Jundishapur Journal of Microbiology
Volume:16 Issue: 7, Jul 2023

 A number of ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) viruses commonly circulating among vertebrates, such as influenza H1N1, respiratory syncytial virus (RSV), adenoviruses, and human coronavirus (HCoV)-229E, cause symptoms similar to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). These viruses are important causes of cold, pneumonia, and shortness of breath in humans, which have been overlooked during the coronavirus disease 2019 (COVID-19) pandemic. Furthermore, the diagnosis of infection with these viruses mostly relies on physical examination and clinical history, despite the fact that accurate molecular diagnosis is available.

 This study aimed to evaluate the presence of respiratory viruses in patients who were suspected to be infected with COVID-19 yet initially tested negative for SARS-CoV-2, as it could be beneficial in developing effective control measures and more reliable testing and surveillance of such viruses.

 In this study, laboratory samples of 123 patients referred to Ghaem Hospital of Mashhad, Iran, were evaluated that tested negative for SARS-CoV-2 in the initial assessment while showing the clinical symptoms of COVID-19. Initial testing for SARS-CoV-2 was carried out by the TaqMan real-time polymerase chain reaction (PCR) method using a kit approved by the Ministry of Health (Pishtaz Teb, Iran). Further analysis for the presence of 17 respiratory viruses was carried out using Genova kits based on the virus genome conserved sequences of influenza H1N1, influenza B, influenza A, SARS-CoV-2, HCoV-HKU1, HCoV-OC43, HCoV-NL63, HCoV-229E, metapneumovirus, RSV, human bocavirus 1, 2, 3, parainfluenza 1, 2, 3, and adenovirus.

 According to the results of the present evaluations, out of 123 samples that were acquired using nasal and throat swabs and that initially tested negative for SARS-CoV-2, 8 cases of influenza A (47.1%), 1 case of parainfluenza (5.9%), 1 case of HKU1/OC-43 (5.9%), 4 cases of RSV (23.5%), 1 case of HCoV-NL63/HCoV-229-E (5.9%), and 2 cases of SARS-CoV-2 (11.8%) were detected.

 Based on the results of real-time PCR tests obtained from patients who had clinical symptoms of SARS-CoV-2 infections, it can be mentioned that due to the similar symptoms of patients with respiratory viral infections, individuals with respiratory symptoms could be examined for other viral infections in addition to SARS-CoV-2 infection, and a suitable basis for their prevalence in the community could be provided.

 More than 768 million people have been affected by COVID-19. Identifying lymphocyte subsets and cytokine level abnormalities in COVID-19 patients is essential to gain new insights and data on immunity mechanisms against viral infections.

 We used flow cytometry to determine the relationship between disease severity, lymphocyte subsets distribution, and cytokine level alterations in COVID-19 patients.

 Totally 94 COVID-19 patients (32 mild, 31 moderate, and 31 severe) and 27 healthy individuals were included in the cross-sectional study. The distribution of peripheral lymphocyte subsets and cytokine levels was assessed by flow cytometry.

 The percentages of CD56+ Natural Killer (NK) cells in all patient groups and total T lymphocytes in moderate and severe groups were significantly lower than those in the control group (P < 0.001). Also, IL-2 (P < 0.001), IL-17A (P < 0.001), IL-4 (P < 0.001), IL-6 (P < 0.001), TNF-α (P = 0.004), IP-10 (P < 0.001), IFN-λ1 (IL-29) (P < 0.001), IFN-λ2/3 (IL-28A/B) (P = 0.011), IFN-β (P < 0.001), IL-10 (P < 0.001), and IFN-γ (P < 0.001) levels were statistically higher in patients than in the controls.

 Our data revealed that increased levels of certain cytokines in peripheral blood contribute to disease severity. Increased CRP (OR: 1.012, %95 CI: 1.002 - 1.023, P = 0.038) and IL-10 (OR: 1.068, %95 CI: 1.000 - 1.141, P = 0.049) levels, decreased CD56+ NK percentage (OR: 0.576, %95 CI: 0.376 - 0.882, P = 0.011) and lymphocyte count (OR: 0.02, %95 CI: 0.001 - 0.368, P = 0.009), and the presence of diabetes mellitus and mechanical ventilation were independent predictors of mortality.

 The medical community is facing a new challenge with the coronavirus disease 2019 (COVID-19) pandemic, as the severity of the disease is largely determined by the overexpression of proinflammatory cytokines, leading to endothelial dysfunction and organ damage, especially in the lungs.

 It is believed that mutations might be linked to severe illness. This cross-sectional study aimed to explore the correlation between COVID-19 severity in Iranian pediatric patients who were referred to Namazi Hospital (Shiraz, Iran) and interleukin 10 (IL-10) gene polymorphisms (rs1800896, rs1800871, and rs1800872).

 The study comprised 53 pediatric patients with COVID-19, who were divided into mild/moderate (n = 44) and severe (n = 9) groups. Nasal swabs and whole blood samples were collected from each patient who participated in the study. Real-time polymerase chain reaction (PCR) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) confirmation (E, RdRp) and PCR-restriction fragment length polymorphism (RFLP) were used for IL-10 gene polymorphism genotyping.

 The study investigated the association between IL-10 gene polymorphisms and COVID-19 severity in pediatric patients. The results showed that the GA genotype at the IL10-1082 locus was protective against severe symptoms and that all severe cases were male with the AA/GA genotype. The other two loci, IL10-819 and IL-10-592, did not show any significant association with COVID-19 severity. The study also showed that shortness of breath was the only symptom significantly associated with COVID-19 severity and that age and gender did not affect the disease outcome.

 The most common symptoms in the mild/moderate group were cough and fever; however, shortness of breath and cough were the most common in the severe group. Coronavirus disease 2019 severity is related to the IL-10 (rs1800872) gene polymorphism, with the GA genotype providing protective effects.

 Herpes simplex virus type-1 (HSV-1) is a highly infectious neurotropic virus. The data on HSV-1 infection in Saudi Arabia, including the seroprevalence of HSV-1 antibodies, are scarce.

 This is the first study to evaluate the prevalence of anti-HSV-1 immunoglobulin G (IgG) in donated blood in Sakaka, Aljouf, Saudi Arabia.

 A total of 300 donated blood samples were collected from the Blood Bank of Prince Mutaib Bin Abdulaziz Hospital in Sakaka. Sensitive and specific enzyme-linked immunosorbent assay (ELISA) was used to detect anti-HSV-1 IgG. A comparison of the age, gender, education, occupation, income, hand hygiene, travel history, and cupping practice of blood donors stratified for the extent of anti-HSV-1 IgG was made.

 There was a low prevalence of anti-HSV-1 IgG (20%; n = 60/300). Moreover, 50.0% of IgG-positive participants were in the age group of 41 - 45 years, and 81.7% of the participants had a household income of < 10000 SAR (statistically highly significant; P < 0.001*). All the participants performed hand washing with soap before handling food and after using the toilet. Furthermore, IgG-positive participants had a bachelor’s degree (50.0%), were governmental employees (60.0%), were international travelers (50.0%), and practiced cupping (50.0%) with statistically significant associations (P < 0.05*).

 The current study’s findings support previous reports about the key importance of improving socioeconomic conditions and hygiene measures in reducing the spread of HSV-1. The present study provides an alarm regarding reaching the age of sexual debut without acquiring protective anti-HSV-1 immunoglobulins, consequently becoming more susceptible to acquiring HSV-1 infection through the genital route. These data support the urgent need to develop an effective anti-HSV-1 vaccine.

 Since the beginning of the recent pandemic in December 2019, the growing waves of SARS-CoV-2 infection have been a major concern. Also, SARS-CoV-2 itself is increasingly developing during the pandemic. The development of a virus leads to emergent mutations and might change the virus-host interaction.

 The current study was conducted to investigate the prevalence of the circulating lineage of SARS-CoV-2 in Iranian COVID-19 patients.

In a cross-sectional study, nasopharyngeal samples of 83 SARS-CoV-2 positive patients, collected between December 2020 to May 2021 from multiple geographical locations in Iran, were studied. The nasopharyngeal samples were used for RNA extraction, and the extracted RNA was used for one-step RT-PCR analysis. Also, a specific primer pair for the spike was used for the amplification and sequencing via Sanger sequencing.

 Our findings revealed a high prevalence of the B 1.1.7 lineage of the SARS-CoV-2 variant after February 2020 in Iranian COVID-19 patients. The results showed some rare mutations, including M177I, I100C, I100T, L452R, N679K, Q173H, Y145H, A222V, and H49Y in evaluated samples.

 As a preliminary multicenter study in Iran, our study indicated the dominancy of the B 1.1.7 lineage in Iranian COVID-19 patients after February 2020 in all the evaluated provinces. Furthermore, 11 isolates represented deletion mutations in positions 209-211 of the Spike protein, similar to the Omicron (21K) variant (211 del only reported in the Omicron 21K clade). Follow-up studies are recommended for more comprehensive results.

 Evaluation of viral pathogenicity is an important part of research in every viral disease, and one of the most important parts of pathogenicity is cell and tissue tropism of viruses, which can help us to have a clear picture of the viral replication cycle and viral disease.

 This study aims to evaluate the possibility of SARS-CoV-2 replication in peripheral blood mononuclear cells (PBMCs) of hospitalized patients with COVID-19.

 Twenty-six whole blood samples (5 mL) were collected from 70 hospitalized patients infected with SARS-CoV-2. Plasma and PBMCs were collected and subjected to total RNA extraction using the alcohol-chloroform precipitation method by the RNX solution. After complementary DNA (cDNA) synthesis, all samples were subjected to real-time and nested polymerase chain reactions (PCRs) to detect the viral genome.

 The nested PCR method showed a higher rate of positivity in plasma samples (42.3%) compared to real-time PCR (30.7%), suggesting nested PCR exhibited better sensitivity. This rate in PBMC samples was 57.7% by nested PCR and 7.7% by real-time PCR. Minus-strand viral genome was detected in PBMCs, demonstrating that these cells can support virus replication and act as a virus transporter through blood.

 PBMCs can be infected with SARS-CoV-2. Plasma and serum samples are also not useful samples for virus detection because all of the positive plasma samples in this study showed low viral load with a low cycle threshold (Ct) value.