Iranian Journal of Virology
Volume:16 Issue: 2, 2022

Non-conserved sequences in the parvoviruses' genome are involved in the virus-host interactions, so analysis of the complete genome sequence of the parvoviruses broadens our perspective about parvoviruses' host tropism and evolution. This study aimed to analyze the phylogeny of the 25 parvoviruses that infect invertebrates from Densovirinae and Hamaparvovirinae subfamilies based on the complete genome and NS1 gene sequences. According to the whole-genome phylogenetic tree, hamaparvoviruses are close to each other; however, they are in the middle of densoviruses clades. Applying non-NS1 sequences for constructing the phylogenetic tree causes Hamaparvovirinae to disperse among Densovirinae members, which shows the possible ancestor relationship of these two subfamilies. The divergence difference between the NS1 nucleotide sequence and the whole genome was higher in Densovirinae compared with Hamaparvovirinae. In Hamaparvovirinae, there is approximately no difference in divergence of NS1 gene sequence compared with the whole genome, which indicates that non-NS1 sequences in densoviruses are more diverse than these sequences in Hamaparvovirinae members. The evolutionary divergence between Hamaparvovirinae and Densovirinae was slightly higher in the whole genome compared with NS1 sequences. As both Hamaparvovirinae and Densovirinae used in this study infect invertebrates, the low difference in divergence value between them could be related to their host. Each parvovirus in this study has its unique 5´ and 3´ untranslated regions, which could be used as a genetic fingerprint indicator for parvovirus detection.

Selecting appropriate antigens, suitable delivery vehicles and proper immune adjuvants are important items in vaccine designing. According to the previous studies, Carcinoembryonic antigen (CEA) and Adenoviral vector are considered as proper antigen and reliable delivery vehicle for cancer vaccines, respectively. Directing antigens to DCs with antibody single-chain fragment variable (scFv) against to DEC-205 (scDEC) can play the role of adjuvant. The aim of this study was to produce a construct encoding CEA targeted to DCs by scDEC in Adenovirus vector platform.

scDEC were cloned into p-track-CEA-GFP. Linearized p-track-scDEC-CEA-GFP and pAdenoVator ∆E1/E3 were co-transformed into BJ5183 cells. Resulting pAd scDEC-CEA-GFP was transfected into HEK293 cells to produce Adenoviruses (Ad scDEC-CEA-GFP). The presence of scDEC-CEA gene in the recombinant virus and expression of CEA protein was detected by PCR and electrochemiluminescence tests, respectively. Flow cytometry tests were used to confirm the attachment of scDEC-CEA protein to DCs. Adenovirus infectivity in cells other than HEK293 was confirmed by transduction of Ad scDEC-CEA-GFP into L929 cells.

PCR test showed the presence of scDEC-CEA gene in adenovirus genome. Electrochemilu-minescence and flow cytometry analysis confirmed expression of CEA protein and attachment of scDEC-CEA protein to DCs, respectively. GFP expression in L929 cells indicated Ad scDEC-CEA-GFP could effectively infect cells other than HEK293.

As construction of a suitable construct for immunotherapy is a major goal of many research groups, the Ad scDEC-CEA-GFP engineered in this study, which properly targets DCs, can be applied in future in vivo cancer immunotherapy investigations in mice.

Adenoviruses are dsDNA viruses known for causing respiratory, gastrointestinal, ocular, and genitourinary infections. Epidemiological insights are crucial for public health interventions. This study focuses on the epidemiology of adenoviruses in acute respiratory cases, aiming to enhance preventive and therapeutic strategies.

This cross-sectional study was performed on collected throat swab samples from individuals under 19 with acute respiratory symptoms. Nested-PCR was used to detect adenovirus presence in 328 samples. DNA extraction, quality assessment, and statistical analyses were conducted to determine prevalence, clinical manifestations, in the papulation under study.

Among the 328 samples analyzed, 72 samples (22%) including 25 male and 47 female tested positive for adenovirus infection using Nested-PCR. Clinical symptoms evaluation revealed distinct manifestations. Fever was presented in 72.6% of cases, cough in 64.6%, and muscular pain in 64%. Gender differences emerged, with 56.3% of infected individuals being females and 34.7% males. Statistical analyses confirmed these associations, providing valuable insights into the prevalence and clinical aspects of adenovirus infections.

The identification of distinct clinical manifestations, coupled with gender-specific prevalence, underscores the complexity of adenovirus infections. These findings contribute crucial knowledge to the understanding of adenovirus epidemiology, highlighting the need for targeted interventions and public health strategies to address their substantial burden on affected populations. Further research and ongoing surveillance are imperative for the effective management and mitigation of adenovirus-related respiratory diseases.

Highly pathogenic avian influenza (HPAI) is responsible for severe outbreaks in domestic and wild poultry. Furthermore, the disease has zoonotic potential posing great risk to human’s health worldwide. In current study the spatial and temporal distribution of HPAI outbreaks in Iran during 2015 to 2021 were evaluated using the information obtained from the OIE World Animal Health Information Database (WAHIS). During the period of study, 90 outbreaks were reported from 17 (54%) provinces. The highest number of outbreaks were reported from South Khorasan province (28%) followed by Mazandaran (14%). The outbreaks occurred throughout the year with no significant difference between two semesters (p>0.05). The majority of outbreaks occurred in domestic poultry (85%). The identified subtypes were H5N8 (90%) followed by H5N1 (3%) and H5N6 (1%). Co-occurrence of H5N8 and H5N1 subtypes observed in 5% of outbreaks. The incidence of subtypes with zoonotic potential (H5N1, H5N6) pose a continued risk to public health. One health approach and inter-sectoral cooperation is recommended for early detection and reporting of HPAI outbreaks with more focus on high-risk areas.

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), originated more likely from Wuhan, China and spread across the world. According to WHO reports, the virus is responsible for the death of almost seven million people around the world until now. Considering the same clinical manifestations of SARS-CoV-2 and influenza virus, simultaneous infection of these two viruses may affect the treatment process of the patient. Thus, we investigated coinfection of SARS-CoV-2, influenza A (IAV) and B (IBV) in patients with respiratory syndrome from June to August 2021. Nasopharyngeal samples were obtained from 84 COVID-19 patients and were tested for detection of SARS-CoV-2, IAV and IBV by using Reverse Transcriptase Real-time Polymerase Chain Reaction. Out of 84 patients, we found 46 and three COVID-19 and influenza positive cases, respectively. Coinfection was only found in two cases. Both cases were female and aged above 60 years. Findings of the currents study represent low prevalence of the influenza virus infection in the 2021 influenza season as well as low coinfection rates with SARS-CoV-2. This low prevalence may be due to the preventive measurements against the COVID-19.

To prepare human plasma for therapeutic purposes and serum with a low risk of contamination for cell culture use, a technique is needed to reduce blood borne pathogens. Silver nanoparticles (AgNPs) are a suitable option due to their low-risk of microbial resistance and strong antimicrobial activity.

As representative microorganisms, we tested Herpes simplex type 1 (HSV-1), Escherichia coli (ATCC 25922), and Staphylococcus aureus (ATCC 1413). The cytotoxicity of biosynthesized AgNPs was assessed on the Vero cell line. The Maximum Non-Toxic Dose (MNTD) of AgNPs did not affect the virus. In order to address the high toxicity of AgNPs and utilize the highest colloidal concentration of AgNPs (300 µg/ml) that did not precipitate within the 24-hour examination period, we developed a removal process. AgNPs were removed after being exposed to viruses and bacteria. This removal step was done by addition of magnetic iron oxide nanoparticles (iron oxide NPs). Then, treated virus and bacteria were exposed to neodymium magnet, and were used for cell inoculation.

Both AgNPs and iron oxide NPs reduced the titer of virus by at least 3.5 log when used together. Additionally, they inactivated 106 CFU/ml of bacteria in human plasma. While each nanoparticle exhibited antiviral activity individually, but also their effect was enhanced when used simultaneously.

Human plasma pathogens were reduced using AgNPs and/or iron oxide NPs. The plasma could be treated with these nanoparticles, and subsequently the magnetic nanoparticles that adsorbed silver nanoparticles were separated from the plasma using a neodymium magnet, as one of the techniques for pathogen reduction.

Rotavirus is one of the most important causes of acute diarrhea in children under five years. Therefore, the diarrhea samples examination in children is necessary to diagnose the prevalence of rotavirus and determine the predominant genotype. The focus of this study was to investigate the prevalence of rotavirus and its predominant genotype in the population of children under five years with acute gastroenteritis in Kermanshah, Iran.

Between October to March 2017, 100 samples were collected and the rotavirus positivity was evaluated by VP6 expression. Then, the dominant genotype in the positive samples was examined by Multiplex seminested PCR with specially designed primers.

100 stool samples of children under 5 years with gastroenteritis were taken, 21 sample positive for rotavirus. The highest frequency of genotype was G1P8 (38.1%) and the lowest was G2P4 (14.3%). The most positive rotavirus samples were in the age group of 1-2 years and no rotavirus positive samples were found in the 4-5 age group.

Rotavirus should be considered as an important agent in diarrhea of children, especially children under 1 year, and inappropriate use of antibiotics should be avoided. It is also recommended to determine the dominant genotype to provide a suitable situation for immunization of children against rotavirus in Iran.

Foot-and-mouth disease virus (FMDV) causes severe infection in livestock and makes considerable economic impacts. Therefore, a rapid, highly specific, and accurate method for the diagnosis of FMDV infections is required to ensure that appropriate treatment is administered to reduce economic losses. In this study, the diagnostic tests for FMDV detection by enzyme-linked immunosorbent (Ag-ELISA), reverse transcription–PCR (RT-PCR), and real-time RT-PCR (rRT-PCR) were carried out as the World Organization for Animal Health recommended and were based on the VP1 gene. Positive samples were detected by RT-PCR and rRT-PCR (73.16%) and by ELISA test (55.99%). According to the information obtained from the present study molecular methods provide much more reliable and definitive results than Immune assay methods.

Apple stem grooving virus (ASGV) is one of the economically important latent viruses infecting pome fruit trees worldwide. The investigation on the distribution of ASGV and its molecular properties can give us more information about the epidemiology and control of this latent and graft-transmissible virus.

The presence of ASGV in apple and pear orchards in Mazandaran province (Northern Iran) was investigated using serological and molecular approaches. The phylogenetic tree was constructed by the Neighbor-Joining method implemented in MEGAX. Two-dimensional nucleotide diversity plot constructed using CP sequences by SDTv1.2 version 12. RDP4 and Dnasp software were used for recombination, and genetic diversity and demographic analysis, respectively v. 6.10.04.

ASGV was detected in 10.2% of leaf samples by ELISA test. A DNA amplicon with the expected size of 780 bp corresponding to the ASGV coat protein (CP) gene was amplified using RT-PCR assay. Phylogenetic analysis showed that the ASGV isolates clustered into two main groups, which is confirmed by the nucleotide identity plot. Group II (GII) includes two Chinese and Korean pear isolates with an apple isolate from India. However, most of the ASGV isolated from different geographical regions including Iranian isolates fell into group I (GI). High nucleotide identity (91 to 100%), low nucleotide, and high haplotype diversities indicate the recent distribution of ASGV. No clustering was found according to the hosts or where the ASGV was isolated. Using dN/dS values it was found that the different populations of ASGV are under negative (purifying) selection with the ω ratio less than 1. The highest gene flow was determined between American and South Asian populations. Moderate or low genetic differentiation, and frequent gene flow (FST < 0.33 and Nm > 1) also confirmed with Ks*, Kst* Z, Z* and Snn statistics values, except between West Asia and East Asia populations which may suggesting these isolates are older than the others. 

To our knowledge, this is the first report of ASGV infecting apple and pear trees in North Iran, which extends the geographical range of this viral disease. Accordingly, larger-scale ASGV investigations must be conducted to determine the distribution and prevalence of this virus in Iran.

The genetic variability and population structure of Grapevine leafroll-associated virus 3 (GLRaV-3) have not already been studied in mid-Eurasia Iran. The investigations will contribute to developing efficient and durable control strategies of latent and graft-transmissible virus.

During the winter of 2018-2019, a total of 229 dormant cutting samples were collected from 15 vineyards in West Azarbaijan province. All the samples were analyzed by serological and RT-PCR assays. The phylogenetic tree and two-dimensional nucleotide diversity plot were constructed using CP sequences by the SplitsTree4 v.4.12.6, and SDTv1.2 soft wares, respectively. Dnasp v.6.10.04 was used for genetic diversity and demographic analysis. We provide analyses of the codon usage and composition of GLRaV-3 based on 517 nucleotide sequences of the CP gene including 11 full CP sequences from Iran. 

Using serological assay 31.87% GLRaV-3 infection was detected. Neighbor-Net method analysis of the virus complete CP gene showed that the Iranian isolates fell into phylogroup I (GI) “as it is dominant in the rest of the world”. High haplotype diversities indicate the recent expansion of GLRaV-3. No clustering was found according to where the GLRaV-3 was isolated. Using dN/dS values it was found that the different populations of this virus is under negative (purifying) selection. The highest gene flow was determined between Europe and East Asia. Moderate or low genetic differentiation, and frequent gene flow (FST < 0.33 and Nm > 1) also confirmed with Ks*, Kst* Z, Z* and Snn statistics values. The frequency of amino acid coded by A/G ended optimal codon indicates the overlapping influences of natural selection and mutational pressure on the codon preferences in the CP gene. Codon bias of the CP gene was strongly affected by natural selection rather than mutation according to the effective number of codons-ENC vs. GC3s plot. Principal component plot analysis (PCA), illustrated the possible origin of GLRaV-3 in the Old World.

This analysis is the first demonstration of the population structuring of GLRaV-3 in mid-Eurasian Iran. Indeed, these consequences explain selectively driven codon bias in GLRaV-3 species; and reveal the potential importance of expression-mediated selection in shaping the genome evolution of this virus.

There have been several known neurologic manifestations of COVID-19, such as headache, anosmia, etc. Rare cases of restless legs syndrome (RLS) associated with the disease have been reported. Here, the authors describe a patient with six-day nighttime discomfort in both legs that improved with moving them, with dry cough and myalgia added to her symptoms and she was hospitalized due to low oxygen saturation and suspicion of COVID-19. During hospitalization, antiviral and anti-inflammatory drugs were used and after a short time of discharge, RLS was eliminated without any specific drug. We hypothesize that since angiotensin-converting enzyme (ACE2) is highly expressed in Substantia Nigra, SARS-Cov-2 may disturb iron metabolism and homeostasis of dopaminergic neurons which leads to the development of RLS and inflammation exacerbates the condition.

The emergence of the novel human coronavirus (SARS-CoV-2) has been one of the most overwhelming human challenges of recent decades. Despite global efforts to stop or slow down the spread of the disease, it has infected millions of people across the world within a short period of time. Research on human coronaviruses has not been received adequate attention and there is currently no specific treatment or vaccine available for coronaviruses in humans. Interestingly, evolution, pathogenesis, and immunogenicity of coronaviruses in livestock and poultry have been described for many years and they are controlled by mass vaccination programs. Moreover, elevating immune responses to coronaviruses, a major hurdle in virulent human-coronaviruses, has been studied by several investigators in cat populations. Indeed, cross-species transmission and tropism of animal coronaviruses have been investigated by several research groups. It is estimated that three out of every four new emerging infectious diseases are zoonotic. Preliminary reports indicate that like other human coronaviruses, SARS-CoV-2 has been transmitted from bats to humans by an intermediate animal host. Hence, interdisciplinary collaborations among veterinary and medical researchers and clinicians, biologists, and environmental scientists are essential for identifying the possible animal reservoir of the viruses in general and discovering the evolutionary pathway of SARS-CoV-2 in particular. This can also result in the designing of effective prevention and control measures against SARS-CoV-2. In this review, advances in the understanding of different features of animal coronaviruses that can facilitate effective measures in dealing with the SARS-CoV-2 pandemic have been discussed.