Sequence variation of the Epstein-Barr virus nuclear antigen 1 (EBNA1) gene in chronic lymphocytic leukemia and healthy volunteer subjects

Epstein-Barr virus-related malignancies have been linked to variations in the sequences of EBV genes, notably EBNA1. Therefore, the purpose of this study was to examine the DBD/DD domain and USP7 binding domain sequences at the C-terminus of the EBNA1 gene in patients with chronic lymphocytic leukemia (CLL). This study included 40 CLL patients and 21 healthy volunteers. Using commercial kits, total DNA was extracted from buffy coat samples, and each sample was tested for the presence of the EBV genome. The C-terminus of EBNA1 was then amplified from positive samples, using nested PCR. Sanger sequencing was used to identify mutations in the PCR products, and the results were analyzed using MEGA11 software. The mean ages of CLL patients and healthy individuals were 61.07 ± 10.2 and 59.08 ± 10.3, respectively. In the EBNA-1 amplicons from CLL patients and healthy individuals, 38.5% and 16.7%, respectively, harbored mutations in the DBD/DD domain of the C-terminal region of the EBNA1 gene (P = 0.378). The mutation frequency at locus 97,320 was significantly higher in CLL patients than in healthy individuals (P = 0.039). Three EBV subtypes based on residue 487 were detected. The frequency of alanine, threonine, and valine in both groups was 88, 8, and 4 percent, respectively (P = 0.207). Moreover, all of the isolates from healthy donors had alanine at this position. The findings indicated that the presence of threonine or valine at residue 487 as well as a synonymous substitution at residue 553 in the C-terminal region of EBNA1 might be involved in the pathogenesis of EBV in CLL patients.

Investigation of the frequencies of various B cell populations in non-responder healthcare workers in comparison with responders to hepatitis B virus vaccination

BACKGROUND

Hepatitis B is a major global health problem. More than 90% of hepatitis B-vaccinated immunocompetent adults become fully immune. The main purpose of vaccination is immunization. Whether non-responders have a lower percentage of total or antigen-specific memory B cells in comparison with responders is still controversial. We aimed to assess and compare the frequency of various B cell subpopulations in non-responders and responders.

METHODS

Fourteen responders and 14 non-responders of hospital healthcare workers were enrolled in this study. We used flow cytometry to evaluate various CD19+ B cell subpopulations using fluorescent-labeled antibodies against CD19, CD10, CD21, CD27 and IgM and ELISA to evaluate total anti-HBs antibodies.

RESULTS

We found no significant differences in the frequency of various B cell subpopulations between the non-responder and responder groups. Furthermore, the frequency of the isotype-switched memory B cell population was significantly higher in the atypical memory B cell subset compared with the classical memory B cell subset in the responder and total groups (p=0.010 and 0.003, respectively).

CONCLUSIONS

Responders and non-responders to HBsAg vaccine had comparable memory B cell populations. Whether anti-HBs Ab production has a correlation with the level of class switching in B lymphocytes in healthy vaccinated individuals needs further investigation.

Sequence Analysis of Hot Spot Regions of Spike and RNA-dependent-RNA polymerase (RdRp) Genes of SARS-CoV-2 in Kerman, Iran

Background

Mutations in the SARS-CoV-2 genome might influence pathogenicity, transmission rate, and evasion of the host immune system. Therefore, the purpose of the present study was to investigate the genetic alteration as well as assess their effects on the receptor binding domain (RBD) of the spike and the putative RNA binding site of the RdRp genes of SARS-CoV-2 using bioinformatics tools.

Materials and Method

In this cross-sectional study, 45 confirmed COVID-19 patients using qRT-PCR were included and divided into mild, severe, and critical groups based on the severity of the disease. RNA was extracted from nasopharyngeal swab samples using a commercial kit. RT-PCR was performed to amplify the target sequences of the spike and RdRp genes and sequence them by the Sanger method. Clustal OMEGA, MEGA 11 software, I-mutant tools, SWISS-MODEL, and HDOCK web servers were used for bioinformatics analyses.

Results

The mean age of the patients was 50.68±2.73. The results showed that four of six mutations (L452R, T478K, N501Y, and D614G) in RBD and three of eight in the putative RNA binding site (P314L, E1084D, V1883T) were missense. In the putative RNA binding site, another deletion was discovered. Among missense mutations, N501Y and V1883T were responsible for increasing structural stability, while others were responsible for decreasing it. The various homology models designed showed that these homologies were like the Wuhan model. The molecular docking analysis revealed that the T478K mutation in RBD had the highest binding affinity. In addition, 35 RBD samples (89.7%) and 33 putative RNA binding site samples (84.6%) were similar to the Delta variant.

Conclusion

Our results indicated that double mutations (T478K and N501Y) in the S protein might increase the binding affinity of SARS-CoV-2 to human ACE2 compared to the wild-type (WT) strain. Moreover, variations in the spike and RdRp genes might influence the stability of encoded proteins.

Investigation of the Seroprevalence of Antimeasles Immunoglobulin G Antibody in Students at Shiraz University of Medical Sciences

Measles is an acute, highly contagious disease with a high mortality rate in children. Although vaccination has reduced measles incidence, outbreaks still occur. Therefore, in this study, we aimed to investigate the frequency of antimeasles immunoglobulin G (IgG) antibody (Ab) among students at Shiraz University of Medical Sciences (SUMS). Four hundred fifty SUMS students were enrolled in this cross-sectional study. Information on demographics and measles vaccination history was collected using a questionnaire. Participants were divided into two groups, including A and B, according to routine doses of measles vaccine and the national measles/rubella immunization program. The antimeasles IgG Abs were tested using a commercial Enzyme-Linked Immunosorbent Assay Kit. Participants ranged in age from 18 to 48 years, with a mean age of 22.2 (±4.3). Fifty percent of the subjects were male. Our results showed that 63.6% of the cases were positive for antimeasles IgG Abs. The seroprevalence of IgG Abs between groups A and B did not differ significantly (p = 0.612). There was also no significant correlation between the seroprevalence of antimeasles IgG Abs and the age (p = 0.43) or sex (p = 0.24) of the subjects. The results showed that the frequency of antimeasles IgG Abs is lower than required to prevent the measles virus from circulating. Therefore, a booster vaccination may be necessary.

The Sero-Prevalence of Hepatitis B and C Viruses in Municipal Waste Collectors in Southwest of Iran

Aims

The present study aimed to investigate the frequency of hepatitis B virus (HBV) and hepatitis C virus (HCV) serological markers among waste collectors in the municipality of Shiraz city, southwest of Iran, 2018.

Settings and Design

In this cross-sectional study, a total of 385 waste collectors from all 10 districts of Shiraz city, southwest of Iran were enrolled. A questionnaire was used to gather occupational and demographic information as well as awareness about viral hepatitis.

Methods and Material

Their blood samples were collected, and the sera were investigated for the presence of hepatitis B surface antigen (HBsAg), anti-HBs antibody, and anti-HCV antibody using enzyme-linked immunosorbent assay (ELISA).

Results

All the participants were men with a mean age of 41 ± 8 years. Out of 385 participants, 6 (1.5%) subjects were positive for HBsAg, indicative of HBV infection. Moreover, 38 (9.9%) had a protective level of anti-HBs antibodies, while more than 90% had a low level of anti-HBs antibodies. All participants were negative for HCV antibodies.

Conclusion

According to these findings, evaluation of HBsAg and anti-HBs levels is recommended in the healthy program of waste collector workers (WCWs). However, this occupation might not be a risk factor for the acquisition of HBV and especially HCV infections.

Association of IFITM1 Promoter Methylation with Severity of SARS-CoV-2 Infection

BACKGROUND

During viral infections such as SARS-CoV-2, epigenetic changes within the promoter region of the immune system genes would possibly occur and have an effect on the immune system response as well as disease outcome. We aimed to evaluate and compare the methylation level of the IFITM1 gene promoter in different stages of COVID-19 disease with a healthy control group.

METHODS

In this cross-sectional study, 75 COVID-19 patients (25 mild, 25 severe, and 25 critical in addition to 25 age- and gender-matched healthy volunteers) have been included. DNA was extracted from the peripheral white blood cells using a commercial DNA extraction kit. PCR was performed using two types of primers designed for the methylated and unmethylated forms of the IFITM1 gene promoter.

RESULTS

The mean age of the patient and healthy volunteer groups was 52.733 ± 13.780 and 49.120 ± 12.490, respectively. Out of a hundred participants, 52 were male. The results demonstrated that severe (p = 0.03, OR 6.729) and critical (p = 0.001, OR 11.156) patients were much more likely to show methylation of the IFITM1 gene in contrast with mild patients. Moreover, IFITM1 methylation was significantly higher in COVID-19 patients in comparison with the healthy volunteer group (p = 0.004, OR 3.17). Furthermore, IFITM1 methylation in male patients with critical status, (p = 0.01) was significantly higher than in male patients with mild status. In addition, IFITM1 methylation of male (p = 0.03) and female (p = 0.01) critical patients was considerably higher compared to males and females of volunteer group.

CONCLUSIONS

Increased methylation of the IFITM1 gene in the severe and critical stage of COVID-19 diseases may indicate the role of SARS-CoV-2 infection in increasing methylation of this antiviral gene. This might be involved in suppressing the immune system, promoting SARS-CoV-2 replication and disease outcome.

A Preliminary Sequence Analysis of the Epstein-Barr Virus Nuclear Antigen 1 (EBNA1) Carboxy-Terminal Region in Cervical and Ovarian Cancers

Background & Objective

Epstein-Barr virus nuclear antigen-1 (EBNA1) is one of the most important proteins of Epstein-Barr virus (EBV) that might be mutated in various related cancers. The purpose of this study was to compare EBNA1 mutations in the C-terminal region between patients with cervical and ovarian cancer and healthy individuals.

Methods

As test and control groups, 18 EBV-positive paraffin-embedded samples of cervical and ovarian cancer and 10 age- and gender-matched healthy volunteers who did not have cancer but were EBV-positive were both used. Utilizing a commercial DNA extraction kit, total DNA was extracted following deparaffinization. The entire C-terminal region of the EBNA1 sequence was amplified using an in-house nested PCR. Phylogenetic analysis and Sanger sequencing were used to analyze the sequences using MEGA 7 software and through NJ method.

Results

Sequence analysis revealed that the P-Ala subtype of EBNA1 was present in all samples. In two and one samples, respectively, of cervical cancer patients, the mutations A1887G and G1891A were found. The G1595T mutation was also detected in four sequences taken from ovarian cancer patients. No statistically significant difference could be found between the frequency of mutations in patients and controls (P>0.05). No known amino acid substitutions were found in the USP7-binding region and the DBD/DD domain.

Conclusion

The findings showed that P-Ala is the predominant EBV subtype across all samples. Additionally, as the sequence of EBNA1's C-terminal region is so stable, it's possible that it had little impact on the pathogenesis of ovarian and cervical malignancies. It is advised to conduct additional research to verify these findings.

The molecular epidemiology, genotyping, and clinical manifestation of prevalent adenovirus infection during the epidemic keratoconjunctivitis, South of Iran

PURPOSE

Adenoviral-mediated keratoconjunctivitis is among the emergency diseases of ophthalmology with long-term sequels. The role of adenovirus infection, ocular-related genotypes, and association with ocular symptoms need to be investigated for epidemiological as well as clinical purposes.

METHODS

The affected patients from two close keratoconjunctivitis epidemics were included in the study. The swab samples were taken from patients; the total DNA was extracted and then used as a template for in-house Real-time PCR. Besides, partial Hexon genes of 11 adenovirus positive samples were amplified and submitted to sanger sequencing. Moreover, they were finally evaluated by phylogenetic analysis.

RESULTS

Of 153 patients, 92 (60.1%) were males and 47 cases (30.7%) had a history of eye infection in the family or colleagues. Real-time PCR tests of 126 samples (82.4%) were positive for adenovirus, and all eleven cases that underwent sequencing analysis were determined to be group 8 (HAdV-D8). Adenovirus infection has a significant relationship with infection among family or colleagues (p = 0.048), membrane formation (p = 0.047), conjunctival bleeding (p = 0.046), tearing, and pain(p < 0.05).

CONCLUSIONS

The results indicated that Adenovirus is the major cause of keratoconjunctivitis, and HAdV-D8 was the most common genotype in the area. There were some clinical manifestations associated with Adenovirus infection of the conjunctiva.

Polymorphism Analysis of Interleukin-18 and Interleukin-37 Genes in Hepatitis B Infections with Different Outcomes: A Preliminary Report from an Iranian Population

OBJECTIVE

Given the vital role of cytokines in influencing the outcomes of hepatitis B virus (HBV) infections, this study aimed to investigate the association between polymorphisms of interleukin (IL)-18 and IL-37 and the outcomes of HBV infection.

METHODS

In this study, we enrolled 300 subjects with chronic HBV infection, including those with cirrhosis/hepatocellular carcinoma (C/HCC), chronic active hepatitis B (CAH) infection, or asymptomatic carriers (AC), and 58 individuals whose infection was spontaneously cleared (SC). Genomic DNA was extracted, and IL-18/IL-37 genotyping was performed using PCR-RFLP and ARMS-PCR.

RESULTS

The frequency of genotypes and alleles of IL-18 single nucleotide polymorphisms (SNPs) at positions rs1946519, rs1946518, and rs187238 and IL-37 at position rs4241122 were not statistically different among the four studied groups (P>0.05). Furthermore, the frequency of different haplotypes was similar among the studied groups (P>0.05).

CONCLUSIONS

Polymorphisms of IL-18 SNPs at positions rs1946519, rs1946518, and rs187238 and variation of IL-37 at position rs4241122 do not appear to influence the outcome of HBV infection.

EBNA1 Upregulates P53-Inhibiting Genes in Burkitt's Lymphoma Cell Line

Background

Suppression of p53 is an important mechanism in Epstein-Barr virus associate-tumors and described as EBNA1-USP7 which is a key axis in p53 suppression. Thus, in this study, we aimed to evaluate the function of EBNA1 on the expression of p53-inhibiting genes including HDAC-1, MDM2, MDM4, Sirt-3, and PSMD10 and the influence of USP7 inhibition using GNE-6776 on p53 at protein/mRNA level.

Methods

The electroporation method was used to transfect the BL28 cell line with EBNA1. Cells with stable EBNA1 expression were selected by Hygromycin B treatment. The expression of seven genes, including PSMD10, HDAC-1, USP7, MDM2, P53, Sirt-3, and MDM4, was evaluated using a real-time PCR assay. For evaluating the effects of USP7 inhibition, the cells were treated with GNE-6776; after 24 hours and 4 days, the cells were collected and again expression of interest genes was evaluated.

Results

MDM2 (P=0.028), MDM4 (P=0.028), USP7 (P=0.028), and HDAC1 (P=0.015) all showed significantly higher expression in EBNA1-harboring cells compared to control plasmid transfected cells, while p53 mRNA expression was only marginally downregulated in EBNA1 harboring cells (P=0.685). Four-day after treatment, none of the studied genes was significantly changed. Also, in the first 24-hour after treatment, mRNA expression of p53 was downregulated (P=0.685), but after 4 days it was upregulated (P=0.7) insignificantly.

Conclusion

It seems that EBNA1 could strongly upregulate p53-inhibiting genes including HDAC1, MDM2, MDM4, and USP7. Moreover, it appears that the effects of USP7 suppression on p53 at protein/mRNA level depend on the cell nature; however, further research is needed.

A comprehensive narrative review of the cutaneous manifestations associated with COVID-19

The systemic and respiratory clinical manifestations of coronavirus disease 2019 (COVID-19) include fever, coughing, sneezing, sore throat, rhinitis, dyspnea, chest pain, malaise, fatigue, anorexia and headache. Moreover, cutaneous manifestations have been reported in 0.2% to 20.4% of cases. Early diagnosis of COVID-19 leads to a better prognosis; knowledge of its cutaneous manifestations is one way that may help fulfil this goal. In this review, PubMed and Medline were searched with the terms "dermatology", "skin" and "cutaneous", each in combination with "SARS-CoV-2" or "COVID-19". All articles, including original articles, case reports, case series and review articles published from the emergence of the disease to the time of submission, were included. In this comprehensive narrative review, we tried to provide an analysis of the cutaneous manifestations associated with COVID-19, including maculopapular rash, urticaria, Chilblain-like, vesicular lesions, livedo reticularis and petechiae in asymptomatic/symptomatic COVID-19 patients that might be the first complication of infection after respiratory symptoms. Immune dysregulation, cytokine storms, side effects of antiviral drugs, environmental conditions and high-dose intravenous immunoglobulin (IVIG) therapy might be involved in the pathogenesis of the cutaneous manifestations in COVID-19 patients. Therefore, knowledge of cutaneous COVID-19 manifestations might be vital in achieving a quick diagnosis in some COVID-19 patients, which would help control the pandemic. Further research is very much warranted to clarify this issue.

Association between expression of ZBP1, AIM2, and MDA5 genes and severity of COVID-19

Antiviral and inflammatory responses following the detection of the virus genome by nucleic acid sensors play a vital role in the pathogenesis and outcome of diseases. In this study, we investigated the ZBP1, AIM2, and MDA5 expression levels in COVID-19 patients with different intensities of the disease. 75 quantitative Real-Time PCR (qRT-PCR)-confirmed COVID-19 patients were included consecutively and divided into 3 groups of mild, severe, and critical based on the severity of the disease. Also, 25 healthy volunteer subjects were included. PBMCs were collected from the whole blood, and RNA was extracted using commercial kit. The expression of ZBP1, AIM2, and MDA5 genes was investigated using qRT-PCR technique. The mean age of the patients and healthy volunteers was 52.73±13.78 and 49.120±12.490, respectively. In each group, 13 out of 25 participants were male. The expression levels of ZBP1 (P=0.001), AIM2 (P=0.001), and MDA5 (P= 0.003) transcript were significantly higher in COVID-19 patients than the control group. The results also revealed that the expression levels of ZBP1, AIM2, and MDA5 were significantly higher in the critical and severe COVID-19 patients compared to those with mild disease (P<0.05). Moreover, regarding the gender, the expression levels of AIM2 and MDA5 were significantly elevated in male severe (P=0.04 and P=0.003, respectively) and critical (P=0.005 and P=0.0004, respectively) patients than the female ones. The results indicated that ZBP1, AIM2, and MDA5 genes might have an important role in the severity of COVID-19 disease. Moreover, the severity of COVID-19 disease in male and female patients might be related to AIM2, and MDA5 expression levels. More studies are recommended to be conducted to clarify this issue.

Lower frequency of T stem cell memory (TSCM) cells in hepatitis B vaccine nonresponders

Despite the availability of an effective vaccine and antiviral treatments, hepatitis B is still a global public health problem. Hepatitis B vaccination can prevent the disease. Vaccination induces long-lasting protective immune memory, and the identification of memory cell subsets can indicate the effectiveness of vaccines. Here, we compared the frequency of CD4⁺ memory T cell subsets between responders and nonresponders to HB vaccination. Besides, the frequency of IFN-γ⁺ memory T cells was compared between studied groups. Study participants were grouped according to their anti-HBsAb titer. For restimulation of CD4⁺ memory T cells, peripheral blood mononuclear cells (PBMCs) were cultured in the presence of HBsAg and PHA for 48 h. Besides, PMA, ionomycin, and brefeldin were added during the last 5 h of incubation to induce IFN-γ production. Flow cytometry was used for analysis. There was a statistically significant difference in the frequency of CD4⁺CD95⁺, CD4⁺CD95^Hi, and CD4⁺CD95^low/med T stem cell memory (T_SCM) cells between responder and nonresponder groups. However, the comparison of the frequency of memory T cells producing IFN-γ showed no differences. Our results identified a possible defect of immunological CD4⁺ memory T cell formation in nonresponders due to their lower frequency of CD4⁺ T_SCM cells.

Serosurvey of hepatitis A virus and E virus infection among municipal sweepers working in the largest city in the south of Iran

This study was conducted to determine the exposure rate of Hepatitis A and Hepatitis E viruses in urban solid waste collectors/sweepers in the south of Iran. The 385 samples (serums) were collected from Shiraz Municipality waste sweepers.. A questionnaire was used to gather data on their demographic and occupational characteristics, as well as their awareness of viral hepatitis disease. The viral seroprevalence was determined by commercial IgG ELISA kit. All participants were male, mean age of 41 ± 8 years. ELISA assay showed that all of them were positive for anti-HAV IgG. Also, 62 out of 385 individuals were positive for anti-HEV IgG. The statistical analysis showed that the frequency of HEV IgG antibody among age groups 20-30, 31-40, 41-50 and >50 years old had an increasing trend, 4.5%, 10.1%, 17.4%, and 36.7%, respectively, indicating age factor significance (p = .001). Based on some investigated factors including the duration of work experience, current and previous jobs, habitation, personal hygiene status, and knowledge on viral hepatitis diseasees/their transmission, there was no statistically significant difference between anti-HEV IgG positive versus negative sweepers. The results indicated a slighty higher frequency of anti-HAV and anti-HEV IgG among sweepers compared to other pre-investigated population. It doesn't seem that garbage collecting/sweeping could be a significant risk factor for HAV and HEV infection.

Epstein-Barr Virus Nuclear Antigen 1 Increases the Expression of Viral Oncogenes and Cellular Genes in the HeLa Cell Line

Epstein-Barr virus (EBV) represents one of the most important viral carcinogens. EBV nuclear antigen-1 (EBNA1) can induce the expression of different cellular and viral genes. In this study, we evaluated the EBNA1 effects on the expression patterns of human papillomavirus type 18 (HPV-18) E6 and E7 oncogenes and three cellular genes, including BIRC5, c-MYC, and STMN1, in a cervical adenocarcinoma cell line. HeLa cells were divided into three groups: one transfected with a plasmid containing the EBNA1 gene, one transfected with a control plasmid, and one without transfection. In all three groups, the expression levels of E6, E7, BIRC5, c-MYC, and STMN1 genes were checked using real-time PCR. Pathological staining was used to examine changes in cell morphology. Real-time PCR results showed that the expression level of HPV-18 E6 (P=0.02) and E7 (P=0.02) oncogenes significantly increased in HeLa cells transfected with the EBNA1 plasmid compared to cells transfected with control plasmid. Also, the presence of EBNA1 induced the expression of BIRC5 and c-MYC, which increased tenfold (P=0.03) and threefold (P=0.02), respectively. Regarding the STMN1 cellular gene, although the expression level in HeLa cells transfected with EBNA1 plasmid showed a twofold increase, this change was insignificant (P=0.11). Also, EBNA1 expression caused the creation of large HeLa cells with abundant cytoplasm and numerous nuclei. The EBV-EBNA1 could increase the expression levels of HPV-18 E6 and E7 viral oncogenes as well as c-MYC and BIRC5 cellular genes in the HeLa cell line. These findings indicate that the simultaneous infection of cervical cells with HPV-18 and EBV might accelerate the progression of cervical cancer.

The seroepidemiology and risk factors of West Nile virus infection in blood donors of Fars province, southwest of Iran

Aim: To evaluate the frequency of West Nile virus (WNV) in blood donors of the blood transfusion center of Fars province, Iran. Materials & methods: A total of 337 participants referred for blood donation to Fars blood centers were included. The presence of anti-WNV antibodies was analyzed using the WNV IgG ELISA kit. Results: Out of all participants, 76 (22.6%) were positive for anti-WNV IgG antibodies. Our results also showed that the frequency of WNV was associated with the age, educational level, job and city of residency of participants (p < 0.05). Conclusion: The results indicated the high frequency of WNV seropositivity among blood donors in southwest Iran. Accordingly, there is an urgent need to establish an integrated surveillance system for monitoring WNV infection in Iran.

Relative frequency of hepatitis B virus, human papilloma virus, Epstein-Barr virus, and herpes simplex viruses in the semen of fertile and infertile men in Shiraz, Iran: A cross-sectional study

Background

About 8-12% of couples on reproductive age suffers from infertility worldwide. Since 1993, the role of genital tract infections by microbes, including viruses that can infect the sperm, in human infertility has been proposed.

Objective

To investigate the frequency of hepatitis B virus (HBV), human papilloma virus (HPV), Epstein-Barr virus (EBV), and herpes simplex virus (HSV) infection in the semen of fertile and infertile men referred to the Mother and Child Hospital, Shiraz, Iran.

Materials and Methods

In this cross-sectional study, 350 men including 200 infertile and 150 fertile men were included. All semen samples were allowed to liquefy, followed by the assessment of sperm parameters. DNA was extracted using a DNA extraction kit (CinaGene, Tehran, Iran) according to the manufacturer's instructions. Detection of HBV, HPV, EBV, and HSV1/2 was done by the PCR method.

Results

The mean age of the participants was 36 ± 7 yr. Molecular results showed that 16 samples (8%) of infertile men and 5 (3.3%) of fertile men were positive for HBV, which was not statistically significant (p = 0.069). Only one sample of the fertile participants was positive for HPV. None of the semen samples of the infertile or fertile groups was positive for the presence of EBV or HSV1/2.

Conclusion

The results of this study indicated that HBV, HPV, EBV, and HSV might not be involved in men's infertility. Further studies are recommended for clarifying the role of these viruses in infertility.

Human gene polymorphisms and their possible impact on the clinical outcome of SARS-CoV-2 infection

The SARS-CoV-2 pandemic has become one of the most serious health concerns globally. Although multiple vaccines have recently been approved for the prevention of coronavirus disease 2019 (COVID-19), an effective treatment is still lacking. Our knowledge of the pathogenicity of this virus is still incomplete. Studies have revealed that viral factors such as the viral load, duration of exposure to the virus, and viral mutations are important variables in COVID-19 outcome. Furthermore, host factors, including age, health condition, co-morbidities, and genetic background, might also be involved in clinical manifestations and infection outcome. This review focuses on the importance of variations in the host genetic background and pathogenesis of SARS-CoV-2. We will discuss the significance of polymorphisms in the ACE-2, TMPRSS2, vitamin D receptor, vitamin D binding protein, CD147, glucose-regulated protein 78 kDa, dipeptidyl peptidase-4 (DPP4), neuropilin-1, heme oxygenase, apolipoprotein L1, vitamin K epoxide reductase complex 1 (VKORC1), and immune system genes for the clinical outcome of COVID-19.

IL-17 Genetic Variations Increase The Risk of Cirrhotic/Hepatocellular Carcinoma in Patients with Hepatitis B Virus Infection

BACKGROUND

Genetic variation in immune regulatory genes might influence the HBV infection outcome.

OBJECTIVE

This study aimed to determine the association of IL-17A rs2275913 (G197A), IL-17F rs763780 (A7488G), and IL-23R rs10889677 (C2370A) gene polymorphisms, as well as the emerged haplotypes in the individual infected by HBV and to investigate their association with the infection outcome.

MATERIALS AND METHODS

300 chronic HBV infections with Cirrhotic/Hepatocellular carcinoma(C/HCC), chronic active (CA), and asymptomatic carrier (AC) and 38 individuals whose infection was spontaneously cleared (SC) were enrolled. Genomic DNA was extracted, and IL-17A/F and IL-23R genotyping were performed by using the PCR-RFLP method.

RESULTS

Out of 338 subjects, 238 and 100 were respectively male and /female with a mean age of 47.61±13.41. The frequency of GA genotype (p=0.01) and A alleles (p=0.001) of IL-17A rs2275913 (G197A), as well as the frequency of AA genotype (p=0.014) and A alleles (p=0.018) of IL-17F rs763780 (A7488G) gene locus, was found to be significantly higher in the C/HCC than CA and AC groups. Furthermore, the frequency of GA and AG haplotype in CA individuals was higher than those with C/HCC and AC (p=0.003). Also, the GG haplotype was higher in AC individuals than those with C/HCC (P=0.022), and the AA haplotype was higher in C/HCC individuals than the CA patients (P=0.001).

CONCLUSION

Our findings suggest that A allele and GA genotype at IL-17A rs2275913 (G197A), as well as A allele and AA genotype at IL-17F rs763780 (A7488G) locus, might be associated with increased risk of C/HCC among patients with hepatitis B virus infection.

The Prevalence of Hepatitis B Virus Markers among Students of Shiraz University of Medical Sciences

Background

Protection against hepatitis B virus (HBV) is based on the presence of antibodies against hepatitis B surface antigen (HBsAg). Vaccination of newborns is the most effective means of prevention. This study aimed to evaluate the frequency of anti-HBs antibody (anti-HBsAb), anti-HB core Ab (anti-HBcAb), HBsAg, and HBV DNA among university students in Fars province, Southern Iran.

Materials and Methods

In this cross-sectional study, 272 students of Shiraz University of Medical Sciences, were enrolled. Venous blood (5 mL) was collected from each participant and centrifuged; the sera were stored at -20°C until use. Anti-HBsAb, Anti-HBcAb, and HBsAg were measured using a commercial enzyme-linked immunosorbent assay kit. HBV DNA load was also measured by a real-time polymerase chain reaction.

Results

The mean age of the participants was 19 ± 1 years. There were 171 (62.9%) females and 101 (37.1%) males. Anti-HBsAb at a protective level (>10 mIU/mL) were detected in the sera of 104 (38.5%) of the cases. Of the anti-HBsAb seropositive participants, 82 were female and 22 were male; the difference between the gender and seropositivity to anti-HBsAb was statistically significant (P = 0.001, odds ratio: 3.3, 95% confidence interval = 1.89-5.79). Anti-HBcAb was detected in only one participant that was negative for both HBsAg and HBV DNA.

Conclusion

Findings of the current study show that more than half of the students do not have a protective level of anti-HBsAb and might be susceptible to HBV infection, indicating the necessity of checking the level of anti-HBsAb as well as a booster dose in high-risk groups.

Serosurvey of parvovirus B19 and cytomegalovirus infections among female university students in Shiraz, Southern Iran

Infection with parvovirus B19 and cytomegalovirus (CMV) during pregnancy might lead to fetal infection, resulting in congenital abnormalities. This study aimed to investigate the frequency of IgM and IgG antibodies against parvovirus B19 and CMV in female university students in Shiraz, in Fars province, Southern Iran. In this cross-sectional study, 370 female university students were included. Blood samples were collected from each participant and tested for anti-parvovirus B19 and CMV IgG and IgM antibodies, using commercial ELISA kits. The mean age of the participants was 24 (±7)years. Out of 370 participants, 327 (88.4%) and 9 (2.4%) were positive for IgG and IgM antibodies against CMV. Moreover, 211 (57.0%) and 4 (1.1%) of the participants were respectively positive for IgG and IgM antibodies against parvovirus B19. The difference in CMV or parvovirus B19 seropositivity between different age groups was not statistically significant (P>0.05). The findings of our study showed that more than 50% of the female university students are seropositive to CMV and parvovirus B19 infections. It highlights the importance of health education and also the laboratory screening of females at childbearing age to reduce the risk of congenital infections resulting from these viral infections.

The Inflammatory and Fibrotic Patterns of Hepatic Stellate Cells Following Coagulation Factors (VII or X)-Shielded Adenovirus Infection

The role of coagulation factors on the inflammatory effect of adenovirus (Ad) is an unresolved question that was considered herein. Adenovirus-36(Ad36) and adenovector-5-GFP(Ad5-GFP) were prepared; then, they were loaded with VII or FX factors. The size/charge parameters and transduction efficiency were evaluated using fluorescent microscopy and Zetasizer, respectively. The Ad36-coagulation factor complexes were added on the stellate cells, LX-2. Thereafter, the expression levels of inflammatory and fibrotic genes including PKR, IL-1β, TNF-α, TIMP-1, collagen, and TGF-β were measured by qPCR and ELISA assays. The loading of FVII or FX factors not only increased the size/charge of Ad5-GFP but also enhanced the transduction rate up to 60% and 75%, respectively, compared to the controls (45%). The PKR expression analysis showed an upregulation following treatment with all Ad36 forms (P = 0.0152). The IL-1β and TNF-α cytokines analyses demonstrated that the Ad36-FVII complex elicited the highest inflammatory response (P = 0.05). Similarly, the fibrosis-related expression analysis revealed a more inductive role of FVII when loaded on Ad36, compared to the FX factor. The findings suggested that adenovirus elicited the innate inflammatory and activation state in the hepatic stellate cell. In addition, adenovirus shielded by FVII exhibited more innate inflammation as well as activation of the stellate cells than the FX-loaded virus.

The Prevalence of Bacteriospermia in Infertile Men and Association with Semen Quality in Southwestern Iran

INTRODUCTION

Infertility considered as a social and public health issue and estimated that most of these infertile couples are residents of developing countries. Infectious diseases including the history of Sexually Transmitted Infections (STIs) may impact on male reproductive function. Therefore, the present study aimed to investigate the prevalence of bacterial contaminants of semen and probable association with sperm quality of infertile men in Iranian population.

METHODS

The study population consisted of 200 infertile men and 150 fertile men attending an infertility Center in southwestern Iran during the study period in 2015. The assessment of sperm parameters was according to the World Health Organization (WHO) guidelines. The presumptive pathogens were identified using standard microbiology tests and confirmed by specific PCR primers.

RESULTS

The prevalence of bacteriospermia in the semen of the infertile group was significantly higher than that in the fertile group (48% vs. 26.7%, P <0.001). The microbiological analysis of samples showed that the most abundant species of bacteria in semen of infertile men were Chlamydia trachomatis (12.5%) followed by Neisseria gonorrhoeae (11%). On the other hand, in the control group, Lactobacillus spp. (17.3%) was the most isolated pathogen. Results showed that the presence of N. gonorrhoeae, C. trachomatis, Mycoplasma genitalium, Haemophilus, and Klebsiella was significantly associated with sperm abnormality.

CONCLUSIONS

Based on our findings, it seems that bacteriospermia is associated with alterations in the properties of semen which may lead to a decrease in the fertilization potential of sperm. Therefore, immediate and appropriate treatment is necessary before investigating every other possible cause of infertility.

Serosurvey of HBV surface antigen and anti-HBV surface antibody among HIV-infected patients in Fars province, southern Iran

HBV infection is a major public health issue that can lead to liver cirrhosis and hepatocellular carcinoma. The current study evaluated the prevalence of HBsAg and anti-HBsAb among HIV/AIDS patients in Shiraz, southern Iran. The subjects in this study comprised 251 participants previously confirmed for HIV infection registered at the Shiraz HIV/AIDS center in southern Iran. Peripheral whole blood (5 ml) was obtained from each participant and evaluated for HBsAg and anti-HBs antibodies, utilizing commercial ELISA kits. The 251 participants consisted of 158 (63.5%) males and 91 (36.5%) females. HBsAg and anti-HBsAb were detected in 16 (6.4%) and 117 (46.6%) cases, respectively, while five cases (2%) were positive for both viral markers. No statistically significant association was observed between patients' age, sex, or CD4+ cell count and seropositivity to HBsAg or anti-HBsAb. The findings of the study revealed a relatively high seroprevalence of HBsAg and anti-HBsAb among HIV patients, highlighting the importance of preventive and therapeutic programs in such patients.

Association of HBsAg mutation patterns with hepatitis B infection outcome: Asymptomatic carriers versus HCC/cirrhotic patients

INTRODUCTION AND OBJECTIVES

The hepatitis B virus (HBV) surface antigen (HBsAg) variations suggested having some effects on infection outcome. Due to some controversial issues, the aim of this study was to compare the pattern of HBsAg variation between asymptomatic carriers and HCC/cirrhosis patients.

MATERIALS AND METHODS

In this cross-sectional study, 19 HCC/cirrhotic and 26 asymptomatic patients were enrolled. After viral DNA extraction, HBs gene was amplified using an in-house nested-PCR. Then, PCR products were introduced into bi-directional Sanger sequencing. The retrieved sequences were compared with references, to investigate the variation of immunologic sites, major hydrophilic region (MHR) of HBsAg as well as reverse transcriptase (RT), and also to determine genotype/subtype.

RESULTS

The analysis of MHR and epitopes on HBsAg showed dozens of substitution, which occurred more prevalently in I110, P120, Y134, G159, S193, Y206, S207, I208, L213 and P214 positions. However, Y134N/F/L (P=0.04) and P120T/S (P=0.009) were significantly detected in MHR and B-cell epitope of HCC/Cirrhotic group. A number of truncation-related mutations were higher in HCC/Cirrhotic group (P>0.001), albeit only C69* stop codon was statistically significant (P=0.003). In RT, some potentially resistant substitutions such as Q215S, V191I and V214A, were revealed. Phylogenetic analysis showed that all of isolates belonged to genotype D, and the major serotype was ayw1.

CONCLUSION

The higher frequency of substitutions in MHR and immune epitopes at positions such as Y134 and P120 as well as stop codons such as C69* in HCC/cirrhotic group might candidate them as predictive factors for infection outcome.

Seroprevalence of anti-hepatitis E antibodies and antigens among HIV-infected patients in Fars Province, southern Iran

Objective

HIV-infected patients have immunological and clinical features that might affect the pathogenesis, as well as the outcome of the HIV/HEV co-infection. The current study aimed to determine the seroprevalence of anti-HEV antibodies and HEV antigens among HIV-infected patients in Fars Province, Southwest Iran.

Methods

Blood samples (5 mL) were collected from 251 HIV-confirmed patients. Respective data, including patients’ demographic information, were obtained for each patient. The presence of HEV antigens and anti-HEV antibodies (IgG) were assessed by commercial ELISA kits, based on the manufacturers’ instructions.

Results

Out of 251 cases, 158 (62.9%) were male and 91 (36.3%) were female. Patients’ age varied from 14 to 83 (mean: 40 ± 9.7) years. Out of 251 HIV positive cases, 26 (10.4%) were positive for anti-HEV IgG antibodies and 6 (2.4%) were positive for HEV-antigens. Also, 2 (0.8%) of the patients were positive for both anti-HEV IgG antibodies and antigens. Statistical analysis revealed no significant association between sex and seropositivity to either HEV antigen or antibodies. Moreover, no significant association was seen between age and seropositivity to HEV antigen or antibody (P = 0.622 and 0.945, respectively).

Conclusion

Our results showed a relatively low prevalence of HEV-antibodies in HIV-infected patients, indicating that HIV positive patients may not be at greater risk of HEV infection than the general population. Moreover, HEV-antigen was detected in a few cases of HIV-infected individuals which indicate an acute or chronic HEV infection in these patients.

Association of Human Papilloma Virus and Epstein-Barr Virus with Ovarian Cancer in Shiraz, Southwestern Iran

Background & Objective:

Ovarian cancer is one of the most common cancers amongst women. The association of Human papillomavirus (HPV) and Epstein-Barr virus (EBV) with ovarian cancer is inconclusive; therefore, the aims of this study were to evaluate the frequency of HPV and EBV in malignant, borderline, benign and normal ovarian tissues.

Methods:

In this case-control study, 205 Paraffin-embedded ovarian tissue specimens including 68 malignant, 27 borderline, 65 benign, and 45 normal tissues were included from December 2014 to January 2018 and subjected to DNA extraction. The β-globin gene was amplified using PCR to confirm the quality of the extracted DNA. The genomes of HPV (genotypes 16 and 18) and EBV were identified, using specific primers by PCR.

Results:

The mean age of participants was 43.42 ± 15.4 years. The frequency of HPV was statistically significant between malignant versus benign (P=0.02) and control groups (P=0.002), but not with borderline tumor group (P=0.78). Amongst HPV infected samples, 1 (4.5%) and 14 (63.6%) samples were infected with types 16 and 18, respectively. Also 4 (18.2 %) samples were infected with both genotypes. Eleven samples including 7(10.3%) malignant, 1 (3.7%) borderline, 3 (4.6%) benign and none (0%) of normal control groups were infected with EBV, which was statistically different between malignant and the normal control group (P=0.03).

Conclusion:

The results of our study showed the possible role of high risk HPVs as well as EBV in pathogenesis of ovarian cancer, and further studies are recommended to confirm these findings.

Impact of IL28 Genotypes and Modeling the Interactions of HCV Core Protein on Treatment of Hepatitis C

BACKGROUND

Mutations in the core CVR region of hepatitis C virus (HCV) and polymorphisms of interleukin 28B (IL28B) are associated with progression toward liver disease and in response to therapy. In addition, interactions of the core protein with some cell interactors can be related to HCV liver damage.

AIM

This study aimed to evaluate the effect of core mutations as well as IL28B polymorphism on clinical features, sustained virological response (SVR) in 1a and 3a HCV genotypes amongst Iranian HCV infected patients, and the impact of mutations on core protein properties, antigenic properties, and interactions with HCV inhibitors, using several bioinformatics tools.

METHODS

Seventy-nine Iranian patients infected with HCV genotypes 1a and 3a and diagnosed with chronic active hepatitis were examined. Plasma viral RNA was used to amplify and sequence the HCV Core gene; also, HCV viral load, molecular genotyping, and the liver enzymes were determined for all samples. The sequencing results were analyzed by several reliable bioinformatics tools to determine the physicochemical properties, B cell epitopes, post-modification changes, and secondary/tertiary structures; and evaluate the interactions with 4 drugs by docking method.

RESULT

There were some substitutions in core CVR related to ALT and AST enzymes that can lead to HCV advanced liver disease. The most prevalent mutation for 3a genotypes was a substitution in aa 162 (I to V) while we did not find any mutation in 1a responder group. Polymorphism of the rs8099917 showed that the majority of patients had TG heterozygous and carried CT genotype at the rs12979860. Analysis indicated several phosphorylation sits for core protein as well as two important disulfide bonds. Immunogenic prediction showed that core protein can strongly induce the immune system. Interaction analysis, using the docking method revealed two potential interactors (Vitronectin and SETD2).

CONCLUSION

Generally, mutations in all core CVR regions in all patients showed a relationship between such substitutions and higher liver enzymes that can result in advanced liver disease progression in HCV infected patients. Furthermore, immunoinformatics analysis determined the possible immunodominant regions to be considered in HCV vaccine designs. Furthermore, no association between SVR and IL28B polymorphism was shown. In silico analysis determined modification sites, structures, B-cell epitopes of core protein and interactions with several interactors can lead to persistent HCV infection in the cell and the progress of liver diseases.

Phylogenetic analysis and circulation pattern of human metapneumovirus strains in children with acute respiratory infection in Iran, 2014–2015

Aim: The aim of the present study was to investigate the prevalence and genetic variation of the human metapneumovirus (HMPV) G gene in children less than 8 years old with acute respiratory tract infections in Iran during 2014–2015. Materials & methods: To this end, 110 nasal swabs were tested for HMPV F gene. All positive samples were tested for the full length of HMPV G gene, then sequenced and analyzed for phylogenetic grouping. Results: Six (5.45%) out of 110 samples were positive for HMPV gene. Our HMPV sequences clustered into two main clusters: A2b (five isolates) and B1 (one isolate). The dN/dS ratio showed the presence of negative selective pressure. Conclusion: A2b was the predominant genotype during the study period in southwest of Iran.

Co-existing of HSV1/2 or EBV Infection with the Presence of High-Risk HPV DNA in Cervical Lesions in the Southwest of Iran

Objective:

While the vast majority of the cervical lesions have been attributed to the HPVs, the role of EBV and HSV1/2 as co-factors in the progression of these abnormalities needs more investigation. In this study, we aimed to determine the co-existence of EBV or HSV in cervical lesions infected with high-risk HPVs.

Methods:

Totally, 102 formaline-fixed cervical lesions with different pathological grades (LSIL, HSIL, and SCC) were enrolled in this study. DNA was extracted, and its integrity was examined by PCR assay. Two conventional PCRs were performed for the detection of EBV and HSV1/2 genomes in the tissue specimens. Besides, an in-house Real-Time PCR, as well as a nested PCR assays following sequencing, was performed to detect HPV genotypes in EBV or HSV positive samples.

Results:

The mean age of the participants was 42.8±13 years. Out of 102 samples, 32% (n=33) were confirmed to be LSIL, 42.2% (n=43) were HSIL, 22.5% (n=23) were SCC and 2.9% (n=3) were adenocarcinoma. EBV genome was detected in 13(12.7%) samples including 2 of LSIL, 8 of HSIL and 3 of SCC. All EBV positive samples harbored high risk HPV types 16,18 and/or 31 co-infections. However, the HSV genome was not found in any of the samples.

Conclusion:

Our result revealed that the frequency of EBV infection is higher in HISL than LSIL. Moreover, the amount of HPV load showed an elevated level among co-infected patients, which indicates that EBV might be an enhancing factor of disease progression. In contrast, HSV may not has a role as a co-factor in cervical lesions pathogenesis.

Knowledge and Awareness Regarding Hepatitis B, Hepatitis C, and Human Immunodeficiency Viruses Among College Students: A Report From Iran

Globally, high-risk illnesses including Hepatitis B, Hepatitis C, and human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) are major health problems causing considerable impact on health systems. Knowledge and awareness are very important factors for controlling these illnesses in society. Regarding the transmission routes of these viruses, young people are at the highest risk of infection. Therefore, our objectives were to determine the college students' awareness of hepatitis B virus (HBV), hepatitis C virus (HCV), and HIV/AIDS with regard to basic information, transmission, and prevention. A total of 810 students from 7 universities, from September to March 2017, were included in the study. All participants were categorized into three groups (medical, biology, and other fields). The subjects were evaluated by a standardized questionnaire and results analyzed in SPSS software using the χ² test. In total, 43% of respondents were male and the majority of them were 20 to 25 years old. Our results showed the suitable level of awareness about HBV and remarkable about HIV. In contrast, insufficient level of awareness was indicated about HCV. Given the low levels of awareness or knowledge about HCV, it can be suggested that educational programs for this important disease are necessary especially for university students. On the other hand, high awareness of participants about HBV and HIV/AIDS might be the results of the proper functioning of educational programs for students in Iran.

Serum levels of anti-hepatitis B surface antibodies among vaccinated children aged 1 to 12 years in a rural community in Fars Province, southern Iran

The present study aimed to find out the levels of anti-HBsAb among vaccinated children in a rural community in Fars Province, Southern Iran. Blood samples were taken from 550 children, aged 1-12 years (mean 6.4 ± 3.5), in 2017 from three villages in the area. A structured questionnaire was used to get the sociodemographic data of the subjects along with determinants concerning the Hepatitis B. Sera samples were examined for anti-HBsAb, using an ELISA commercial kit. Anti-HBsAb were detected in 468 (85.1%) of the subjects. Of the seropositive subjects, 37 (45.1%) were female and 45 (54.9%) were male. In the age group of 0-5 years, 88.7% of the subjects were seropositive. This rate was 84.3% and 78.1% in the age group of 6-10 years old and older than 10 years, respectively. There was a significant association (p < .05) between the anti-HBsAb and age. Findings of the current study revealed that children living in a rural community in southern Iran have appropriate protection against HBV even more than 10 years after being vaccinated. The decline in seropositivity rate of anti-HBsAb with age may further point out the need for a booster dose of HBV vaccine.

The Investigation of Drug Resistance Substitutions in NS3 Protease Sequence of Hepatitis C Virus from Non-Responder Patients

Background:

Even with the fantastic successes of direct-acting antivirals (DAA) in the treatment of Hepatitis C Virus (HCV) infection, natural drug resistance remains a challenging obstacle for their impacts. The data regarding protease inhibitors (PIs) resistance in Iran population are limited. The aim of this study was to investigate the variations in NS3 protease of HCV from non-responder patients.

Methods:

In this cross-sectional study, 14 HCV infected patients with genotype 1(N=5) and 3(N=9) who have not responded to Interferon-related regime were enrolled from Liver Clinic, Shiraz. The NS3 protease region was amplified by Nested-PCR followed by product gel extraction. Besides, some amplified protease regions were cloned into a cloning vector to improve the sensitivity of mutation detection. Both crude and cloned sequences were then introduced into sequencing. The obtained sequences were compared with the NS3 reference sequences and analyzed by Geno2pheno available software to find possible substitutions. In the end, the phylogenetic tree was constructed.

Results:

Among variations responsible for PIs resistance, only one out of 14 (7%) sample who was infected with genotype 1a, harbored R117C+N174S double mutation, which causes reduced susceptibility to Telaprevir. Any another resistance mutation was not found among the studied population. The most frequent substitutions were determined as I52M(N=9), S102A(N=9), S166A(8) and V170I(8) for genotype 3a, and F147S/A(4) for genotype 1. However, some uncharacterized substitutions on scored position, including I132L(N=1), I170V(N=3) and N174S(N=2) were also determined among sequences. Phylogenetic analysis demonstrated that the protease region has enough power to correctly classify enrolled samples into relevant clusters on the tree. There were 2, 3 and 9 cases of sub-genotypes 1a, 1b, and 3a, respectively.

Conclusion:

A low frequency of PIs resistance mutations in our HCV infected population is a hopeful point of starting these drugs in HCV infected patients.

Signature of natural resistance in NS3 protease revealed by deep sequencing of HCV strains circulating in Iran

A tremendous upscale of screening and treatment strategies is required to achieve elimination of the hepatitis C virus (HCV) in Iran by 2030. Among treated patients, at least 5-10% is expected to experience treatment failure. To efficiently retreat cases with prior exposure to NS5A and NS5B drugs, knowledge on the natural prevalence of NS3 resistance is key. The NS3 region of 32 samples from sixteen Iranian HCV patients, among which 6 injecting drug users, was amplified and subjected to deep sequencing. Amplification and sequencing were successful in 29 samples. The reads were assembled to consensus sequences and showed that 6 patients were infected with HCV1a (37.5%), 7 with HCV1b (43.8%) and 3 with HCV3a (18.7%). Nucleotide identities were shared for >97% between intra-host sequences. Two patients were infected with natural resistant viruses, of which one solely comprising low frequency variants. Inferred phylogenies showed that Iranian sequences clustered together for HCV1a and HCV1b, while for HCV3a a potential recombination event was detected. We firstly report the use of deep sequencing for HCV in Iran, demonstrate the use of NS3 inhibitors as salvage therapy in case of retreatment and stress the importance for Iran to prioritize drug users for screening and treatment.

The Very Low Frequency of Epstein-Barr JC and BK Viruses DNA in Colorectal Cancer Tissues in Shiraz, Southwest Iran

Viruses including Epstein-Barr virus (EBV), JCV and BKV have been reported to be associated with some cancers. The association of these viruses with colorectal cancers remains controversial. Our objective was to investigate their infections association with adenocarcinoma and adenomatous polyps of the colon. Totally, 210 paraffin-embedded tissue specimens encompassing 70 colorectal adenocarcinoma, 70 colorectal adenomatous and 70 colorectal normal tissues were included. The total DNA was extracted, then qualified samples introduced to polymerase chain reaction (PCR). The EBV, JCV and BKV genome sequences were detected using specific primers by 3 different in-house PCR assays. Out of 210 subjects, 98 cases were female and the rest were male. The mean age of the participants was 52 ± 1.64 years. EBV and JCV DNA was detected just in one (1.42%) out of seventy adenocarcinoma colorectal tissues. All adenomatous polyp and normal colorectal tissues were negative for EBV and JCV DNA sequences. Moreover, all the patients and healthy subjects were negative for BKV DNA sequences. The results suggested that EBV and JCV genomes were not detectable in the colorectal tissue of patients with colorectal cancer in our population. Hence, BKV might not be necessitated for the development of colorectal cancer. The findings merit more investigations.

High prevalence of vancomycin and high-level gentamicin resistance in Enterococcus faecalis isolates

Multiple drug-resistant enterococci are major cause of healthcare-associated infections due to their antibiotic resistance traits. Among them, Enterococcus faecalis is an important opportunistic pathogen causing various hospital-acquired infections. A total of 53 E. faecalis isolates were obtained from various infections. They were identified by phenotypic and genotypic methods. Determination of antimicrobial resistance patterns was done according to CLSI guidelines. The isolates that were non-susceptible to at least one agent in ≥3 antimicrobial categories were defined as multidrug-resistant (MDR). Detection of antimicrobial resistance genes was performed using standard procedures. According to MDR definition, all of the isolates were MDR (100%). High-level gentamicin resistance was observed among 50.9% of them (MIC ≥ 500 μg/ml). The distributions of aac(6')-Ie-aph(2'')-Ia and aph(3')-IIIa genes were 47.2% and 69.8%, respectively. The aph(2'')-Ib, aph(2'')-Ic, aph(2'')-Id, and ant(4')-Ia genes were not detected. Vancomycin resistance was found in 45.3% of strains. The vanA gene was detected in 37.7% of isolates, whereas vanB and vanC₁ genes were not observed in any strain. Erythromycin resistance rate was 79.2% and the frequencies of ermB and ermC genes were 88.6% and 69.8%, respectively. The ermA and msrA genes were not present in any of the isolates. Our data indicate a high rate of MDR E. faecalis strains. All of high-level gentamicin-resistant isolates carried at least one of aac(6')-Ie-aph(2'')-Ia or aph(3')-IIIa genes. Distribution of vanA was notable among the isolates. In addition, ermB and ermC were accountable for resistance to erythromycin.

No detection of EBV, BKV and JCV in breast cancer tissue samples in Iran

OBJECTIVE

The most common cancer amongst women is breast cancer. Reports on the role of EBV, BKV, and JCV in the development of breast cancer are controversial. Hence, the aim of this study was to determine the frequency of EBV, BKV, and JCV in malignant breast tumors in comparison with benign ones.

RESULTS

A total of 300 breast biopsy tissues were included, of which 150 were malignant and 150 benign. After deparaffinization, tissues were subjected to DNA extraction. β-globin gene was amplified by PCR to evaluate the quality of extracted DNA. In house PCRs assay was performed to detect EBV, JCV, and BKV genome fragment. The mean age of malignant and benign groups was 45.0 ± 9.4 and 35.2 ± 12.1 years old. Out of 150 malignant samples, 146 were ductal, two lobular and two samples both invasive ductal and lobular carcinoma. In the benign group, 96, 52 and two samples were fibroadenoma, fibrocystic, and adenosis types, respectively. Genomic DNA fragment of EBV, BKV, and JCV was not found in any of the malignant and benign breast tissues.

CONCLUSION

According to our finding, there is the possibility that EBV, BKV, and JCV are not involved in breast cancer pathogenesis.

Comparison of ISG15, IL28B and USP18 mRNA levels in peripheral blood mononuclear cells of chronic hepatitis B virus infected patients and healthy individuals

AIM

The purpose of this study was to evaluate the expression level of Interferon-stimulated Gene 15 (ISG15), Interleukin28B (IL28B) or IFN-lambda-3 and Ubiquitin specific peptidase 18 (USP18) genes in Peripheral Blood Mononuclear Cells (PBMCs) of patients with chronic active and inactive hepatitis B in comparison with healthy individuals.

BACKGROUND

Despite the presence of the vaccine for hepatitis B virus (HBV), it remains a public health challenge. The effort to uncover the immune genes attributed to infection outcome is going through.

METHODS

This Cross-sectional study was conducted on hepatitis B infected patients that were admitted to the Clinic of Liver diseases, Shiraz, January-November 2016. Patients were divided into two groups including active and inactive chronic regarding relevant World Gastroenterology Organization Global Guideline. They were mono-infected with HBV, and HCV or HIV co-infection was excluded from the study. Gene expression analysis was performed on fresh PBMCs samples with the help of Real-time PCR method.

RESULTS

Interleukin 28B gene expression showed no statistically significant difference between the three studied groups (P>0.05). The expression level of ISG15 was significantly higher in the healthy control group compared to active (P= 0.0068) and inactive chronic subjects (P<0.0001). Similarly, USP18 expression level in the control group was also significantly higher compared to the active (P= 0.0228) and inactive chronic patients (P=0. 0226).

CONCLUSION

The results of this study showed that the expression level of ISG15 and USP18 but not IL28B were higher in healthy individuals than in those infected with HBV. This difference expression may highlight the role of ISG15 and USP18 in the immune-related mechanism of HBV infection.

Recombinant NS3 Protein Induced Expression of Immune Modulatory Elements in Hepatic Stellate Cells During Its Fibrotic Activity

There is a growing body of studies that show the important role of NS3 protein from hepatitis C virus in fibrosis. However, mechanisms of the effects of this protein on immune modulation of stellate cells remain to be investigated. Herein, the effect of NS3 protein on the expression level of suppressor of cytokine signaling (SOCS)1/3 and interleukin-24 (IL-24)-related genes was investigated in hepatic stellate cell (HSC), LX-2. Recombinant NS3 protein was added to LX-2 HSC culture. Leptin and standard medium treatments were also included in experiments as positive and negative controls, respectively. Total RNA was extracted from each well at 6, 12, and 24 h after NS3 addition. The expression levels of the fibrotic (transforming growth factor beta 1 [TGF-β], alpha-smooth muscle actin [α-SMA], and COL1A1), inflammatory (IL-6 and IL-24), IL-20R, IL-22R, and immunosuppressive genes (SOCS1 and SOCS3) were evaluated by real-time polymerase chain reaction (PCR). Recombinant NS3 protein induced activated phenotypes of LX-2 with a significant increase in the expression level of α-SMA COL1A1 (p < 0.0001) and TGF-β. Moreover, this exposure led to a meaningful elevation in the expression of IL-6. Furthermore, compared with leptin (control), after the stellate cell treatment with NS3, SOCS1 and SOCS3 gene expression induced at a comparable level. Compared with the control sample, the NS3 protein significantly increased the expression level of IL-24 and its related receptors, IL-20R and IL-22R. This study not only confirmed the previously proved inflammatory and fibrotic effect of this protein but also indicated that high expression levels of SOCS1, SOCS3, and IL-24 have a significant effect on HSC activation. Therefore, these two molecules can be used as a potential therapeutic target candidate.

Association of PD-1 gene with outcome of hepatitis C virus infection

Primary hepatitis C virus infection might be spontaneously cleared or become chronic. Polymorphisms in immune regulatory genes might influence the outcome. The aim of this study was to determine the frequency of genotypes and alleles of PD-1.3 and PD-1.5 gene loci in HCV infected patients and their association with the disease outcome. In this study 167 patients with chronic hepatic C and 42 individuals whose infection was spontaneously cleared, and a healthy control group comprising of 300 participants were included. The presence of chronic or spontaneously cleared infection amongst the participants was determined in advance by serologic and molecular methods. Genomic DNA was extracted using salting out method. PD-1 gene polymorphisms assay was performed using PCR-RFLP method. The frequency of alleles of PD-1.3 gene locus was significantly higher in the spontaneously cleared HCV infected group (P = 0.03) as well as the healthy control group (P = 0.04) in comparison to the chronic infected participants. In the case of PD-1.5 locus, there was no association between the frequency of inherited genotype or alleles and HCV infection outcome amongst the three groups. Haplotype analysis showed no statistically significant differences in the frequencies of different haplotypes between the three studied groups. Our finding collectively inferred that individuals with A allele at PD-1.3 locus might clear HCV infection more frequently than those with T allele. Instead, polymorphisms at PD-1.5 locus as well as haplotypes emerged from PD-1.3 G/A and PD-1.5 C/T might not be significant in the HCV infection outcome.

Emerge of blaNDM-1 and blaOXA-48-like harboring carbapenem-resistant Klebsiella pneumoniae isolates from hospitalized patients in southwestern Iran

BACKGROUND

One of the most important emerging carbapenem-resistant bacteria is Klebsiella pneumoniae (K. pneumoniae). The present study aimed to investigate the antibiotic susceptibility pattern of K. pneumoniae isolates and detection of carbapenemase producing K. pneumoniae obtained from Iranian hospitalized patients.

METHODS

This cross-sectional study was performed on 211 K. pneumoniae isolates which were recovered from different clinical specimens from 2014 to 2015. Modified Hodge test (MHT) and double disk synergy test (DDST) were done for detection of carbapenemase and metallo-beta-lactamase (MBL) producing K. pneumoniae. The presence of antibiotic resistance determinants was investigated by polymerase chain reaction (PCR) method.

RESULTS

The results of antibiotic susceptibility showed that all isolates were resistant to ampicillin, and then mostly resistant to piperacillin and ceftazidime with 76.3% and 66.8%, respectively. On the other hand, the highest sensitivity was toward polymyxin B, followed by carbapenems. Of 29 carbapenem-resistant isolates, all were high-level imipenem-resistant isolates (Minimum inhibitory concentration ≥4), except 4 isolates. The results of MHT and DDST showed that 93.1% (27/29) of carbapenem-resistant isolates were carbapenemase and MBL producing isolates, respectively. The presence of bla_NDM-1 and bla_OXA-48-like genes was detected in 27 (10.9%) and 2 (0.9%) isolates, respectively.

CONCLUSION

This is the first identification of bla_NDM-1 and bla_OXA-48-like in K. pneumoniae in Southwestern Iran and the highest reported prevalence of bla_NDM in this bacterium from Iran. Since carbapenem-resistant isolates containing New Delhi metallo-beta-lactamase 1 (NDM-1) were almost resistant to all the tested antibiotics, the resistance due to this gene may be increased in the near future as a potential health threat.

A survey of the frequency of cytomegalovirus-associated diarrhea in immunocompromised patients using a non-invasive method

BACKGROUND AND OBJECTIVES

Cytomegalovirus (CMV) infection is the most common viral opportunistic infection causing gastrointestinal diseases such diarrhea and colitis in immunocompromised patients. The development and performance of a robust and sensitive PCR assay are usually evaluated to detect CMV DNA in human fecal specimens. In this study, our aim was to detect CMV DNA in stool samples taken from patients with HIV/AIDS, cancer, and transplant recipient patients with chronic and persistent diarrhea using a non-invasive method.

MATERIALS AND METHODS

A total of 633 immunocompromised patients (451 males and 182 females) suffering from persistent or chronic diarrhea were included in this study. Among them, 392 were HIV/AIDS patients, 151 had cancer and were receiving chemotherapy, and 90 were recipients of a solid organ or bone marrow transplant. CMV genome was extracted from the stool samples using phenol: chloroform: isoamyl alcohol method. CMV DNA was identified by polymerase chain reaction using sequence specific primers on genomic DNA.

RESULTS

Looking at the frequency of CMV DNA in 392 HIV/AIDS patients, we found that only 5 patients (1.27%) were positive for CMV genome, while this frequency was 4.63% (7/151) and 5.5% (5/90) in patients with cancer receiving chemotherapy and in those with solid organ or bone marrow transplant, respectively.

CONCLUSION

The results of this study revealed that the cause of chronic or persistent diarrhea in HIV/AIDS, cancer, and graft recipient patients might be related to CMV infection. Accordingly, we recommend a non-invasive method, such as stool sample, as a first line of diagnosis of enteritis when the physician suspects that a patient has CMV infection.

Almost Complete Lack of Human Cytomegalovirus and Human papillomaviruses Genome in Benign and Malignant Breast Lesions in Shiraz, Southwest of Iran

Breast cancer ranks as the most common cancer among women worldwide. There have been controversial reports regarding contributions of human papillomaviruses (HPVs) and human cytomegalovirus (HCMV) to its development. The aim of this study was to determine the frequency of HPV and HCMV positivity in benign and malignant breast tumors.

Frequency of human parvovirus 4 (PARV4) viremia among HBV-infected patients and healthy donors in Shiraz, Iran

BACKGROUND/AIM

PARV4, a small DNA virus belonging to the family Parvoviridae, was first isolated in an HBV injecting drug user. Several studies have investigated PARV4 co-infection with HBV and HCV and its effect on the progression of liver disease. The aim of this study was to determine the frequency of PARV4 among HBV-infected patients and healthy individuals.

MATERIALS AND METHODS

A group of 90 HBV patients and a group of 90 healthy subjects were included in this study. Samples were selected after screening tests such as HBsAg ELISA, anti-HCV ELISA, and anti-HIV ELISA. Nested-PCRs were conducted to detect the PARV4 genome. Positive samples were then subjected to DNA sequencing.

RESULTS

PARV4 DNA was detected in 4.4% of HBV patients in comparison with 1.1% of healthy individuals (P-value: 0.36). DNA sequencing results revealed that PARV4 in all five positive samples was genotype I.Conclusions: Although this pilot study showed no significant difference between the frequency of PARV4 among HBV patients and healthy donors, further studies with a larger sample size are suggested to determine the association of PARV4 with HBV co-infection and the impact of this virus on the progression of liver disease in patients with hepatitis B.

The possible role of NS3 protease activity of hepatitis C virus on fibrogenesis and miR-122 expression in hepatic stellate cells

The various roles of hepatitis C virus (HCV) NS3 protein in viral pathogenesis are emphasized, especially in the progression of fibrosis and tumors. The levels of miR-122 have been widely accepted as a critical factor in viral pathogenesis and disease progression. However, the possible correlation between miR-122 levels and fibrosis state has been less investigated. Therefore, in this study, plasmids expressing protease competent and protease mutated non-structural proteins 3 (NS3) were transfected into LX-2 cell line. Subsequently, the total RNA was extracted and real-time PCR was performed to measure the expression level of miR-122, collagen type 1 alpha 1 (COL1A1), alpha smooth muscle actin (α-SMA), and tissue inhibitor of metaloproteinase 1 (TIMP-1). Moreover, the transforming growth factor beta (TGF-β) levels in the supernatants of transfected cells were evaluated by ELISA. The gene expression analysis of fibrotic genes and TGF-β cytokine in LX-2 cells showed that protease competent NS3 had a significant fibrogenic impact when compared to protease defective NS3 or GFP control plasmids (P <0.001). The results also demonstrated that the expression of miR-122 was downregulated in both versions of the cells transfected with NS3 plasmids (P <0.01) irrespective of protease function. These results suggested that the protease function of NS3 protein is a crucial factor for the induction of hepatic fibrosis but it doesn't play a complete role in the expression of miR-122.

Analysis of TLR7, SOCS1 and ISG15 immune genes expression in the peripheral blood of responder and non-responder patients with chronic Hepatitis C

AIM

To evaluate the baseline expression of the immune genes in PBMCs of responder and non-responder patients with chronic Hepatitis C.

BACKGROUND

Although the contribution of peripheral blood mononuclear cell (PBMC) gene expression in treatment outcome of hepatitis C virus (HCV) infection is supposed, it has remained to be distinctly delineated. The baseline expression of the immune genes inside PBMCs may reflect the responsiveness status following IFN treatment.

METHODS

Totally, 22 chronic HCV encompasses 10 responders and 12 non-responsive cases enrolled randomly regarding medical records. The PBMCs from the peripheral blood samples were isolated and then incubated for 6 hours in the culture media. The baseline expression of TLR7, SOCS1 and ISG15 was measured by Real time PCR.

RESULTS

The gene expression pattern in PBMCs of both groups showed a similar trend. The expression of SOCS1 and TLR7 genes showed higher levels in non-responder group (P>0.05). The result of ISG15 showed a higher but non-significant expression in the responder group (P>0.05).

CONCLUSION

The similar pattern of TLR7, SOCS1 and ISG15 expression in the responder and non-responder patients indicated their poor discriminating and predictive value in PBMCs sample.