Partial sequence conservation of SARS-CoV-2 NSP-2, NSP-12, and Spike in stool samples from Abadan, Iran.

Since the onset of the coronavirus disease 2019 (COVID-19) pandemic, the clinical manifestations of the virus have undergone many changes. Recently, there have been many reports on gastrointestinal symptoms in COVID-19 patients. This study is aimed to perform a detailed phylogenetic study and assessment of different SNVs in the RNA genome of viruses isolated from fecal samples of patients with COVID-19 who have gastrointestinal symptoms, which can help better understand viral pathogenesis. In the present study, 20 fecal samples were collected by written consent from COVID-19 patients. According to the manufacturer's protocol, virus nucleic acid was extracted from stool samples and the SARS-CoV-2 genome presence in stool samples was confirmed by RT-PCR assay. Three viral genes, S, nsp12, and nsp2, were amplified using the reverse transcription polymerase chain reaction (RT-PCR) method and specific primers. Multiple sequencing alignment (MSA) was performed in the CLC word bench, and a phylogenetic tree was generated by MEGA X based on the neighbor-joining method. Of all cases, 11 (55%) were males. The mean age of the patients was 33.6 years. Diabetes (70%) and blood pressure (55%) were the most prevalent comorbidities. All 20 patients were positive for SARS-CoV-2 infection in respiratory samples. Molecular analysis investigation among 20 stool samples revealed that the SARS-CoV-2 genome was found among 10 stool samples; only three samples were used for sequencing. The polymorphism and phylogenetic analysis in SARS-CoV-2 showed great similarity among all of the evaluated genes with the Wuhan reference sequence and all of the current variants of concern (VOCs). The current study represents a great similarity in polymorphism and phylogenetic analysis of the SARS-CoV-2 isolates with the Wuhan reference sequence and all of the current VOC in the particular evaluated partial sequences of S, nsp12, and nsp2.

The role of SARS-CoV-2 accessory proteins in immune evasion.

Many questions on the SARS-CoV-2 pathogenesis remain to answer. The SARS-CoV-2 genome encodes some accessory proteins that are essential for infection. Notably, accessory proteins of SARS-CoV-2 play significant roles in affecting immune escape and viral pathogenesis. Therefore SARS-CoV-2 accessory proteins could be considered putative drug targets. IFN-I and IFN-III responses are the primary mechanisms of innate antiviral immunity in infection clearance. Previous research has shown that SARS-CoV-2 suppresses IFN-ß by infecting host cells via ORF3a, ORF3b, ORF6, ORF7a, ORF7b, ORF8, and ORF9b. Furthermore, ORF3a, ORF7a, and ORF7b have a role in blocking IFNα signaling, and ORF8 represses IFNß signaling. The ORF3a, ORF7a, and ORF7b disrupt the STAT1/2 phosphorylation. ORF3a, ORF6, ORF7a, and ORF7b could prevent the ISRE promoter activity. The main SARS-CoV-2 accessory proteins involved in immune evasion are discussed here for comprehensive learning on viral entry, replication, and transmission in vaccines and antiviral development.

Letter to the Editor Regarding "An Overview on Serology and Molecular Tests for COVID-19: An Important Challenge of the Current Century (doi: 10.22034/iji.2021.88660.1894.)".

Recently in a review article by Mansourabadi et al. published in the Iranian Journal of Immunology, the authors described the serological and molecular tests for COVID-19 (1). The mentioned review considered helicase (Hel) as a structural protein of SARS-CoV-2 (1). However, based on evidence, the genome of novel coronavirus is approximately 30kb in length and encodes only four structural proteins, including spike (S), envelope (E), membrane (M), and nucleoprotein (N) (2, 3), although helicase (NSP13) as a nonstructural protein such as RNA-dependent RNA polymerases (NSP12) encoded by the ORF region and is involved in the replication of the virus (3).In addition, authors reported that hemagglutinin esterase could be used as a favorite target for SARS-CoV-2 Real-time PCR (1); however, scientific evidence shows that SARS-CoV-2 as a betacoronavirus lineage B like SARS-CoV lacks hemagglutinin esterase (4-6); thus this protein cannot be a target for detection of SARS-CoV-2.

Comment on Alfassam et al. Development of a Colorimetric Tool for SARS-CoV-2 and Other Respiratory Viruses Detection Using Sialic Acid Fabricated Gold Nanoparticles. Pharmaceutics 2021, 13, 502.

In a published article in Pharmaceutics, researchers developed a sialic acid (SA) stabilized Au nanoparticle system based on SA's binding ability that exists on the surface of lungs epithelial cells. The authors reported that many respiratory viruses including influenza, Middle-East respiratory syndrome (MERS-CoV), and the current coronavirus (SARS-CoV-2) bind to SA as one of the main binding targets of the surface protein hemagglutinin (HA).

VDR gene polymorphisms are associated with the increased susceptibility to COVID-19 among iranian population: A case-control study.

Coronavirus disease 2019 (COVID-19) is an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but the pathogenesis is unclear. Host genetic background is one of the main factors influencing the patients' susceptibility to several viral infectious diseases. This study aimed to investigate the association between host genetic polymorphisms of two genes, including vitamin D receptor (VDR) and vitamin D binding protein (DBP), and susceptibility to COVID-19 in a sample of the Iranian population. This case-control study enrolled 188 hospitalized COVID-19 patients as the case group and 218 suspected COVID-19 patients with mild signs as the control group. The VDR (rs7975232, rs731236 and rs2228570) and DBP (rs7041) gene single nucleotide polymorphisms (SNPs) were genotyped by Polymerase Chain Reaction Restriction - Fragment Length Polymorphism (PCR-RFLP) method. A significant association between rs2228570 SNP in the VDR gene and the susceptibility of COVID-19 was found between case and control groups. The CT genotype (Heterozygous) of rs2228570 C > T polymorphism showed significant association with a 3.088 fold increased odds of COVID-19 (p < .0001; adjusted OR: 3.088; 95% CI: 1.902-5.012). In addition, a significant association between CC genotype of rs2228570 CT polymorphism and increased odds of COVID-19 in male and female groups (p = .001; adjusted OR: 3.125; 95% CI: 1.630-5.991 and p = .002; adjusted OR: 3.071; 95% CI: 1.485-6.354 respectively) were determined. Our results revealed no significant differences in the frequency of genotype and allele of VDR (rs7975232 and rs731236) and DBP (rs7041) between SARS-CoV-2-infected patients and controls (p > .05). Our results showed that polymorphism of VDR (rs2228570) probably could influence individual susceptibility to COVID-19. The polymorphisms of VDR (rs7975232 and rs731236) and DBP (rs7041) were not associated with SARS-CoV-2 infection susceptibility.

Ribosome Profiling: A Useful Approach to Discover Hidden Corners of SARS-CoV-2.

Following SARS-CoV-2 China epidemic in the December 2019, researches have attended to the genome of novel coronavirus. Hidden corners of SARS-CoV-2, maybe a shiny way to discover its pathogenicity and virulence. To design therapeutic agents, it is critical to map the complete repertoire of viral-translated proteins. Ribosome profiling is considered as a snapshot of all active ribosomes in a cell at a specific time point.

Worldwide prevalence of fungal coinfections among COVID-19 patients: a comprehensive systematic review and meta-analysis.

Microbial coinfections can increase the morbidity and mortality rates of viral respiratory diseases. Therefore, this study aimed to determine the pooled prevalence of fungal coinfections in coronavirus disease 2019 (COVID-19) patients. Web of Science, Medline, Scopus, and Embase were searched without language restrictions to identify the related research on COVID-19 patients with fungal coinfections from December 1, 2019, to December 30, 2020. A random-effects model was used for analysis. The sample size included 2,246 patients from 8 studies. The pooled prevalence of fungal coinfections was 12.60%. The frequency of fungal subtype coinfections was 3.71% for Aspergillus, 2.39% for Candida, and 0.39% for other. The World Health Organization's Regional Office for Europe and Regional Office for Southeast Asia had the highest (23.28%) and lowest (4.53%) estimated prevalence of fungal coinfection, respectively. Our findings showed a high prevalence of fungal coinfections in COVID-19 cases, which is a likely contributor to mortality in COVID-19 patients. Early identification of fungal pathogens in the laboratory for COVID-19 patients can lead to timely treatment and prevention of further damage by this hidden infection.

Pooled Prevalence Estimate of Ocular Manifestations in COVID-19 Patients: A Systematic Review and Meta-Analysis.

Background: There are reports of ocular tropism due to respiratory viruses such as severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Various studies have shown ocular manifestation in coronavirus disease-2019 (COVID-19) patients. We aimed to identify ophthalmic manifestations in COVID-19 patients and establish an association between ocular symptoms and SARS-CoV-2 infection. Methods: A systematic search of Medline, Scopus, Web of Science, Embase, and Cochrane Library was conducted for publications from December 2019 to April 2021. The search included MeSH terms such as SARS-CoV-2 and ocular manifestations. The pooled prevalence estimate (PPE) with 95% confidence interval (CI) was calculated using binomial distribution and random effects. The meta-regression method was used to examine factors affecting heterogeneity between studies. Results: Of the 412 retrieved articles, 23 studies with a total of 3,650 COVID-19 patients were analyzed. The PPE for any ocular manifestations was 23.77% (95% CI: 15.73-31.81). The most prevalent symptom was dry eyes with a PPE of 13.66% (95% CI: 5.01-25.51). The PPE with 95% CI for conjunctival hyperemia, conjunctival congestion/conjunctivitis, and ocular pain was 13.41% (4.65-25.51), 9.14% (6.13-12.15), and 10.34% (4.90-15.78), respectively. Only two studies reported ocular discomfort and diplopia. The results of meta-regression analysis showed that age and sample size had no significant effect on the prevalence of any ocular manifestations. There was no significant publication bias in our meta-analysis. Conclusion: There is a high prevalence of ocular manifestations in COVID-19 patients. The most common symptoms are dry eyes, conjunctival hyperemia, conjunctival congestion/conjunctivitis, ocular pain, irritation/itching/burning sensation, and foreign body sensation.

CRISPR-Cas System: A Promising Diagnostic Tool for Covid-19.

More than a year has passed since the beginning of the 2019 novel coronavirus diseases (COVID-19) pandemic which has created massive problems globally affecting all aspects of people's life. Due to the emergence of new strains of the SARS-CoV-2, pandemic risk still remains, despite the start of vaccination. Therefore, rapid diagnostic tests are essential to control infection, improve clinical care and stop the spread of the disease. Recently CRISPR-based diagnostic tools have facilitated rapid diagnostic. Here, we review the diagnostic applications of CRISPR-Cas system in COVID-19.

A multicenter retrospective study of clinical features, laboratory characteristics, and outcomes of 166 hospitalized children with coronavirus disease 2019 (COVID-19): A preliminary report from Iranian Network for Research in Viral Diseases (INRVD).

BACKGROUND: The objectives of this study were to analyze the clinical features and laboratory profiles and risk factors associated with critical illness of children with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). METHODS: One hundred and sixty-six coronavirus disease 2019 (COVID-19) Iranian pediatric patients were recruited through a collaborative research network between March and May 2020. Demographics, clinical, laboratory, and radiological results were obtained from patient files. RESULTS: Of 166 patients, 102 (61%) and 64 (39%) were males and females, respectively. Ninety-six (57.8%) and 70 (42.2%), had moderate and severe conditions, respectively. Thirty (18%) of patients died. The common symptoms were fever (73%), cough (54%), and shortness of breath, headache decrease in neutrophil and platelet counts; increase values in lactate dehydrogenase, decrease in the blood pH and HCO3 were significantly associated with the disease severity. 54% and 56% of patients showed abnormal radiographic appearance in Chest X-ray and in chest computed tomography scan, respectively. Sixty-one (36.7%) of patients were referred to intensive care unit (ICU). The coexistence of comorbidity was the main factor associated with ICU admission, shock, arrhythmia, acute kidney injury, acute respiratory distress syndrome, acute cardiac injury, and death. CONCLUSIONS: We describe a higher than previously recognized rate of COVID-19 mortality in Iranian pediatric patients. Epidemiological factors, such as the relatively high case fatality rate in the country and the presence of underlying diseases were the main factors for the high death rate.

Worldwide prevalence of microbial agents' coinfection among COVID-19 patients: A comprehensive updated systematic review and meta-analysis.

BACKGROUND: To provide information about pathogens' coinfection prevalence with SARS-CoV-2 could be a real help to save patients' lives. This study aims to evaluate the pathogens' coinfection prevalence among COVID-19 patients. METHOD: In order to find all of the relevant articles, we used systematic search approach. Research-based databases including PubMed, Web of Science, Embase, and Scopus, without language restrictions, were searched to identify the relevant bacterial, fungal, and viral coinfections among COVID-19 cases from December 1, 2019, to August 23, 2021. In order to dig deeper, other scientific repositories such as Medrxiv were probed. RESULTS: A total of 13,023 studies were found through systematic search. After thorough analysis, only 64 studies with 61,547 patients were included in the study. The most common causative agents of coinfection among COVID-19 patients were bacteria (pooled prevalence: 20.97%; 95% CI: 15.95-26.46; I2 : 99.9%) and less frequent were virus coinfections (pooled prevalence: 12.58%; 95% CI: 7.31-18.96; I2 : 98.7%). The pooled prevalence of fungal coinfections was also 12.60% (95% CI: 7.84-17.36; I2 : 98.3%). Meta-regression analysis showed that the age sample size and WHO geographic region did not influenced heterogeneity. CONCLUSION: We identified a high prevalence of pathogenic microorganism coinfection among COVID-19 patients. Because of this rate of coinfection empirical use of antibacterial, antifungal, and antiviral treatment are advisable specifically at the early stage of COVID-19 infection. We also suggest running simultaneously diagnostic tests to identify other microbiological agents' coinfection with SARS-CoV-2.

The role of lipids in the pathophysiology of coronavirus infections.

Coronaviruses, which have been known to cause diseases in animals since the 1930s, utilize cellular components during their replication cycle. Lipids play important roles in viral infection, as coronaviruses target cellular lipids and lipid metabolism to modify their host cells to become an optimal environment for viral replication. Therefore, lipids can be considered as potential targets for the development of antiviral agents. This review provides an overview of the roles of cellular lipids in different stages of the life cycle of coronaviruses.

Severe acute respiratory syndrome coronavirus 2 and respiratory syncytial virus coinfection in children.

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has infected many people around the world. Children are considered an important target group for SARS-CoV-2, as well as other viral infections such as respiratory syncytial virus infection. Both SARS-CoV-2 and respiratory syncytial virus can affect the respiratory tract. Coinfection of SARS-CoV-2 and respiratory syncytial virus can pose significant challenges in terms of diagnosis and treatment in children. This review compares the symptoms, diagnostic methods, and treatment of COVID-19 and respiratory syncytial virus infection in children.

Clinical Symptoms and Types of Samples Are Critical Factors for the Molecular Diagnosis of Symptomatic COVID-19 Patients: A Systematic Literature Review.

BACKGROUND: Currently, a novel coronavirus found in 2019 known as SARS-CoV-2 is the etiological agent of the COVID-19 pandemic. Various parameters including clinical manifestations and molecular evaluation can affect the accuracy of diagnosis. This review aims to discuss the various clinical symptoms and molecular evaluation results in COVID-19 patients, to point out the importance of onset symptoms, type, and timing of the sampling, besides the methods that are used for detection of SARS-CoV-2. METHODS: A systematic literature review of current articles in the Web of Science, PubMed, Scopus, and EMBASE was conducted according to the PRISMA guideline. RESULTS: Of the 12946 patients evaluated in this investigation, 7643 were confirmed to be COVID-19 positive by molecular techniques, particularly the RT-PCR/qPCR combined technique (qRT-PCR). In most of the studies, all of the enrolled cases had 100% positive results for molecular evaluation. Among the COVID-19 patients who were identified as such by positive PCR results, most of them showed fever or cough as the primary clinical signs. Less common symptoms observed in clinically confirmed cases were hemoptysis, bloody sputum, mental disorders, and nasal congestion. The most common clinical samples for PCR-confirmed COVID-19 patients were obtained from throat, oropharyngeal, and nasopharyngeal swabs, while tears and conjunctival secretions seem to be the least common clinical samples for COVID-19 diagnosis among studies. Also, different conserved SARS-CoV-2 gene sequences could be targeted for qRT-PCR detection. The suggested molecular assay being used by most laboratories for the detection of SARS-CoV-2 is qRT-PCR. CONCLUSION: There is a worldwide concern on the COVID-19 pandemic and a lack of well-managed global control. Hence, it is crucial to update the molecular diagnostics protocols for handling the situation. This is possible by understanding the available advances in assays for the detection of the SARS-CoV-2 infection. Good sampling procedure and using samples with enough viral loads, also considering the onset symptoms, may reduce the qRT-PCR false-negative results in symptomatic COVID-19 patients. Selection of the most efficient primer-probe for target genes and samples containing enough viral loads to search for the existence of SARS-CoV-2 helps detecting the virus on time using qRT-PCR.

Viral Coinfection among COVID-19 Patient Groups: An Update Systematic Review and Meta-Analysis.

BACKGROUND: Coinfections have a potential role in increased morbidity and mortality rates during pandemics. Our investigation is aimed at evaluating the viral coinfection prevalence in COVID-19 patients. METHODS: We systematically searched scientific databases, including Medline, Scopus, WOS, and Embase, from December 1, 2019, to December 30, 2020. Preprint servers such as medRxiv were also scanned to find other related preprint papers. All types of studies evaluating the viral coinfection prevalence in COVID-19 patients were considered. We applied the random effects model to pool all of the related studies. RESULTS: Thirty-three studies including 10484 patients were identified. The viral coinfection estimated pooled prevalence was 12.58%; 95% CI: 7.31 to 18.96). Blood viruses (pooled prevalence: 12.48%; 95% CI: 8.57 to 16.93) had the most frequent viral coinfection, and respiratory viruses (pooled prevalence: 4.32%; 95% CI: 2.78 to 6.15) had less frequent viral coinfection. The herpesvirus pooled prevalence was 11.71% (95% CI: 3.02 to 24.80). Also, the maximum and minimum of viral coinfection pooled prevalence were in AMRO and EMRO with 15.63% (95% CI: 3.78 to 33.31) and 7.05% (95% CI: 3.84 to 11.07), respectively. CONCLUSION: The lowest rate of coinfection belonged to respiratory viruses. Blood-borne viruses had the highest coinfection rate. Our results provide important data about the prevalence of blood-borne viruses among COVID-19 patients which can be critical when it comes to their treatment procedure.