Ali Tahan, Najmaldin Saki, Shirin Azizidoost, Farid Yousefi, Habib Haybar
Background: COVID-19 might worsen preexisting cardiac conditions and cause new heart failure (HF). To appropriately triage and treat patients, an early diagnosis is necessary. Objectives: This study assessed the levels of antibodies immunoglobulin G (IgG) and immunoglobulin M (IgM) required for the coronavirus spike S protein in the serum of individuals with cardiovascular disease (CVD) who developed HF complications from COVID-19. Methods: A total of 104 hospitalized patients with confirmed COVID-19 were equally divided into severe COVID-19 cases with new HF evidence and controls. The levels of IgG and IgM antibodies vs SARS-CoV-2 were measured. The possible correlation of antibody levels with underlying cardiac risk factors was also investigated. Results: It was found that 86% of HF patients and 5% of controls had an IgG level greater than 100 AU/mL (P < 0.05). Ischemic heart disease (IHD) was the most common disease in the patient group, and the highest level of antibodies was also found in this group. Conclusions: Increasing IgG during COVID-19 can be one of the signs of worsening heart disease, which is more prevalent in patients with an underlying IHD and hypertension.
{"title":"COVID-19 as an Aggravator of Cardiovascular Diseases: Increasing Immunoglobulin G, a Valuable Prognostic Factor for Heart Failure","authors":"Ali Tahan, Najmaldin Saki, Shirin Azizidoost, Farid Yousefi, Habib Haybar","doi":"10.5812/jjm-139233","DOIUrl":"https://doi.org/10.5812/jjm-139233","url":null,"abstract":"Background: COVID-19 might worsen preexisting cardiac conditions and cause new heart failure (HF). To appropriately triage and treat patients, an early diagnosis is necessary. Objectives: This study assessed the levels of antibodies immunoglobulin G (IgG) and immunoglobulin M (IgM) required for the coronavirus spike S protein in the serum of individuals with cardiovascular disease (CVD) who developed HF complications from COVID-19. Methods: A total of 104 hospitalized patients with confirmed COVID-19 were equally divided into severe COVID-19 cases with new HF evidence and controls. The levels of IgG and IgM antibodies vs SARS-CoV-2 were measured. The possible correlation of antibody levels with underlying cardiac risk factors was also investigated. Results: It was found that 86% of HF patients and 5% of controls had an IgG level greater than 100 AU/mL (P < 0.05). Ischemic heart disease (IHD) was the most common disease in the patient group, and the highest level of antibodies was also found in this group. Conclusions: Increasing IgG during COVID-19 can be one of the signs of worsening heart disease, which is more prevalent in patients with an underlying IHD and hypertension.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135735401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mastaneh Alinezhadi, M. Arshadi, M. Rasti, N. Neisi, M. Parsanahad
Background: 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. Objectives: This study aims to evaluate the possibility of SARS-CoV-2 replication in peripheral blood mononuclear cells (PBMCs) of hospitalized patients with COVID-19. Methods: 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. Results: 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. Conclusions: 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.
{"title":"Detection of the SARS-CoV-2 Genome in Peripheral Blood Mononuclear Cells of Hospitalized Patients With COVID-19 Infection","authors":"Mastaneh Alinezhadi, M. Arshadi, M. Rasti, N. Neisi, M. Parsanahad","doi":"10.5812/jjm-138125","DOIUrl":"https://doi.org/10.5812/jjm-138125","url":null,"abstract":"Background: 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. Objectives: This study aims to evaluate the possibility of SARS-CoV-2 replication in peripheral blood mononuclear cells (PBMCs) of hospitalized patients with COVID-19. Methods: 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. Results: 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. Conclusions: 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.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":0.6,"publicationDate":"2023-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46209383","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Najmeh Sheikhi, M. Jamalidoust, Arash Letafati, K. Shahzamani, Anahita Sanaei Dashti, G. Talei
Background: 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. Objectives: 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). Methods: 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. Results: 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. Conclusions: 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.
{"title":"Association of IL-10 Gene in Protection Against COVID-19 Disease","authors":"Najmeh Sheikhi, M. Jamalidoust, Arash Letafati, K. Shahzamani, Anahita Sanaei Dashti, G. Talei","doi":"10.5812/jjm-138241","DOIUrl":"https://doi.org/10.5812/jjm-138241","url":null,"abstract":"Background: 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. Objectives: 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). Methods: 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. Results: 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. Conclusions: 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.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":0.6,"publicationDate":"2023-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48112176","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tuğrul Hoşbul, S. Oren, C. Artuk, C. Aydoğan, İrem Unat, S. Şenkal, Gamze İçen, Tugba Fatsa, R. Gumral, F. Şahiner, M. Kızılgun, M. Yavuz
Background: 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. Objectives: We used flow cytometry to determine the relationship between disease severity, lymphocyte subsets distribution, and cytokine level alterations in COVID-19 patients. Methods: 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. Results: 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. Conclusions: 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.
{"title":"Analysis of Immune Profiles Related to Disease Severity in COVID-19 by Flow Cytometry","authors":"Tuğrul Hoşbul, S. Oren, C. Artuk, C. Aydoğan, İrem Unat, S. Şenkal, Gamze İçen, Tugba Fatsa, R. Gumral, F. Şahiner, M. Kızılgun, M. Yavuz","doi":"10.5812/jjm-138835","DOIUrl":"https://doi.org/10.5812/jjm-138835","url":null,"abstract":"Background: 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. Objectives: We used flow cytometry to determine the relationship between disease severity, lymphocyte subsets distribution, and cytokine level alterations in COVID-19 patients. Methods: 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. Results: 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. Conclusions: 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.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":0.6,"publicationDate":"2023-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43003819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. Taha, Amany A Ghazy, A. Almaeen, I. Taher, T. El-Metwally, Mohammad Alayyaf, F. Alrayes, Ahmed Alinad, S. Albulayhid, Abdulrahman D. AlDakhil
Background: 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. Objectives: This is the first study to evaluate the prevalence of anti-HSV-1 immunoglobulin G (IgG) in donated blood in Sakaka, Aljouf, Saudi Arabia. Methods: 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. Results: 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*). Conclusions: 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.
{"title":"Estimation of Seroprevalence of Anti-Herpes Simplex Virus Type-1 IgG Among Healthy Blood Donors in Sakaka City, Aljouf, Saudi Arabia","authors":"A. Taha, Amany A Ghazy, A. Almaeen, I. Taher, T. El-Metwally, Mohammad Alayyaf, F. Alrayes, Ahmed Alinad, S. Albulayhid, Abdulrahman D. AlDakhil","doi":"10.5812/jjm-136606","DOIUrl":"https://doi.org/10.5812/jjm-136606","url":null,"abstract":"Background: 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. Objectives: This is the first study to evaluate the prevalence of anti-HSV-1 immunoglobulin G (IgG) in donated blood in Sakaka, Aljouf, Saudi Arabia. Methods: 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. Results: 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*). Conclusions: 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.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":0.6,"publicationDate":"2023-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46483066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Khoshakhlagh, Arastoo Vojdani, A. Amali, Samaneh Abolbashari, Aida Gholoobi, Z. Meshkat
Background: 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. Objectives: 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. Methods: 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. Results: 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. Conclusions: 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.
{"title":"Evaluation of Viral Respiratory Pathogens Among Patients Initially Tested Negative for SARS-CoV-2","authors":"M. Khoshakhlagh, Arastoo Vojdani, A. Amali, Samaneh Abolbashari, Aida Gholoobi, Z. Meshkat","doi":"10.5812/jjm-136617","DOIUrl":"https://doi.org/10.5812/jjm-136617","url":null,"abstract":"Background: 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. Objectives: 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. Methods: 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. Results: 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. Conclusions: 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.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":0.6,"publicationDate":"2023-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48492590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
W. Shen, Jingjing Sheng, Meng Wang, Xiujiao Xia, Keyu Ling, M. Qian, Zhejiong Wang, P. Du
Background: Candida is the main causative agent of severe mucosal and invasive candidiasis. Different species of Candida have shown varying levels of resistance to antifungal treatments. It is estimated that each 12-hour delay in antifungal treatment is associated with a significant increase in patient mortality and treatment costs. The culture method is regarded as the gold standard for identifying Candida species, but its time-consuming process is a clear disadvantage. Objectives: This study established a method using membrane technology combined with dual-target melting analysis for rapid cultivation and identification of common Candida species. This method is expected to preserve the advantages of the conventional culture method and improve upon its weaknesses while also evaluating the practical application of the method. Methods: A microfiltration membrane-based culture followed by a color indicator method was established to rapidly cultivate Candida cultures. The 5.8S ribosomal DNA region and internal transcribed spacer 2 (ITS2) region were used as target gene regions, for which two sets of primers were employed. Melting analysis following dual-target real-time polymerase chain reaction (PCR) was conducted to distinguish among Candida albicans, C. tropicalis, C. glabrata, and C. krusei. To evaluate its practical application, the method was tested with 72 clinical isolates, and the results were compared with those obtained using the chromogenic culture method and DNA sequencing. Results: Distinctive melting temperatures in the two gene targets were detected among the four common Candida species. The entire process, from cultivation to identification, was completed within 12 hours, about 50% less time than the gold-standard method. The minimum detection limit of Candida species was 10 femtograms. The results of the identification of the clinical isolates were consistent with those of DNA sequencing. Conclusions: The short-term membrane-based cultivation combined with dual-target melting analysis can be used to rapidly, easily, and accurately identify common Candida species, thus reducing the time needed to initiate targeted treatment for patients with severe candidiasis.
{"title":"Development of Short-term Membrane-based Cultivation Combined with Dual-target Melting Analysis for Rapid Differentiation of Common Candida Species","authors":"W. Shen, Jingjing Sheng, Meng Wang, Xiujiao Xia, Keyu Ling, M. Qian, Zhejiong Wang, P. Du","doi":"10.5812/jjm-136710","DOIUrl":"https://doi.org/10.5812/jjm-136710","url":null,"abstract":"Background: Candida is the main causative agent of severe mucosal and invasive candidiasis. Different species of Candida have shown varying levels of resistance to antifungal treatments. It is estimated that each 12-hour delay in antifungal treatment is associated with a significant increase in patient mortality and treatment costs. The culture method is regarded as the gold standard for identifying Candida species, but its time-consuming process is a clear disadvantage. Objectives: This study established a method using membrane technology combined with dual-target melting analysis for rapid cultivation and identification of common Candida species. This method is expected to preserve the advantages of the conventional culture method and improve upon its weaknesses while also evaluating the practical application of the method. Methods: A microfiltration membrane-based culture followed by a color indicator method was established to rapidly cultivate Candida cultures. The 5.8S ribosomal DNA region and internal transcribed spacer 2 (ITS2) region were used as target gene regions, for which two sets of primers were employed. Melting analysis following dual-target real-time polymerase chain reaction (PCR) was conducted to distinguish among Candida albicans, C. tropicalis, C. glabrata, and C. krusei. To evaluate its practical application, the method was tested with 72 clinical isolates, and the results were compared with those obtained using the chromogenic culture method and DNA sequencing. Results: Distinctive melting temperatures in the two gene targets were detected among the four common Candida species. The entire process, from cultivation to identification, was completed within 12 hours, about 50% less time than the gold-standard method. The minimum detection limit of Candida species was 10 femtograms. The results of the identification of the clinical isolates were consistent with those of DNA sequencing. Conclusions: The short-term membrane-based cultivation combined with dual-target melting analysis can be used to rapidly, easily, and accurately identify common Candida species, thus reducing the time needed to initiate targeted treatment for patients with severe candidiasis.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":0.6,"publicationDate":"2023-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43864803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Parastu Satei, S. Fahimirad, E. Ghaznavi-Rad, H. Abtahi
Background: Most Acinetobacter baumannii (A. baumannii) species have become resistant to all common antibiotics. Many antimicrobial peptides (AMPs) have been identified with efficient functions in infection management. E50-52 (UniProtKB: P85148) and Ib-AMP4 (UniProtKB: O24006) AMPs have shown marked antibacterial functions. Objectives: This investigation was designed to produce E50-52 and Ib-AMP4 AMPs through recombinant protein production. Subsequently, the synergistic antimicrobial functions of these two peptides were assessed under in vitro and in vivo circumstances on multidrug-resistant A. baumannii to investigate the antimicrobial effects of Ib-AMP4 and E50-52 AMPs on drug-resistant Acinetobacter. Methods: The gene sequence of E50-52 and Ib-AMP4 AMPs were codon optimized and separately inserted into the pET-32α vector. The recombinant structures were expressed in host bacteria. The antibacterial functions of the individual and combined application of the purified refolded E50-52 and Ib-AMP4 AMPs against multidrug-resistant A. baumannii were evaluated through the time-kill, minimum inhibitory concentration (MIC), growth kinetic assays, and in vivo (mouse body) systemic infection. Results: The minimum concentrations of the produced refolded E50-52 and Ib-AMP4 AMPs against A. baumannii were 0.325 and 0.0625 mg/mL, respectively. Moreover, the checkerboard procedure confirmed the synergic effects of the produced AMPs. The use of E50-52 and Ib-AMP4 AMPs in combination resulted in an over five times reduction in log10 CFU/mL of alive cells during the first 240-min exposure. The antibacterial efficiency of the produced AMPs was confirmed by growth kinetic assays, scanning electron microscopy (SEM) results, and in vivo evaluation tests. The in vivo assay on rats confirmed the significant antibacterial functions of the produced recombinant proteins on A. baumannii systemic infection. Conclusions: The results proved the considerable synergistic antibacterial functions of the produced recombinant Ib-AMP4 and E50-52 AMPs to treat A. baumannii systemic infection effectively.
{"title":"In Vitro and In Vivo Synergistic Antibacterial Functions of the Recombinant Ib-AMP4 and E50-52 Antimicrobial Peptides against Multidrug-Resistant Acinetobacter baumannii","authors":"Parastu Satei, S. Fahimirad, E. Ghaznavi-Rad, H. Abtahi","doi":"10.5812/jjm-136280","DOIUrl":"https://doi.org/10.5812/jjm-136280","url":null,"abstract":"Background: Most Acinetobacter baumannii (A. baumannii) species have become resistant to all common antibiotics. Many antimicrobial peptides (AMPs) have been identified with efficient functions in infection management. E50-52 (UniProtKB: P85148) and Ib-AMP4 (UniProtKB: O24006) AMPs have shown marked antibacterial functions. Objectives: This investigation was designed to produce E50-52 and Ib-AMP4 AMPs through recombinant protein production. Subsequently, the synergistic antimicrobial functions of these two peptides were assessed under in vitro and in vivo circumstances on multidrug-resistant A. baumannii to investigate the antimicrobial effects of Ib-AMP4 and E50-52 AMPs on drug-resistant Acinetobacter. Methods: The gene sequence of E50-52 and Ib-AMP4 AMPs were codon optimized and separately inserted into the pET-32α vector. The recombinant structures were expressed in host bacteria. The antibacterial functions of the individual and combined application of the purified refolded E50-52 and Ib-AMP4 AMPs against multidrug-resistant A. baumannii were evaluated through the time-kill, minimum inhibitory concentration (MIC), growth kinetic assays, and in vivo (mouse body) systemic infection. Results: The minimum concentrations of the produced refolded E50-52 and Ib-AMP4 AMPs against A. baumannii were 0.325 and 0.0625 mg/mL, respectively. Moreover, the checkerboard procedure confirmed the synergic effects of the produced AMPs. The use of E50-52 and Ib-AMP4 AMPs in combination resulted in an over five times reduction in log10 CFU/mL of alive cells during the first 240-min exposure. The antibacterial efficiency of the produced AMPs was confirmed by growth kinetic assays, scanning electron microscopy (SEM) results, and in vivo evaluation tests. The in vivo assay on rats confirmed the significant antibacterial functions of the produced recombinant proteins on A. baumannii systemic infection. Conclusions: The results proved the considerable synergistic antibacterial functions of the produced recombinant Ib-AMP4 and E50-52 AMPs to treat A. baumannii systemic infection effectively.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":0.6,"publicationDate":"2023-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44651283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: Colorectal cancer (CRC) is the third most common cancer worldwide, and its development is influenced by genetic and environmental factors, including the gut microbiota. Recent studies have reported an association between Fusobacterium nucleatum abundance and CRC. Objectives: This study aimed to investigate the abundance of F. nucleatum in CRC and polyp patients and its association with the expression of Chemokine ligand -3(CCL3), Vascular endothelial growth factor (VEGF), and Nuclear factor-kappa B (NF-KB11) genes and the presence of deoxyribonucleic acid (DNA) mutations and polymorphisms in the Kirsten rat sarcoma viral oncogene homolog (KRAS) gene. Methods: A total of 80 biopsy samples were collected from CRC, polyp, and colitis patients. Moreover, F. nucleatum abundance was measured by quantitative polymerase chain reaction (qPCR). The expression of CCL3, VEGF, and NF-KB11 genes was measured by reverse transcription polymerase chain reaction (RT-PCR). Additionally, KRAS gene mutations and polymorphisms were detected by the Mutation Surveyor software (V5.1.2). Results: The results showed that F. nucleatum abundance was significantly higher in CRC and polyp patients than in colitis patients (P < 0.05). The expression of CCL3 and VEGF genes was also significantly higher in F. nucleatum-positive samples (P < 0.05). However, NF-KB11 gene expression was non-significant. F. nucleatum-positive biopsy samples had a higher frequency of KRAS gene mutations and polymorphisms than F. nucleatum-negative CRC patients (odds ratio = 3). Most of the mutations observed in the positive samples were (6144A>AT,31E>E) at exon 2 of the KRAS gene. Conclusions: The study findings suggest that F. nucleatum might play a role in CRC and polyp development and contribute to KRAS gene mutations. Therefore, targeting F. nucleatum in the gut microbiota could be a potential therapeutic strategy for preventing CRC and polyp development.
{"title":"Fusobacterium nucleatum-Mediated Alteration in Expression of VEGF and CCL3 Genes and KRAS Mutation in Colorectal Cancer Patients","authors":"H. J. Taher, F. Kamel","doi":"10.5812/jjm-136914","DOIUrl":"https://doi.org/10.5812/jjm-136914","url":null,"abstract":"Background: Colorectal cancer (CRC) is the third most common cancer worldwide, and its development is influenced by genetic and environmental factors, including the gut microbiota. Recent studies have reported an association between Fusobacterium nucleatum abundance and CRC. Objectives: This study aimed to investigate the abundance of F. nucleatum in CRC and polyp patients and its association with the expression of Chemokine ligand -3(CCL3), Vascular endothelial growth factor (VEGF), and Nuclear factor-kappa B (NF-KB11) genes and the presence of deoxyribonucleic acid (DNA) mutations and polymorphisms in the Kirsten rat sarcoma viral oncogene homolog (KRAS) gene. Methods: A total of 80 biopsy samples were collected from CRC, polyp, and colitis patients. Moreover, F. nucleatum abundance was measured by quantitative polymerase chain reaction (qPCR). The expression of CCL3, VEGF, and NF-KB11 genes was measured by reverse transcription polymerase chain reaction (RT-PCR). Additionally, KRAS gene mutations and polymorphisms were detected by the Mutation Surveyor software (V5.1.2). Results: The results showed that F. nucleatum abundance was significantly higher in CRC and polyp patients than in colitis patients (P < 0.05). The expression of CCL3 and VEGF genes was also significantly higher in F. nucleatum-positive samples (P < 0.05). However, NF-KB11 gene expression was non-significant. F. nucleatum-positive biopsy samples had a higher frequency of KRAS gene mutations and polymorphisms than F. nucleatum-negative CRC patients (odds ratio = 3). Most of the mutations observed in the positive samples were (6144A>AT,31E>E) at exon 2 of the KRAS gene. Conclusions: The study findings suggest that F. nucleatum might play a role in CRC and polyp development and contribute to KRAS gene mutations. Therefore, targeting F. nucleatum in the gut microbiota could be a potential therapeutic strategy for preventing CRC and polyp development.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":0.6,"publicationDate":"2023-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46561793","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: SARS-CoV-2 is a single-stranded RNA virus and a member of a large family of Coronaviruses that are important human pathogens. This virus caused severe acute respiratory syndrome and was initially identified to be transmitted between humans on November 17, 2019. Objectives: To investigate the lineage, mutational patterns, variants, and serotypes of SARS-CoV-2 viruses circulating in the Duhok governorate population and to compare them with those identified in travelers crossing the border from Turkey in order to trace the epidemiological patterns. Methods: Nasopharyngeal swabs were collected from 700 individuals living in Duhok and 700 travelers crossing the border to Duhok-Iraq from Turkey. The subjects were recruited by random sampling and questioned about demographic features and symptoms of upper or lower respiratory tract infections. Exclusion criteria included vaccination with COVID-19 vaccines of any approved previous infection. Samples were subjected to RT-PCR (QIAGEN KIT), and 30 positive samples with the highest viral load (lowest Ct values) were chosen for sequencing of the complete S gene by next-generation sequencing (NGS) (INTERGEN Genetics and Rare Diseases Diagnosis Research and Application Center, Turkey). Three platforms of Nextstrain, GISAID, and PANGO were used to identify variants, clades, and lineages and analyze sequences. Results: Out of 1400 participants, 353 (25.21%) positive samples were identified by RT-PCR, of which 30 representative positive samples (15 from each group: Patients and travelers) were sent for complete sequencing of the S spike gene using NGS. Nineteen samples were successfully sequenced and retrieved, including nine samples from Duhok residents and ten samples from travelers. Nextclade results revealed that 12 samples belonged to the delta strain (Pango lineages: B1.617.2.78, B1.617.2, B1.617.126, and B.1.617.121) distributed among the two groups while 5 omicron (BA.1.1) and 2 alpha (B.1.1.7) strains were found among travelers. A total of 76 mutations, including 52 non-synonymous, 16 synonymous, and 8 deletions, were detected without identifying a unique mutation. Sequencing results were submitted to GISAID, and accession numbers were obtained. A phylogenetic tree was constructed using the sequences obtained from Iraqi and non-Iraqi variants from GISAID. Conclusions: The present research presents a description and observation of the genetic and epigenetic status of SARS-CoV-2 in Iraq based on sequencing results. The study revealed the impact of travels in introducing new variants to the country, including those with mutations in the S1 domain of the spike protein that can enhance viral attachment to receptors.
{"title":"Comparison of Sequencing and Phylogenetic Analysis of SARS-CoV-2 Spike Proteins Extracted from Patients and Travelers in Duhok-Iraq","authors":"Omar Mohammed Younus, A. Parmaksız, A. Goreal","doi":"10.5812/jjm-138053","DOIUrl":"https://doi.org/10.5812/jjm-138053","url":null,"abstract":"Background: SARS-CoV-2 is a single-stranded RNA virus and a member of a large family of Coronaviruses that are important human pathogens. This virus caused severe acute respiratory syndrome and was initially identified to be transmitted between humans on November 17, 2019. Objectives: To investigate the lineage, mutational patterns, variants, and serotypes of SARS-CoV-2 viruses circulating in the Duhok governorate population and to compare them with those identified in travelers crossing the border from Turkey in order to trace the epidemiological patterns. Methods: Nasopharyngeal swabs were collected from 700 individuals living in Duhok and 700 travelers crossing the border to Duhok-Iraq from Turkey. The subjects were recruited by random sampling and questioned about demographic features and symptoms of upper or lower respiratory tract infections. Exclusion criteria included vaccination with COVID-19 vaccines of any approved previous infection. Samples were subjected to RT-PCR (QIAGEN KIT), and 30 positive samples with the highest viral load (lowest Ct values) were chosen for sequencing of the complete S gene by next-generation sequencing (NGS) (INTERGEN Genetics and Rare Diseases Diagnosis Research and Application Center, Turkey). Three platforms of Nextstrain, GISAID, and PANGO were used to identify variants, clades, and lineages and analyze sequences. Results: Out of 1400 participants, 353 (25.21%) positive samples were identified by RT-PCR, of which 30 representative positive samples (15 from each group: Patients and travelers) were sent for complete sequencing of the S spike gene using NGS. Nineteen samples were successfully sequenced and retrieved, including nine samples from Duhok residents and ten samples from travelers. Nextclade results revealed that 12 samples belonged to the delta strain (Pango lineages: B1.617.2.78, B1.617.2, B1.617.126, and B.1.617.121) distributed among the two groups while 5 omicron (BA.1.1) and 2 alpha (B.1.1.7) strains were found among travelers. A total of 76 mutations, including 52 non-synonymous, 16 synonymous, and 8 deletions, were detected without identifying a unique mutation. Sequencing results were submitted to GISAID, and accession numbers were obtained. A phylogenetic tree was constructed using the sequences obtained from Iraqi and non-Iraqi variants from GISAID. Conclusions: The present research presents a description and observation of the genetic and epigenetic status of SARS-CoV-2 in Iraq based on sequencing results. The study revealed the impact of travels in introducing new variants to the country, including those with mutations in the S1 domain of the spike protein that can enhance viral attachment to receptors.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":0.6,"publicationDate":"2023-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41794628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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