sFas and TNF-alpha as compared to both control groups. Plasma levels of sFas in patients with chronic HCV infection showed significant positive correlations to ALT and TNF-alpha levels. TNF-alpha levels also showed a significant positive correlation with ALT levels. CONCLUSIONS: PBMC in HCV infection exhibit decreased susceptibility to Fas ligand induced cell death. This may signify a means by which HCV escapes immune surveillance. This phenomenon merits further investigation. The strong correlations observed between plasma sFas, ALT and TNF-alpha suggest a potential role for these markers as an alternative to an invasive liver biopsy.

HPV 16 E6 sequence variations in Indian patients with cervical neoplasia.

In a cross-sectional study performed between June 2001 and November 2003, the HPV 16 E6 gene of 50 women with cervical neoplasia and 20 cytologically normal women ('controls') was sequenced following amplification by PCR. The 350T to G variant was seen in 35 (70%) of 50 patients' isolates while it was seen in only 3 (15%) of the 20 isolates from the 'controls'. The higher occurrence of the 350G variant among the patients was statistically significant (P<0.01). Isolates from patients were grouped into the European (E), Asian-American (AA) and North-American (NA-1) phylogenetic clusters with 46 (92%) belonging to the E cluster. All the 20 isolates from 'controls' belonged to the E cluster. This study suggests an association of the HPV 16 350G variant with a higher risk of cervical neoplasia and a predominance of E lineage strains among Indian HPV 16 isolates.

Evaluation of a rapid assay as an alternative to conventional enzyme immunoassays for detection of hepatitis C virus-specific antibodies.

A rapid membrane flow-through immunoassay to detect antibodies to hepatitis C virus was compared with a commercial enzyme immunoassay (EIA) and microparticle enzyme immunoassay (MEIA) using 2,590 serum samples. Sensitivity and specificity of the "rapid assay" in comparison to the EIA/MEIA were 99.3 and 99.0%; the correlation coefficient being 0.91. This assay is suitable where infrastructure and laboratory expertise are limited.

HPV DNA in plasma of patients with cervical carcinoma.

BACKGROUND: HPV DNA has been detected in metastatic tumour and HPV plasma viraemia may indicate a poor prognosis and a high risk for metastasis. OBJECTIVE: Detection of HPV DNA in plasma of patients with cervical carcinoma. STUDY DESIGN: A cross-sectional study was done, wherein cervical biopsies and plasma samples were collected from 58 women with invasive cervical carcinoma, 10 women with cervical intraepithelial neoplasia (CIN) and 30 control women in the same age range. Polymerase chain reaction (PCR) was employed to detect the presence of HPV DNA. Samples positive for HPV DNA were typed by restriction fragment length polymorphism (RFLP). To confirm that the HPV sequence in plasma was identical to that in tissue, sequencing was done on all the paired plasma and tissue samples. RESULTS: All the 30 paired cervical tissue and plasma samples from the controls were negative for HPV DNA. HPV DNA was detectable in cervical tissues of 55 (94.8%) of 58 patients with invasive cervical carcinoma and in all 10 patients (100%) with CIN and in eight (11.8%) of the total 68 plasma samples from patients. All eight plasma samples were from women with invasive cervical carcinoma with three each in stages IIIB and IV and one each in stages IIB and IB, respectively. Of the eight positive samples, seven were typed as HPV-16 and 1 as HPV-58. HPV types detected in cervical tissue and plasma pairs from these eight patients correlated as revealed by RFLP and sequencing. A patient with stage IB cancer had detectable HPV DNA in the external iliac lymph node, removed at Wertheims hysterectomy, which was histopathologically free of tumour. The HPV type in the node, was the same as that present in the paired tissue and plasma sample. CONCLUSIONS: HPV DNA is detectable in the plasma of patients with advanced cervical cancer.

E2 sequence variations of HPV 16 among patients with cervical neoplasia seen in the Indian subcontinent.

OBJECTIVES: Specific nucleotide variations in the E2 DNA sequence were looked for in samples with an intact human papillomavirus (HPV) 16 episomal E2 DNA. METHODS: Ninety-two women, 76 with invasive cervical carcinoma and 16 with cervical intraepithelial neoplasia (CIN) were recruited. HPV DNA typing was performed by polymerase chain reaction (PCR) based restriction fragment length polymorphism (RFLP). Intact episomal E2 DNA of HPV 16 was detected by PCR. Important nucleotide variations in samples with amplifiable E2 DNA were detected by RFLP. Nucleotide sequencing was performed on representative samples to confirm RFLP findings. RESULTS: A total of 89 (96.7%) women were positive for HPV DNA. Of these, 56 (63%) were positive for HPV 16, and of these, 38 (68%) were positive for intact episomal HPV 16 E2 DNA while 18 (32%) were negative. Samples with intact episomal HPV 16 E2 DNA sequences were grouped into four different digestion profiles I to IV based on RFLP patterns. Digestion patterns revealed absence of any sequence variations in samples with digestion profile I and presence of a 2983 A-G variation in those with profile II. Samples with digestion profiles III and IV revealed three variations in the hinge region (3516 C-A, 3538 A-C, 3566 T-G) and two in the DNA binding domain (3684 C-A, 3694 T-A) of the E2 sequence. Sequencing performed on representative samples confirmed RFLP findings. CONCLUSIONS: PCR-RFLP helped in the identification of important HPV 16 E2 sequence variations, circumventing the need for sequencing. The presence of the nucleotide variations in positions that could alter the biological and immunological functions of the E2 protein combined with its increased occurrence in this study bring out the importance of these variations.

Human papillomavirus 16 E6/E7 transcript and E2 gene status in patients with cervical neoplasia.

BACKGROUND: The viral transforming genes E6 and E7 of human papillomavirus (HPV) 16 cause the degradation of tumor suppressor proteins. Expression of these oncoproteins increases following the integration of viral DNA into the host cell, resulting in the disruption of the E2 open reading frame (ORF). AIM: To detect and correlate HPV-16 oncogene transcripts and HPV-16 E2 DNA in cervical biopsies obtained from women (n = 68) with cervical neoplasia. METHODS: HPV-16 E6/E7 transcript and HPV-16 E2 DNA detection was performed on the cervical biopsies of 42 women positive for HPV-16 (36 with invasive cervical carcinoma and 6 with cervical intraepithelial neoplasia [CIN]). PCR was used to detect HPV DNA in cervical biopsies then restriction fragment length polymorphism (RFLP) was used to type the HPV DNA. Reverse-transcription (RT)-PCR for HPV-16 E6/E7 oncogene mRNA transcripts and a PCR to detect the HPV-16 E2 DNA was performed on HPV-16-positive samples. RESULTS: HPV-16 E6/E7 mRNA transcripts were not detected in any of the CIN I or II biopsies, but were detected in all cases of CIN III and invasive cancer in different combinations (E6 alone, E6*I, E6*I/E6*II, E6/E6*I/E6*II) except for one patient with stage IIB cancer treated with radiotherapy. The incidence of episomal E2 DNA was high in this study with 52.4% of the samples positive for episomal E2. It was even detected in patients with advanced stage cancer with 50%, 42%, and 66.6% of samples positive in stages IIB, IIIB, and IV, respectively. DISCUSSION: HPV-16 E6/E7 mRNA oncogene transcripts, in various combinations, were uniformly detectable in the majority of the high-grade cervical lesions examined. Intact episomal E2 DNA was seen in a high proportion of samples, even from advanced cervical lesions. Conservation of the E2 gene with concomitant expression of viral oncogenes in advanced cervical lesions may point to alternate mechanisms, other than integration, bringing about the enhanced expression of E6/E7 mRNA. CONCLUSIONS: This study suggests that the detection of the HPV-16 oncogene transcripts could serve as an indicator for assessing the prognosis of patients on radiotherapy. The majority of HPV-16-positive cervical neoplastic lesions are transcriptionally active and express the oncogene transcripts. The increased occurrence of intact HPV-16 episomal E2 DNA in advanced lesions further substantiates the fact that the disruption of E2 ORF is not mandatory for increased oncogene expression. Thus, this study underscores the significance of investigating alternative mechanisms of oncogene expression in HPV-16.

An outbreak of echovirus meningitis in children.

An outbreak of aseptic meningitis in children as evidenced by increase in the number of admissions in a tertiary care hospital is described. Clinical data and stool samples were collected from 25 hospitalized infants and young children. The stool samples were subjected to virological investigations. Fever and vomiting were the commonest symptoms. Cerebrospinal fluid (CSF) showed lymphocytic pleocytosis in majority of cases. Of the 25 stool samples, 14 showed an enterovirus specific cytopathogenic effect (CPE) in rhabdomyosarcoma (RD) cell line. All the 14 samples were positive for enterovirus RNA by reverse transcription-polymerase chain reaction (RT-PCR). Partial sequencing of the Virion protein 1 (VPI) region of the enterovirus genome carried out on the first 7 isolates revealed 5 isolates to be echovirus serotype 4 and one each to be echovirus serotypes 3 and 30. All children showed a rapid recovery and were discharged within 3 days of admission.

Occurrence of false positives during testing for antibodies to hepatitis C virus among volunteer blood donors in India.

The hepatitis C virus antibody statuses of only 11 (21.5%) of 51 initially reactive samples from volunteer blood donors could be confirmed by using additional screening and confirmatory assays; 23 (45%) were negative by all subsequent assays. Seventeen samples (33.3%) gave variable results in the different assays. The core and NS5 antigens were most immunogenic. An algorithm for serological screening of volunteer blood donors in blood banks of developing countries is suggested.

Rapid particle agglutination test for human immunodeficiency virus: hospital-based evaluation.

The performance of a rapid particle agglutination test for human immunodeficiency virus (HIV) (Capillus HIV type 1 [HIV-1]/HIV-2) on hospital samples is compared with enzyme-linked immunosorbent assays. The test had a sensitivity and specificity of 99 and 98.9%, respectively. In addition, the test was reactive on plasma samples from all individuals infected with HIV-1 subtype C. This test can safely be used for voluntary counseling and testing in India.