Pasteur Institute of Iran

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Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive-sense single-strand RNA virus belonging to the Coronaviridae family, responsible for coronavirus infectious disease 2019 (COVID-19) with the rapid transmission. This study aimed to characterize and compare SARS-CoV-2 and SARS-CoV major viral proteins and predict antigen proteasomal cleavage patterns, MHC class I processing and presentation, and B T-cell and anti-inflammatory epitopes. Methods: The amino acid sequences of spike surface (S) glycoprotein, membrane (M) glycoprotein, envelop (E) protein, and nucleocapsid (N) phosphoprotein was obtained from NCBI. The sequences were aligned by MEGA 7.0 and modeled by SWISS-MODEL. The proteasomal cleavage pattern, MHC class I processing, and T-cell epitopes were predicted via IEDB analysis and EPISOFT. The B-cell epitopes were predicted by BepiPred 2.0. Also, the prediction of anti-inflammatory epitopes was performed by AntiInflam. Results: Two major antigen proteins, S glycoprotein and M glycoprotein of SARS-CoV-2, respectively, showed 26.57% and 20.59% less efficiency in proteasomal cleavage and presentation to MHC class I, comparing SARS-CoV. There were fewer B-cell predicted epitopes in SARS-CoV-2, comparing SARS-CoV. The anti-inflammatory properties of SARS-CoV-2 S glycoprotein and N protein were higher than SARS-CoV. Conclusion: It seems that the evolution of SARS-CoV-2 is on the way to reducing antigen-presenting to MHC class I and escaping cellular immunity. Moreover, the predicted hotspot epitopes potentially can be used to induce adaptive cellular immunity against SARS-CoV-2. Besides, SARS-CoV-2 appears to be less immunopathogenic than SARS-CoV due to its higher anti-inflammatory proteins.

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Introduction: The angiotensin-converting enzyme 2 (ACE2) is the effective primary receptor for SARS-CoV-2. The interaction between ACE2 and the spike protein of the virus is the crucial step for virus entry into the target cells. ACE2 receptor can be blocked by neutralizing antibodies (nAbs) such as CR3022 which targets the virus receptor-binding site. Enhancing the binding affinity between CR3022 and ACE2 would lead to a more efficient blockade of virus entry. Methods:  In this regard, the amino acids with central roles in the binding affinity of CR3022 antibody to spike protein were substituted. The best mutations to increase the affinity of antibodies were also selected based on protein-protein docking and molecular dynamics simulations. Result: The variants 45 (H:30I/G, H:55D/F, H: 103S/Y, L:59T/F, L:98Y/A), 60(H:31T/D, H:55D/E,  H:103S/Y, L:59T/D, L:98Y/F), 67(H:30I/G, H:55D/F, H:103S/Y, L:56 W/L, L:59T/Y, L:61E/G), 69(H:31T/D,  H:55D/F,   H:103S/Y, L:59T/F, L:98Y/A), and 71(H: 31T/D, H:55D/F, H:103S/Y) with respective binding affinities of -167.3, -167.5, -161.6, -173.0, and -169.8 Kcal/mol had higher binding affinities against the RBD of the SARS-CoV2 spike protein compared to the wild-type Ab. Conclusion: The engineered antibodies with higher binding affinities against the target protein can improve specificity and sensitivity. Thus, a more successful blockade of the ACE2 is achieved, resulting in a better therapeutic outcome. In silico studies can pave the way for designing these engineered molecules avoiding the economic and ethical challenges.
 

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The coronavirus infectious disease-2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has become a severe global health challenge. The primary target for this virus is the lung. However, SARS-CoV-2 can also attack other organs, including the kidney and liver.  Some COVID-19 case reports demonstrated elevated liver enzymes such as aspartate aminotransferase (AST), alanine aminotransferase (ALT), and total bilirubin. Indeed, higher levels of liver enzymes occur in severe cases compared with mild to moderate cases. The relationship between liver injury and COVID-19 might be due to various possible reasons such as reactivation of pre-existing liver disease, viral replication in hepatic cells causing direct cytotoxicity, liver ischemia and hypoxia, cytokine storm, and drug-induced liver injury (DILI). Thus, hepatitis prevention and care services are necessary during the COVID-19 pandemic. For instance, drugs that might reactivate hepatitis B should not be prescribed for treating COVID-19. Generally, the long-term effects of SARS-CoV-2 on human health and various organs are not well understood. This review briefly discusses the relationship between SARS-CoV-2 and liver injury (hepatitis), coinfection of hepatitis and COVID-19, and SARS-CoV-2 infection in autoimmune hepatitis.

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Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spilled over to humans via wild mammals, entering the host cell using angiotensin-converting enzyme 2 (ACE2) as receptor through Spike (S) protein binding. While SARS-CoV-2 became fully adapted to humans and globally spread, some mammal species were infected back. The present study evaluated the potential risk of mammals becoming hosts for SARS-CoV-2 through bioinformatics prediction based on ACE2 receptors. Methods: We used evolutionary bioinformatic approaches and comparative analysis of ACE2 critical residues that bind SARS-CoV-2 S-protein and predicted potential SARS-CoV-2 hosts among mammals and assessed their risk. Results: ACE2 phylogenetic tree placed primates close to rodents and rabbits. Felines, rodents, and rabbits had higher ACE2 similarities than human ACE2 (hACE2). Farmed animals, such as bovids, swine, and equids, had similar ACE2 compared to hACE2; however, these animals showed low SARS-CoV-2 susceptibility. Some cetaceans also presented high similarities in ACE2 key residues with hACE2. Conclusion: Here, we showed wild and domestic mammals with a low divergence of ACE2 compared to humans, discussing their possible chance of being infected, especially those animals kept as livestock or pets. Regarding the feasible transmission through contaminated water, cetaceans can be at risk of SARS-CoV-2 infection. Extensive surveillance of SARS-CoV-2 should be applied to prevent new coronavirus outbreaks and preserve mammals from infectious threats.

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In the SARS-CoV-2 pandemic, the seasonal viral respiratory infections had a minimum prevalence due to public health precautions to reduce the risk of getting Coronavirus Disease 19 (COVID-19). There have been reports of COVID-19 coinfection with influenza, respiratory syncytial virus (RSV), and seasonal coronaviruses during the pandemic. Here, we report a case in which the patient had sequential respiratory infections of human coronavirus HKU1 (HCoV-HKU1) and SARS-CoV-2 in a fully vaccinated, healthy person. It should be noted that other seasonal coronaviruses that could cause symptomatic RTIs might be misdiagnosed clinically with COVID-19. Hence, we highly recommend monitoring and follow-up of symptomatic patients with negative SARS-COV-2 RT-PCR results.
 

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Introduction: In Sub-Saharan Africa, the data on the mutations and variants of circulating SARS-CoV-2 is limited. This study aimed to screen specific mutations and variants of SARS-CoV-2 circulating in Burkina Faso. Methods: This study included symptomatic and asymptomatic individuals who underwent diagnostic testing for SARS-CoV-2 by RT-PCR on nasopharyngeal and oropharyngeal swabs from 7 December 2021 to 12 January 2022. Samples from individuals with a Ct value ≤ 33 were selected for the variants-specific mutation screening. The screening was performed using two kits, “SNPsig^® SARS-COV-2 (Escape PLEX)" and "SNPsig® VariPLEX™ (COVID-19) Real-Time PCR Assay". Results: SARS-CoV-2 prevalence was 18.9% (332/1758). A total of 113 samples (34.04%) had a Ct value less than (≤ 33), with only 20.35% (23/113) belonging to symptomatic patients. The mean age was 39.01±13 years. The Beta variant (B.1.351) was the most detected one comprising 78.8% (89/113) of variants. Gamma and Delta variants were detected at a low proportion of 0.9% (1/113). No mutation or variant was detected in seven (6.2%) samples. Conclusion: Specific mutation screening detected Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2) variants of SARS-CoV-2 circulating in Burkina Faso. The absence of mutations in some samples might suggest variants other than those detected.
 

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Precision tracking and monitoring viral genome mutations are critical during a viral pandemic such as COVID-19. As molecular assays for diagnosing numerous infectious agents are being developed, RT-PCR is still deployed as the gold standard for detecting SARS-CoV-2. Despite its proofreading capability, SARS-CoV-2, like other RNA viruses, adopts several changes in its genome. If these mutations, especially deletions, occur in the target areas of primers and probes, they will hinder molecular detection methods from identifying the given gene. The authors describe the cases in which, despite the lack of the N gene detection, the ORF1ab gene was discovered with a relatively low cycle of threshold (Ct). Following sequencing, changes were discovered in the annealing region of the forward and reverse primers and probes used in the SARS-CoV-2 detection kit. Among the most significant mutations is a large deletion of 15 nucleotides in the N gene, which has never been seen in prior variants. This highlights the importance of persistent monitoring of hypervariable regions in the SARS-CoV-2 genome through sequencing and updating the molecular detection kits during the COVID-19 pandemic.

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The SARS-COV-2 virus is the cause of the 2020 pandemic that has infected and killed millions worldwide. While the upper respiratory tract cells are the primary targets of COVID-19, the virus can infiltrate other tissues and organs, leading to potentially serious complications. The new coronavirus primarily affects angiotensin II receptor and cytokine pathways, which can result in acute pulmonary inflammation, pulmonary edema, acute respiratory distress syndrome, vascular endothelial dysfunction, pulmonary embolism in the lungs, and cardiomyopathy, arrhythmia, heart failure, and intravenous thrombosis in the heart. COVID-19 infection can be associated with gastrointestinal symptoms such as diarrhea, vomiting, and abdominal pain. Also, reports of mild and transient liver damage, polyneuropathy, encephalitis, stroke, acute renal failure, hypocortisolism, and damage to the hypothalamus and pituitary system are available. COVID-19 can also be associated with skin symptoms such as rash, urticaria, maculopapular lesions, and vascular lesions such as chill blain, petechiae purpura, and scalpopathy. This narrative review evaluates the pathogenesis of novel coronavirus on body organs based on relevant published papers and reference books.

 

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Introduction: This quantitative study aims to conduct a literature evaluation on COVID-19 and pregnancy published since September 2022. Methods: The data was retrieved from the Web of Science database. Authors, co-cited authors, publishing journals, keywords, countries, affiliations, H indexes, citation numbers, and connections between these parameters were used to identify and analyze the data. Microsoft Excel was used to assess the descriptive characteristics of publications, and VOSviewer was used to analyze and visualize selected criteria. Results: We extracted 1574 publications on COVID-19 and pregnancy according to search criteria. The majority (81.96%) were published in Science Citation Index Expanded journals, and 670 (42.56%) were published in 2021. Although 100 countries contributed to this topic, the highest number f articles was published by the United States of America (n=473), followed by the United Kingdom, Italy, China, and India. The University of London and Harvard University were the most productive affiliations, and the American Journal of Obstetrics and Gynecology published the most (n=84). The publications received 17,406 citations, an average of 11.06 per document. Conclusion: Since the emergence of COVID-19 and pregnancy, numerous countries, affiliations, and academics have focused on this issue, resulting in a rapid expansion of publications in this field of literature. So far, American, British, and Italian scientists have collaborated the most on COVID-19 and pregnancy research internationally.

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Introduction: COVID-19, caused by the SARS-CoV-2 virus, had a widespread impact on lives worldwide. Its global impact has transcended geographical barriers, affecting people of all ages, races, and genders. Pregnancy induces critical physiological changes in women that can increase their susceptibility to infections. As a result, pregnant women may be at a higher risk of acquiring infections compared to non-pregnant individuals. This retrospective study aimed to determine the prevalence of COVID-19 among pregnant women from April 2020 to January 2022. Methods: Screening was performed on a total of 4929 pregnant women nearing their expected delivery date. Nasopharyngeal and/or oropharyngeal samples were collected and analyzed for SARS-CoV-2 detection using real-time RT-PCR. Result: Pregnant women in the study had a mean age of 30.28 years, and the overall prevalence of COVID-19 was 3.6%. Positivity rates varied between zero and 23.2% during different intervals, with increases in positivity coinciding with the peaks of the country's first, second, and third waves of COVID-19. Pregnant females exhibited a higher positivity rate for COVID-19 compared to the general population. Conclusions: The presence of COVID-19-positive patients in our study group, which comprised entirely of asymptomatic individuals, underscores the importance of active screening among at-risk populations, particularly during periods of increased activity in the general population. These findings can be of vital importance for the management of COVID-19 in pregnant patients, as well as policymaking at all levels.
 

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Introduction: The global COVID-19 pandemic has disproportionately impacted people with weakened immune systems. Non-communicable diseases, which include diabetes and cancer, are the top causes of weakened immune systems, recording up to 74% of all deaths globally. Studying the seroprevalence is crucial in understanding the epidemiology of the virus and contributes to the improved management of COVID-19 amongst patients with cancer and diabetes. Methods: The study was a single-center prospective study that tested serum samples for routine chemical analysis from March to July 2022 at NHLS, Chemical Pathology, Polokwane laboratory using the COVID-19 IgG/IgM Rapid Test Cassette - Orient Gene Biotech, Zhejiang, China. The assay tests antibodies against SARS-CoV-2 in the early (lgM) and later stage (lgG) of infection. Results: Of the 207 patients with diabetes, 84% had detectable IgG and IgM antibodies against SARS-CoV-2. Similarly, 81% of the 283 cancer patients had detectable IgG and IgM antibodies against SARS-CoV-2. The patients with diabetes had a median age of 56 years (range: 0-91), and 60% were females. The cancer patients had a median age of 62 years (range: 49-72), and 40% were females. Conclusion: The study demonstrates a high SARS-CoV-2 IgG and IgM antibody seroprevalence in diabetic and oncology patients at Pietersburg Hospital, Limpopo, South Africa. These findings emphasize the importance of ongoing serologic testing to track the pandemic, particularly among immunocompromised patients, and inform the development of effective public health strategies to mitigate COVID-19 transmission.

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Introduction: The COVID-19 pandemic has significantly impacted global health, and vaccines have been crucial in mitigating severe outcomes. However, the effect of type 2 diabetes on vaccine-induced immune responses is not fully understood. This study aims to analyze SARS-CoV-2 antibody levels in individuals with type 2 diabetes and compare them to individuals without diabetes to elucidate the complex interactions between diabetes and immune responses. Methods: At GMC Srinagar, India, a study involving 299 healthcare workers reviewed their vaccination status, SARS-CoV-2 infection history, and diabetes status. Blood samples were analyzed for HbA1c and IgG antibodies using ELISA and chemiluminescence assays. Descriptive and inferential statistics were used to analyze demographic data and compare groups. Results: More than two-thirds of the participants had prior COVID-19 infections, and vaccination rates were high. Diabetes significantly impacted antibody levels, with diabetic individuals showing lower IgG titers compared to non-diabetic individuals. Age and gender also influenced antibody levels: individuals aged 41-50 and 51-60 had higher anti-S antibody titers than younger age groups (t-test = 52.603, df = 15, P < 0.001). Males exhibited higher anti-S antibody titers compared to females (t-test = 7.483, df = 5, P = 0.007). Booster doses of the vaccine significantly enhanced antibody responses. Conclusion: This study highlights the impact of diabetes, age, gender, and vaccination history on SARS-CoV-2 antibody levels in healthcare workers. Diabetic individuals had lower antibody titers, while age and gender differences also affected antibody responses. These findings suggest the need for personalized vaccination strategies, especially for diabetic healthcare workers, to optimize COVID-19 prevention and ensure effective immunity.