Characteristics, outcome, duration of hospitalization, and cycle threshold of patients with COVID-19 referred to four hospitals in Babol City: a multicenter retrospective observational study on the fourth, fifth, and sixth waves.

BACKGROUND: The aim of the present study was to compare the epidemiological patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infections, hospitalizations, deaths, and duration of hospitalization during the fourth, fifth and sixth epidemic waves of coronavirus disease 2019 (COVID-19) in Iran. METHODS: A multicenter retrospective observational study was conducted on hospitalized patients in four hospitals in the Babol district of northern Iran. The study periods were during the fourth, fifth, and sixth waves of the epidemic in Iran, (March 2021 to March 2022). A total of 13,312 patients with suspected COVID-19 were included. Patient demographics, medical history, length of hospital stay, and clinical outcomes were obtained from the hospital information system. Data on the cycle threshold (Ct) and SARS-CoV2 variant were collected for SARS-CoV2-positive cases. RESULTS: The highest number of hospitalized patients was reported during the fifth (Delta) wave (5231; 39.3%), while the lowest number of hospitalized patients was reported during the sixth (Omicron) wave (2143; 16.1%). In total, 6459 (48.5%) out of 13,312 hospitalized patients with suspected COVID-19 had a positive rRT-PCR result. The fifth (Delta) wave had the highest number of SARS-CoV2 rRT-PCR-positive hospitalized patients (3573, 55.3%), while the sixth (Omicron) wave had the lowest number (835, 12.9%). Moreover, 238 (3.7%) patients with laboratory-confirmed COVID-19 died. The hospital mortality rate was 6.8% in the fourth (Alpha) wave, which reduced to 2.7 and 3.5% in the fifth (Delta) and sixth (Omicron) waves, respectively (p < 0.001). CONCLUSIONS: This is the most comprehensive study evaluating the epidemiologic characteristics of laboratory-confirmed SARS-CoV2 cases in Iran during the Alpha, Delta, and Omicron waves. The highest number of SARS-CoV2-positive hospitalized patients was in the fifth wave of COVID-19 (dominance of the Delta variant), while the sixth wave (dominance of the Omicron variant) had the lowest number. Comorbidities were similar, and cardiovascular disease, diabetes, kidney disease, and hypertension were the main risk factors in all waves.

Evaluation of human papillomavirus type 16 viral load and genome physical status in Iranian women with cervical disease.

BACKGROUND: This study examined the viral load and physical status of the human papillomavirus 16 (HPV-16) genome in non-cancerous, precancerous and cancerous cervical lesions. METHODS: Quantitative real-time PCR was performed to determine HPV-16 E2 and E6 viral load in 132 cervical specimens. E2/E6 viral load ratio was used to determine the physical status of HPV-16 genome. RESULTS: E2 gene viral load was a significant (P < 0.001) predicting biomarker in differentiating non-cancerous from precancerous and cancerous samples. E6 gene viral load was significantly different between the groups (P < 0.001). The specificity and sensitivity of E2 and E6 in distinguishing SCC samples were 100% and 95% respectively. CONCLUSION: HPV-16 viral load measured through E2 and E6 genes is a reliable indicator of lesion type.

COVID-19: A trigger of autoimmune diseases.

The SARS-coronavirus-2 (SARS-CoV-2) that causes coronavirus disease 2019 (COVID-19), has spread worldwide and caused a global health emergency. SARS-CoV-2 is a coronaviridae virus that infects target cells by interacting with the plasma membrane-expressed angiotensin-converting enzyme 2 (ACE2) via the S1 component of the S protein. Effective host immune response to SARS-CoV-2 infection, which includes both innate and adaptive immunity, is critical for virus management and elimination. The intensity and outcome of COVID-19 may be related to an overabundance of pro-inflammatory cytokines, which results in a "cytokine storm" and acute respiratory distress syndrome. After SARS-CoV-2 infection, the immune system's hyperactivity and production of autoantibodies may result in autoimmune diseases such as autoimmune hemolytic anemia, autoimmune thrombocytopenia, Guillain-Barré syndrome, vasculitis, multiple sclerosis, pro-thrombotic state, and diffuse coagulopathy, as well as certain autoinflammatory conditions such as Kawasaki disease in children. We have reviewed the association between COVID-19 and autoimmune disorders in this article.

A Large Retrospective Study of Epidemiological Characteristics of COVID-19 Patients in the North of Iran: Association between SARS-CoV-2 RT-PCR Ct Values with Demographic Data.

Objectives: To avoid worsening from mild, moderate, and severe diseases and to reduce mortality, it is necessary to identify the subpopulation that is more vulnerable to the development of COVID-19 unfavorable consequences. This study aims to investigate the demographic information, prevalence rates of common comorbidities among negative and positive real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) patients, and the association between SARS-CoV-2 cycle threshold (Ct) at hospital admission, demographic data, and outcomes of the patients in a large population in Northern Iran. Methods: This large retrospective cross-sectional study was performed from 7 March to 20 December 2020. Demographic data, including gender, age, underlying diseases, clinical outcomes, and Ct values, were obtained from 8,318 cases suspected of COVID-19, who were admitted to four teaching hospitals affiliated to Babol University of Medical Sciences (MUBABOL), in the north of Iran. Results: Since 7 March 2020, the data were collected from 8,318 cases suspected of COVID-19 (48.5% female and 51.5% male) with a mean age of 53 ± 25.3 years. Among 8,318 suspected COVID-19 patients, 3,250 (39.1%) had a positive rRT-PCR result; 1,632 (50.2%) patients were male and 335 (10.3%) patients died during their hospital stay. The distribution of positive rRT-PCR revealed that most patients (464 (75.7%)) had a Ct between 21 and 30 (Group B). Conclusion: Elderly patients, lower Ct, patients having at least one comorbidity, and male cases were significantly associated with increased risk for COVID-19-related mortality. Moreover, mortality was significantly higher in patients with diabetes, kidney disease, and respiratory disease.

Neonatal Outcomes in Pregnant Women Infected with COVID-19 in Babol, North of Iran: A Retrospective Study with Short-Term Follow-Up.

During the coronavirus disease 2019 (COVID-19) pandemic, the number of pregnant women and neonates suffering from COVID-19 increased. However, there is a lack of evidence on clinical characteristics and neonatal outcomes in pregnant women with COVID-19. We evaluated short-term outcomes (4 weeks postdischarge) and symptoms in neonates born to mothers infected with COVID-19. In this retrospective cohort study, we included all neonates born to pregnant women with COVID-19 admitted to Ayatollah Rohani Hospital, Babol, Iran, from February 10 to May 20, 2020. Clinical features, treatments, and neonatal outcomes were measured. Eight neonates were included in the current study. The mean gestational age and birth weight of newborns were 37 ± 3.19 weeks (30₊6-40) and 3077.50 ± 697.64 gr (1720-3900), respectively. Apgar score of the first and fifth minutes in all neonates was ≥8 and ≥9 out of 10, respectively. The most clinical presentations in symptomatic neonates were respiratory distress, tachypnea, vomiting, and feeding intolerance. This manifestation and high levels of serum C-reactive protein (CRP) in three infants are common in neonatal sepsis. The blood culture in all of them was negative. They have been successfully treated with our standard treatment. Our pregnant women showed a pattern of clinical characteristics and laboratory results similar to those described for nonpregnant COVID-19 infection. This study found no evidence of intrauterine or peripartum transmission of COVID-19 from mother to her child. Furthermore, the long-term outcomes of neonates need more study.

Detection of Epstein-Barr virus encoded small RNA genes in oral squamous cell carcinoma and non-cancerous oral cavity samples.

BACKGROUND: Epstein-Barr Virus (EBV) is a human oncogenic virus that can lead to cancer in lymphoid and epithelial cells and is one of the hypothesized causes of oral cavity lesions including oral squamous cell carcinoma (OSCC), but the etiological association remains undetermined. The present investigation aimed to explore the EBV presence, viral load, and EBV-encoded small RNA (EBER) sequence variation in tissue samples of patients with OSCC and other oral cavity lesions including oral lichen planus (OLP), and oral irritation fibroma (OIF). METHODS: In total, 88 oral cavity samples (23 with OSCC, 29 with OLP, and 36 with OIF diagnosis) were examined by Real-Time PCR technique and some of them were sequenced. RESULTS: Viral EBER sequence was detected in 6 out of the 23 OSCC (31.4%), 6 out of the 29 OLP (20.7%), and 3 out of the 36 OIF cases (8.3%). The mean EBV copy number was higher in OSCC samples (1.2 × 10-2 ± 1.3 × 10-2 copies/cell) compared to OLP (2.2 × 10-3 ± 2.6 × 10-3 copies/cell) and OIF (2.4 × 10-4 ± 2.0 × 10-4 copies/cell) samples, although this difference was not statistically significant (P = 0.318). The EBER gene was amplified and sequenced in 5 OSCC, 3 OLP, and 2 OIF samples with high EBV viral load. One OSCC, two OLP, and two OIF isolates showed different nucleotide variations compared with EBV-WT and AG876 prototype sequences: C6834T, C6870T, C6981T, C7085T, C7085G, and C7094T. CONCLUSION: In our study the presence of more than one genome copies per tumor cell indicates the possible role of EBV infection in oral cancers. However, more studies should be conducted to clarify the role of EBV in OSCC carcinogenesis.

Measurement of serum hepatitis B surface antibody levels in Iranian autistic children and evaluation of immunological memory after booster dose injection in comparison with controls.

BACKGROUND: Responsiveness to hepatitis B vaccine among patients with autism spectrum disorders (ASD) has not been evaluated worldwide. We aimed to determine the anti-HBs antibody duration in autistic and healthy children few years after primary vaccination and evaluate their immunological memory against hepatitis B virus (HBV) vaccine with booster dose administration. METHODS: One hundred seven and 147 HBsAg-negative children from ASD and normal population were recruited, respectively. HBV seromarkers (HBc-Ab, HBsAg, and HBs-Ab) were assessed and subsequently, molecular tests were used on all the subjects. A booster dose of vaccine was injected for those who showed low levels (<10 mIU/mL) of anti-HBs and their antibody levels was measured 4 weeks later. RESULTS: The mean ages of ASD and control groups were 7.14 ± 2.42 and 8.68 ± 1.96, respectively. Seven (6.5%) of the ASD group were positive for anti-HBc and one child was positive for occult hepatitis B infection (HBsAg negative, HBV DNA positive). In ASD, 54 (50.4%) and 53 (49.6%) had adequate (>10 mIU/mL) and low anti-HBs levels, respectively. Among control group, 74 (50.4%) and 73 (49.6%) had sufficient and low antibody levels, respectively. After injection of a booster dose for all children with low antibody, 100% of ASD and 92% (59 of 64) of control pupils contained >10 mIU/mL of antibody, respectively. In both the groups, the HBs-Ab titer increased similarly in response to the booster injection (P < 0.05). CONCLUSION: Despite previous investigations regarding immune impairment in individuals with autism, the immune system of these individuals was able to manage the hepatitis B vaccine challenge.

Low viral load of Merkel cell polyomavirus in Iranian patients with head and neck squamous cell carcinoma: Is it clinically important?

Recent studies show that the human Merkel cell polyomavirus (MCPyV) may be involved in causing cancer. The objective of this study was to assess the impact of MCPyV on the development of head and neck squamous cell carcinoma (HNSCC). In total, 50 paraffin-embedded HNSCC biopsy samples and 50 adjacent non-cancerous samples were evaluated for the presence of MCPyV DNA and RNA. Among patients, the five most frequent histopathologic sites were the tongue (22.0%), lip (16.0%), submandibular (14.0%), cheek (14.0%), and throat (14.0%). MCPyV DNA was positive in eight (16.0%) samples. The median MCPyV LT-Ag copy number in the eight positive samples and in one non-cancerous sample was 4.8 × 10-3 and 2.6 × 10-5 copies/cell, respectively. Quantification of MCPyV LT-Ag revealed increased expression in stage III (5.6 × 10-3 copies/cell) than in the other stages. The MCPyV DNA load in different stages of HNSCC was also statistically significant (P = 0.027). The viral load was low, suggesting that only a fraction of cancerous cells is infected. This result provides evidence confirming the presence of MCPyV in a subset of Iranian patients with HNSCCs, but further studies needed to confirm our findings.

Integron types, gene cassettes and antimicrobial resistance profile of Acinetobacter baumannii isolated from BAL samples in Babol, north of Iran.

Multi-drug resistant isolates of Acinetobacter baumannii have created therapeutic problems worldwide. This current study was intended to determine the Integron types, gene cassettes and antimicrobial resistance profile of A. baumannii isolated from BAL samples in Babol, north of Iran. During a 15-month period, 35 A. baumannii isolates were studied. Different classes of antimicrobial agents were used to determine the resistance ratios. Multiplex-PCR was used to detect different types of integrons and associated gene cassettes. The resistance rates to GM, FEP, AK, TOB, CP, PIP, SAM, IPM, SXT, CTX, CAZ, CL, TIM, MEM, and TZP were 85.7%, 100%, 91.4%, 68.5%, 94.3%, 88.5%, 97.1%, 94.3%, 100%, 100%, 100%, 0.0%, 91.4%, 94.3% and 91.4%, respectively. The distribution analysis of int genes showed that 25.7%, 88.6% and 28.6% of isolates carried the intI, intII and intIII genes, respectively. The prevalence of aadB, dfrA1, bla-OXA30 and aadA1 genes were 94.3%, 77.1%, 40% and 5.7%, respectively. The current study showed that a high level of A. baumannii isolates harbor integrons in our therapeutic center, which may lead to distribution of multiple antimicrobial resistance. The different types of gene cassette arrays in the present study highlight the important role of geographical features in MDR isolates dissemination which could be credited to different profiles of drug consumption in different areas. The findings emphasized that the need for continuous surveillance to prevent distribution of multidrug resistance among A. baumannii strains in Iran.

Evaluation of Merkel cell polyomavirus in non-small cell lung cancer and adjacent normal cells.

Several risk factors have been linked to lung cancer (LC). Nevertheless, a viral etiology has been mentioned for a subset of patients developing LC. The aim of this study was to evaluate the effect of Merkel cell polyomavirus (MCPyV) on developing non-small cell lung cancer (NSCLCs). In total, 96 paraffin-embedded NSCLC biopsies and 96 adjacent non-LC normal specimens were analyzed by quantitative real-time polymerase chain reaction (PCR) for the existence of the MCPyV DNA and the expressions of RNA transcripts. Among the 96 enrolled participants, 42 patients were adenocarcinomas (ADs) and 54 patients were squamous cell carcinoma (SCC). Of the 42 ADs, MCPyV DNA was determined in 15 (35.7%) samples and of the 54 SCC, MCPyV DNA was detected in 22 (40.7%) samples. Only one non-cancerous sample in SCC subjects was positive for MCPyV LT-Ag DNA load (0.216 × 10-3). In MCPyV-positive subjects, the median MCPyV copy number was higher in the patients with ADs (0.016 × 10-3 copies/cell) compared to SCCs (0.005 × 10-3 copies/cell); but this difference was not statistically significant (P = 0.913). In the seven stages of LC, the MCPyV LT-Ag was quantified in stage IV (0.204 × 10-3 copies/cell) more than in other stages. There was statistically significant difference between stages of cancer and MCPyV LT-Ag DNA load (P = 0.002). These results revealed for the first time the presence of MCPyV in a subset of patients with NSCLCs in Iran. Further studies should be carried out to clarify the role of MCPyV in lung carcinogenesis.

Identification and antimicrobial resistance of Enterococcus spp. isolated from the river and coastal waters in northern Iran.

As fecal streptococci commonly inhabit the intestinal tract of humans and warm blooded animals, and daily detection of all pathogenic bacteria in coastal water is not practical, thus these bacteria are used to detect the fecal contamination of water. The present study examined the presence and the antibiotic resistance patterns of Enterococcus spp. isolated from the Babolrud River in Babol and coastal waters in Babolsar. Seventy samples of water were collected in various regions of the Babolrud and coastal waters. Isolated bacteria were identified to the species level using standard biochemical tests and PCR technique. In total, 70 Enterococcus spp. were isolated from the Babolrud River and coastal waters of Babolsar. Enterococcus faecalis (68.6%) and Enterococcus faecium (20%) were the most prevalent species. Resistance to chloramphenicol, ciprofloxacin, and tetracyclin was prevalent. The presence of resistant Enterococcus spp. in coastal waters may transmit resistant genes to other bacteria; therefore, swimming in such environments is not suitable.

Demographics, clinical characteristics, and outcomes in hospitalized patients during six waves of COVID­19 in Northern Iran: a large cohort study.

Since the first report of coronavirus disease 2019 (COVID-19) in Iran, our country has experienced several waves of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Northern Iran was one of the most affected regions of the country by COVID-19. In the current study, the demographic and clinical characteristics and outcomes of hospitalized patients were determined over a 2-year period (during six waves of SARS-CoV-2). This is a large cohort study investigating hospitalized patients with suspected and probable, and confirmed SARS-CoV-2 infection in Babol district, northern Iran, during the two years of COVID-19. The study population included patients admitted to four hospitals affiliated with Babol University of Medical Sciences between March 7, 2020 (start of the first wave) and March 20, 2022 (end of the sixth wave). Epidemiological and demographic characteristics, real-time PCR, cycle thresholds, clinical data and outcomes of COVID-19 were analyzed in 24,287 hospitalized patients. A total of 24,287 hospitalized patients were included in the study: 13,250 (46.6%) patients were suspected of having COVID-19, 11037(45.4%) were confirmed COVID-19 cases. The mean age of confirmed COVID-19 patients was 54.5 ± 18.9 years and 5961 (54%) were female. The median length of hospitalization for COVID-19 survivors and non-survivors was 5 (interquartile range [IQR] 4-8) and 7 (IQR 3-15) days, respectively. Of the patients with confirmed COVID-19, 714 (6.5%) died during hospitalization. In addition, the mortality rate from the first to the sixth wave was 22.9%, 8.1%, 9.9%, 6.8%, 2.7% and 3.5% in confirmed COVID-19 patients. The patients in the fifth wave were significantly younger than the others (mean age and SD of 51.1 ± 17.4 versus 59.2 ± 16.9, 54.7 ± 19.9, 58.4 ± 17.9, 53.5 ± 16.8 and 58.5 ± 25.1 years; p<0.001). The highest in-hospital mortality rate was 22.9% (126/551) in the first wave and the lowest in the fifth wave was 2.7% (96/3573) of cases. In conclusion, in the present study, the in-hospital mortality rate was 6.5% and more than half of the deceased patients were ≥65 years old. Male gender, advanced age and comorbidities significantly increased the mortality rate. The patients in the fifth wave were significantly younger than those in the other waves, and the lowest mortality rate and intensive care unit admission were also observed in the fifth wave.

Critical involvement of circular RNAs in virus-associated cancers.

Virus-related cancer is cancer where viral infection leads to the malignant transformation of the host's infected cells. Seven viruses (e.g., human papillomavirus (HPV), Epstein-Barr virus (EBV), Kaposi's sarcoma herpesvirus (KSHV), Hepatitis B virus (HBV), Hepatitis C virus (HCV), Human T-lymphotropic virus (HTLV), and Merkel cell polyomavirus (MCV)) that infect humans have been identified as an oncogene and have been associated with several human malignancies. Recently, growing attention has been attracted to exploring the pathogenesis of virus-related cancers. One of the most mysterious molecules involved in carcinogenesis and progression of virus-related cancers is circular RNAs (circRNA). These emerging non-coding RNAs (ncRNAs), due to the absence of 5' and 3' ends, have high stability than linear RNAs and are found in some species across the eukaryotic organisms. Compelling evidence has revealed that viruses also encode a repertoire of circRNAs, as well as dysregulation of these viral circRNAs play a critical role in the pathogenesis and progression of different types of virus-related cancers. Therefore, understanding the exact role and function of the virally encoded circRNAs with virus-associated cancers will open a new road for increasing our knowledge about the RNA world. Hence, in this review, we will focus on emerging roles of virus-encoded circRNAs in multiple cancers, including cervical cancer, gastric cancer, Merkel cell carcinoma, nasopharyngeal carcinoma, Kaposi cancer, and liver cancer.

EBV and HPV Infections in Colorectal Cancer and Their Effect on P53 and P16 Protein Expression.

Viral infections contribute to 15-20% of newly diagnosed cancers worldwide. There is evidence of a possible etiological role of Epstein-Barr virus (EBV) and high-risk human papillomaviruses (HR-HPVs) in colorectal carcinoma (CRC). Loss of p53 and p16 function has been found in many cancers and this may occur in many different ways, including gene mutation or interaction with viral oncoproteins. This study aimed to evaluate the presence of EBV and HPV in CRC patients in northern Iran and to assess p53 and p16 protein expression related to these viral infections. Real-time PCR was used to amplify the DNA sequences of these viruses in 55 colorectal tumoral tissues, along with their corresponding non-tumoral adjacent tissues. Additionally, immunohistochemistry (IHC) was utilized to determine p53 and p16 protein expression. EBV DNA was detected in 49.1% of CRC tissues. Furthermore, HPV DNA was present in 7.3% of CRC tissues. Notably, the prevalence of EBV infection in tumoral tissues was significantly higher than in non-tumoral tissues (P=0.001). The EBV DNA polymerase catalytic subunit (BALF5) copy number in tumoral tissues was higher than in non-tumoral tissues and this difference was statistically significant (P=0.008). P53 was positive in 21/26 (80.8%) EBV-positive and in 11/25 (44%) EBV-negative samples and this difference was significant (P=0.007). P16 was positive in 13/26 (50%) EBV-positive and in 14/25 (58.3%) EBV-negative samples (P= 0.668). Our findings suggest that EBV infection can increase the risk of CRC. In addition, EBV seems to stabilize p53 in EBV-positive CRC which needs further research. No significant correlation was detected between EBV infection and p16 expression. Also, we could not find a causal relationship between HPV infection and CRC in the study population.

A Multiple-Center, Retrospective Study of Characteristics and Outcomes of Hospitalized COVID-19 Patients with Cardiovascular Disease in North Iran.

Background: In this retrospective study, we investigated the outcomes and demographic characteristics of COVID-19 patients with and without a history of CVD. Methods: This large retrospective, multicenter study was performed on inpatients with suspected COVID-19 pneumonia who were admitted across four hospitals in Babol, Northern Iran.Demographic data, clinical data, and cycle threshold value (Ct) results of Real Time PCR were obtained. Then, participants were divided into two groups: (1) cases with CVDs, (2) cases without CVDs. Results: A total of 11097 suspected COVID-19 cases with a mean ± SD age of 53 ±25.3 (range: 0 to 99) years were involved in the present study. Out of whom 4599 (41.4%) had a positive RT-PCR result. Of those, 1558 (33.9%) had underlying CVD. Patients with CVD had significantly more co-morbidities such as hypertension, kidney disease, and diabetes. Moreover, 187 (12%) and 281 (9.2%) of patients with and without CVD died, respectively. Also, mortality rate was significantly high among the three groups of Ct value in patients with CVD, with the highest mortality in those with Ct between 10 and 20 (Group A = 19.9%). Conclusions: In summary, our results highlight that CVD is a major risk factor for hospitalization and the severe consequences of COVID-19. Death in CVD group is significantly higher compared to non-CVD. In addition, the results show that age-related diseases can be a serious risk factor for the severe consequences of COVID-19.

Implementation of an In-House Platform for Rapid Screening of SARS-CoV-2 Genome Variations.

BACKGROUND: Global real-time monitoring of SARS-CoV-2 variants is crucial to controlling the COVID-19 outbreak. The purpose of this study was to set up a Sanger-based platform for massive SARS-CoV-2 variant tracking in laboratories in low-resource settings. METHODS: We used nested RT-PCR assay, Sanger sequencing and lineage assignment for 930-bp of the SARS-CoV-2 spike gene, which harbors specific variants of concern (VOCs) mutations. We set up our platform by comparing its results with whole genome sequencing (WGS) data on 137 SARS-CoV-2 positive samples. Then, we applied it on 1028 samples from March-September 2021. RESULTS: In total, 125 out of 137 samples showed 91.24% concordance in mutation detection. In lineage assignment, 123 out of 137 samples demonstrated 89.78% concordance, 65 of which were assigned as VOCs and showed 100% concordance. Of 1028 samples screened by our in-house method, 78 distinct mutations were detected. The most common mutations were: S:D614G (21.91%), S:P681R (12.19%), S:L452R (12.15%), S:T478K (12.15%), S:N501Y (8.91%), S:A570D (8.89%), S:P681H (8.89%), S:T716I (8.74%), S:L699I (3.50%) and S:S477N (0.28%). Of 1028 samples, 980 were attributed as VOCs, which include the Delta (B.1.617.2) and Alpha (B.1.1.7) variants. CONCLUSION: Our proposed in-house Sanger-based assay for SARS-CoV-2 lineage assignment is an accessible strategy in countries with poor infrastructure facilities. It can be applied in the rapid tracking of SARS-CoV-2 VOCs in the SARS-CoV-2 pandemic.

High prevalence of occult hepatitis B virus infection in children born to HBsAg-positive mothers despite prophylaxis with hepatitis B vaccination and HBIG.

BACKGROUND & AIMS: Occult hepatitis B virus (HBV) infection is a well-recognized clinical entity characterized by the detection of HBV DNA in serum and/or liver in the absence of detectable hepatitis B surface antigen (HBsAg). The frequency of the diagnosis depends on the relative sensitivity of both HBsAg and HBV DNA assays. We aimed at determining the prevalence of occult HBV infection in a high risk group of children who developed HBV infection despite immunoprophylaxis. METHODS: The sera of 75 children born to HBsAg-positive mothers previously immunized by HBIG and prophylaxic vaccine regimen were assayed for HBV DNA by real-time PCR. Subsequently, the samples were tested using a sensitive standard PCR, with an independent set of primers for all HBV genes, and analyzed by direct sequencing. RESULTS: HBV DNA was detected in 21/75 (28%) children, and ranged between 77 and 9240 copies/ml. All were positive for anti-HBs. Five (24%) children were found to be positive for anti-HBc, while anti-HBc-only positive individuals were not observed. Eight isolates (38%) did not carry any mutation. Thirteen infected children (62%) had at least one mutation in regions known to be involved in functional and/or immune epitope activity. Ten had G145R mutations. CONCLUSIONS: HBV occult infection seems to be relatively frequent in immunized children born to HBsAg-positive mothers. HBsAg negativity is not sufficient to completely exclude HBV DNA presence. These findings emphasize the importance of considering occult HBV infection in hypo-endemic areas.

Prevalence of Co-infection by Human Papillomavirus, Epstein- Barr Virus and Merkel Cell Polyomavirus in Iranian Oral Cavity Cancer and Pre-malignant Lesions.

Human papillomavirus (HPV) is recognized as the most important risk factor in oral cavity cancer and pre-malignant lesions; however, the etiological association of concomitant infection with other oncogenic viruses as a co-factor has not been definitively proven. The present study aimed to determine the prevalence of co-infection with HPV, Epstein-Barr virus (EBV) and Merkel Cell PolyomaVirus (MCPyV) in oral cavity lesions in Iranian patients. One hundred and fourteen oral cavity samples, including 33 oral squamous cell carcinoma, 28 oral lichen planus, 16 oral epithelial dysplasia and 37 oral irritation fibromas were analyzed for the HPV, EBV and MCPyV infection by quantitative real-time PCR. According to histological features 32.5% and 28.9% of cases were oral irritation fibroma and oral squamous cell carcinoma, respectively. Infection with at least two viruses was detected in 21.1% of patients. In this group, co-infection with HPV/EBV was identified in 37.5% of cases, HPV/MCPyV in 29.2%, EBV/MCPyV in 12.5%, and HPV/EBV/MCPyV in 20.8%. There was no statistically significant difference between multiple infections and anatomical locations of cancer. The prevalence of triple viral infection (HPV/EBV/MCPyV) in well differentiated tumors was higher than EBV or MCPyV single infection. This study revealed that co-infection of HPV, EBV and MCPyV can be detected in both malignant and non-malignant oral cavity tissues, and co-infection with all three viruses in well differentiated tumors can be shown as a synergistic hypothesis of the pathogenic role of these viruses in oral malignant transformation.

Detection of human adenovirus among Iranian pediatric hospitalized patients suspected of COVID-19: epidemiology and comparison of clinical features.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in children typically results in similar symptoms with other viral respiratory agents including human adenoviruses (HAdVs). Mixed HAdV and SARS-CoV-2 infection (co-infection) in children might result in enhanced or reduced disease severity compared with single infections. The present study aims to investigate the rate of SARS-CoV2 and HAdV infection and also their coinfection and compare the two infections regarding their laboratory and clinical characteristics at hospital admission. A total of 360 combined oropharyngeal and nasopharyngeal swab samples from hospitalized children were examined by real-time PCR for the existence of the SARS-CoV-2 and HAdVs. The symptoms, the clinical characteristics and laboratory findings were retrieved and compared in SARS-CoV-2 and HAdVs positive cases. Of the total 360 suspected COVID-19 hospitalized children, 45 (12.5%) and 19 (5.3%) specimens were PCR-positive for SARS-CoV-2 and HAdV respectively. SARS-CoV-2 and HAdV co-infection was detected in 4 cases (1.1%). Regarding symptoms at hospital admission, fever in SARS-CoV-2 positive group was significantly higher than that in HAdV positive group [34 (85%) vs. 7 (46.7%), p = 0.012]. However, percentages of cases with sore throat, headache, fatigue, lymphadenopathy and conjunctivitis in HAdV positive group were significantly higher than those in SARS-CoV-2 positive group. SARS-CoV-2 and HAdV co-infected children showed mild respiratory symptoms. The present study revealed that SARS-CoV-2 positive children often appear to have a milder clinical course than children with respiratory HAdV infection and children co-infected with SARSCoV-2 and HAdV had less-severe disease on presentation.

Quantitative analysis of Merkel cell polyomavirus (MCPyV) genome in non-melanoma skin cancer and normal tumor margins.

Merkel cell polyomavirus (MCPyV) is the cause of approximately 80% of Merkel cell carcinomas (MCC). The common types of non-melanoma skin cancer (NMSC) including squamous cell carcinoma (SCC) and basal cell carcinoma (BCC) are histologically similar to MCC. In the present study, 58 NMSC formalin-fixed paraffin-embedded tissue (FFPE) samples including 12 SCC, 46 BCC, and 58 FFPE samples of adjacent non-tumoral margins as the control were included. Determination of large tumor antigens (LTAg) copy number was performed by qReal-Time PCR as a viral copy number per cell to elucidate MCPyV carcinogenic role in non-melanoma skin cancer. Out of 58 samples, 36 (62%) cancerous and 22 (37.9%) normal tumor margins were positive for MCPyV LTAg. Median copy numbers of MCPyV LTAg among all NMSC samples and non-tumoral margins were 0.308×10-2 and 0.269×10-3 copies per cell respectively (P=0.001). In addition, although the viral load in the majority of samples was detected to be lower than one copy per cell, in 4 BCC samples, a viral load higher than one LTAg copy per cell was detected. The present study revealed that the detection of higher levels of MCPyV LTAg viral load in some BCC and SCC samples may be correlated with the role of MCPyV in some cases of BCC and SCC skin cancer.