scholarly journals Determination of Genetic Characterization and Circulation Pattern of Respiratory Syncytial Virus (Rsv) in Children With a Respiratory Infection, Tehran, Iran, During 2018-2019

2021 ◽  
Author(s):  
Forough Tavakoli ◽  
Anahita Izadi ◽  
Jila Yavarian ◽  
Ali Sharifi‐Zarchi ◽  
Vahid Salimi ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Respiratory Infection ◽  
Circulation Pattern ◽  
Glycosylation Site ◽  
Phylogenetic Characterization ◽  
Glycoprotein Gene ◽  
Virus Genotypes ◽  
Syncytial Virus

Abstract The RSV-associated disease accounts for a significant health burden particularly in infants and young children who need to be hospitalized. Since continuous surveillance of circulating RSV genotypes is critical worldwide, this study aimed to investigate the genetic diversity of RSV circulating strains causing upper or lower acute respiratory infection. Our attention was geared towards studying the cases in hospitalized or outpatient children younger than 2 years of age in Iran during 2018/2019. In this study, nasopharyngeal aspirates collected from 206 children who presented with respiratory infection symptoms, were admitted to the referral pediatric ward of Bahrami children’s hospital in Tehran, Iran. RSV-positive samples were detected via Nested RT-PCR. The glycoprotein gene was sequenced, and virus genotypes were confirmed through phylogenetic analysis by the MEGA X program. A total of 74(35.92%) samples tested positive for RSV. Among them, sequencing was done in 10 specimens from 2018 (RSV-A: RSV-B =4:6) and 19 specimens from 2019 (RSV-A: RSV-B =16:3). According to Phylogenetic analysis, all RSV-A strains were assigned as ON1 genotype and RSV-B strains were assigned as BA9 genotype. A new N-glycosylation site in Iranian BA9 and positive selection in ON1 genotype was observed. Phylogenetic characterization of strains in the current study revealed co-circulation of ON1 and BA9 as the only prevalent genotypes of both RSV-A and –B groups.

scholarly journals Respiratory syncytial virus genotypes NA1, ON1, and BA9 are prevalent in Thailand, 2012–2015

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3970 ◽  
Author(s):  
Ilada Thongpan ◽  
John Mauleekoonphairoj ◽  
Preeyaporn Vichiwattana ◽  
Sumeth Korkong ◽  
Rujipat Wasitthankasem ◽  
...  
Keyword(s):  
Respiratory Syncytial Virus ◽  
Tract Infection ◽  
Respiratory Tract ◽  
Respiratory Tract Infection ◽  
Acute Respiratory Tract Infection ◽  
Glycosylation Site ◽  
Predicted Amino Acid Sequence ◽  
Glycoprotein Gene ◽  
Virus Genotypes ◽  
Syncytial Virus

Respiratory syncytial virus (RSV) causes acute lower respiratory tract infection in infants and young children worldwide. To investigate the RSV burden in Thailand over four consecutive years (January 2012 to December 2015), we screened 3,306 samples obtained from children ≤5 years old with acute respiratory tract infection using semi-nested reverse-transcription polymerase chain reaction (RT-PCR). In all, 8.4% (277/3,306) of the specimens tested positive for RSV, most of which appeared in the rainy months of July to November. We then genotyped RSV by sequencing the G glycoprotein gene and performed phylogenetic analysis to determine the RSV antigenic subgroup. The majority (57.4%, 159/277) of the RSV belonged to subgroup A (RSV-A), of which NA1 genotype was the most common in 2012 while ON1 genotype became prevalent the following year. Among samples tested positive for RSV-B subgroup B (RSV-B) (42.6%, 118/277), most were genotype BA9 (92.6%, 87/94) with some BA10 and BA-C. Predicted amino acid sequence from the partial G region showed highly conserved N-linked glycosylation site at residue N237 among all RSV-A ON1 strains (68/68), and at residues N296 (86/87) and N310 (87/87) among RSV-B BA9 strains. Positive selection of key residues combined with notable sequence variations on the G gene contributed to the continued circulation of this rapidly evolving virus.

scholarly journals First Isolation and Molecular Typing of Pathogenic and Intermediate Leptospira Species from Urine of Symptomatic Dogs

2021 ◽  
Vol 8 (12) ◽  
pp. 304
Author(s):  
Ivana Piredda ◽  
Loris Bertoldi ◽  
Giuseppe Benvenuto ◽  
Bruna Palmas ◽  
Aureliana Pedditzi ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Zoonotic Risk ◽  
Leptospira Spp ◽  
Blood And Urine Samples ◽  
Healthy Dogs ◽  
Polymerase Chain ◽  
Sequence Types ◽  
Leptospira Species

Aim of this study was to evaluate, the presence and diversity of Leptospira spp. in blood and urine samples collected from 175 owned-dogs from Sardinia, Italy. After determination of leptospiral infection by microscopic agglutination test (MAT), urine from MAT-positive dogs were examined by real-time polymerase chain reaction (lipL32 rt-PCR) and then isolated by culture. In order to characterize obtained serovars, positive cultures were then subjected to 16S rRNA and secY sequencing, phylogenetic analysis and Multilocus Sequence Typing (MLST). Results showed that seven dogs (4%; 95% CI: 0–55) had Leptospira DNAs in their urine and five strains were isolated from urine cultures. The three different sequence types (ST17, ST198 and ST24) belonging to Leptospira interrogans genomospecies identified by MLST analyses in this study, confirmed that the leptospiral infection was widespread in Sardinian dogs. We also reported the first characterization of a new Leptospira spp. isolated from urine of one dog living in the study area. Whole genome sequencing and phylogenetic analysis, confirmed that this genospecies was closely related to Leptospira hovindhougenii, an intermediate Leptospira spp. with unknown pathogenicity previously isolated from a rat in Denmark. Further studies are required to clarify whether healthy dogs that shed leptospires in their urine could represent a zoonotic risk for humans in this region.

scholarly journals Phylogenetic Characterization of the Palyam Serogroup Orbiviruses

Viruses ◽  
2019 ◽  
Vol 11 (5) ◽  
pp. 446 ◽  
Author(s):  
Karen Ebersohn ◽  
Peter Coetzee ◽  
Louwrens P. Snyman ◽  
Robert Swanepoel ◽  
Estelle H. Venter
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Data ◽  
Evolutionary Relationship ◽  
Full Genome Sequence ◽  
African Horse Sickness Virus ◽  
Gene Encoding ◽  
Phylogenetic Characterization ◽  
Next Generation Sequencing Ngs ◽  
High Degree

The Palyam serogroup orbiviruses are associated with abortion and teratogenesis in cattle and other ruminants. Of the 13 different serotypes that have been identified, the full genome sequence of only one, Kasba, has been published. We undertook to perform Next Generation Sequencing (NGS) and phylogenetic analysis on 12 Palyam serotypes plus field isolates of the African serotypes in our possession. The Palyam serogroup was found to be most closely related to the African horse sickness virus group and showed the most distant evolutionary relationship to the equine encephalosis viruses (EEV). Amino acid sequence analysis revealed that the gene encoding VP7 was the most conserved within serotypes and VP2 and VP5 showed the highest degree of variation. A high degree of sequence identity was found for isolates from the same geographical region. The phylogenetic analysis revealed two clades where the African serotypes were all very closely related in one clade and the other clade contained the Australian and Asian serotypes and one African serotype, Petevo. It was evident from the sequence data that the geographical origin of Palyam serogroup viruses played an important role in the development of the different serotypes.

scholarly journals Versatile Oxidase and Dehydrogenase Activities of Bacterial Pyranose 2-Oxidase Facilitate Redox Cycling with Manganese PeroxidaseIn Vitro

2019 ◽  
Vol 85 (13) ◽  
Author(s):  
Peter L. Herzog ◽  
Leander Sützl ◽  
Beate Eisenhut ◽  
Daniel Maresch ◽  
Dietmar Haltrich ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Lignin Degradation ◽  
Evolutionary Relationship ◽  
Physiological Role ◽  
Redox Cycling ◽  
Content Type ◽  
Phylogenetic Characterization ◽  
Pyranose Oxidase

ABSTRACTPyranose 2-oxidase (POx) has long been accredited a physiological role in lignin degradation, but evidence to provide insights into the biochemical mechanisms and interactions is insufficient. There are ample data in the literature on the oxidase and dehydrogenase activities of POx, yet the biological relevance of this duality could not be established conclusively. Here we present a comprehensive biochemical and phylogenetic characterization of a novel pyranose 2-oxidase from the actinomycetous bacteriumKitasatospora aureofaciens(KaPOx) as well as a possible biomolecular synergism of this enzyme with peroxidases using phenolic model substratesin vitro. A phylogenetic analysis of both fungal and bacterial putative POx-encoding sequences revealed their close evolutionary relationship and supports a late horizontal gene transfer of ancestral POx sequences. We successfully expressed and characterized a novel bacterial POx gene fromK. aureofaciens, one of the putative POx genes closely related to well-known fungal POx genes. Its biochemical characteristics comply with most of the classical hallmarks of known fungal pyranose 2-oxidases, i.e., reactivity with a range of different monosaccharides as electron donors as well as activity with oxygen, various quinones, and complexed metal ions as electron acceptors. Thus,KaPOx shows the pronounced duality of oxidase and dehydrogenase similar to that of fungal POx. We further performed efficient redox cycling of aromatic lignin model compounds betweenKaPOx and manganese peroxidase (MnP). In addition, we found a Mn(III) reduction activity inKaPOx, which, in combination with its ability to provide H2O2, implies this and potentially other POx as complementary enzymatic tools for oxidative lignin degradation by specialized peroxidases.IMPORTANCEEstablishment of a mechanistic synergism between pyranose oxidase and (manganese) peroxidases represents a vital step in the course of elucidating microbial lignin degradation. Here, the comprehensive characterization of a bacterial pyranose 2-oxidase fromKitasatospora aureofaciensis of particular interest for several reasons. First, the phylogenetic analysis of putative pyranose oxidase genes reveals a widespread occurrence of highly similar enzymes in bacteria. Still, there is only a single report on a bacterial pyranose oxidase, stressing the need of closing this gap in the scientific literature. In addition, the relatively smallK. aureofaciensproteome supposedly supplies a limited set of enzymatic functions to realize lignocellulosic biomass degradation. Both enzyme and organism therefore present a viable model to study the mechanisms of bacterial lignin decomposition, elucidate physiologically relevant interactions with specialized peroxidases, and potentially realize biotechnological applications.

scholarly journals Molecular characterization of circulating respiratory syncytial virus genotypes in Pakistani children, 2010–2013

2020 ◽  
Vol 13 (3) ◽  
pp. 438-445 ◽  
Author(s):  
Uzma Bashir Aamir ◽  
Muhammad Salman ◽  
Nadia Nisar ◽  
Nazish Badar ◽  
Mohammad Masroor Alam ◽  
...  
Keyword(s):  
Respiratory Syncytial Virus ◽  
Molecular Characterization ◽  
Virus Genotypes ◽  
Syncytial Virus

scholarly journals Diversity of Wolbachia Endosymbionts in Heteropteran Bugs

2003 ◽  
Vol 69 (10) ◽  
pp. 6082-6090 ◽  
Author(s):  
Yoshitomo Kikuchi ◽  
Takema Fukatsu
Keyword(s):  
Phylogenetic Analysis ◽  
Fragment Length Polymorphism ◽  
Universal Primers ◽  
Multiple Infections ◽  
Polymorphism Analysis ◽  
Phylogenetic Characterization ◽  
Molecular Phylogenetic ◽  
Pcr Products ◽  
Horizontal Transfers

ABSTRACT An extensive survey of Wolbachia endosymbionts in Japanese terrestrial heteropteran bugs was performed by PCR detection with universal primers for wsp and ftsZ genes of Wolbachia, cloning of the PCR products, restriction fragment length polymorphism analysis of infecting Wolbachia types, and molecular phylogenetic characterization of all the detected Wolbachia strains. Of 134 heteropteran species from 19 families examined, Wolbachia infection was detected in 47 species from 13 families. From the 47 species, 59 Wolbachia strains were identified. Of the 59 strains, 16 and 43 were assigned to A group and B group in the Wolbachia phylogeny, respectively. The 47 species of Wolbachia-infected bugs were classified into 8 species with A infection, 28 species with B infection, 2 species with AA infection, 3 species with AB infection, 5 species with BB infection, and 1 species with ABB infection. Molecular phylogenetic analysis showed little congruence between Wolbachia phylogeny and host systematics, suggesting frequent horizontal transfers of Wolbachia in the evolutionary course of the Heteroptera. The phylogenetic analysis also revealed several novel lineages of Wolbachia. Based on statistical analyses of the multiple infections, we propose a hypothetical view that, in the heteropteran bugs, interactions between coinfecting Wolbachia strains are generally not intense and that Wolbachia coinfections have been established through a stochastic process probably depending on occasional horizontal transfers.

scholarly journals An overview of respiratory syncytial virus infections in Saudi Arabia

2018 ◽  
Vol 12 (11) ◽  
pp. 929-936 ◽  
Author(s):  
Anwar Ahmed ◽  
Shama Parveen ◽  
Sarah M Al-Hassinah ◽  
Salman F. Al-Amery
Keyword(s):  
Saudi Arabia ◽  
Respiratory Syncytial Virus ◽  
Molecular Characterization ◽  
Evolutionary Dynamics ◽  
Winter Season ◽  
Glycosylation Site ◽  
Viral Pathogen ◽  
Geographical Regions ◽  
Syncytial Virus

Respiratory syncytial virus (RSV) is a major pathogen of acute respiratory tract infection (ARI) in different geographical regions including Saudi Arabia. Numerous hospital-based investigations have revealed the RSV prevalence between 0.2-54% in the paediatric population with ARI/ALRI from Saudi Arabia during 1991-2015. Maximum RSV infections occurred in children less than 1 year of age (51-97%) and male children (51-69%) were more commonly affected than females (31-49%). RSV infections are reported mostly during winter season suggesting seasonal distribution of the virus. Other respiratory viruses reported from this region are adenovirus, influenza, parainfluenza, human metapneumovirus and rhinovirus including many mixed infections. A few studies have reported the phylogenetic analysis of the circulating strains of RSV. These studies have revealed that circulating group A-RSV Saudi strains belonged to NA1 and ON1 genotypes and group B-RSV viruses clustered in the BA genotype. Molecular characterization of the Saudi strains was further carried out by mutational, selection pressure and glycosylation site analyses. We have compiled all the eighteen studies of RSV infection from Saudi Arabia in the form of this review and concluded that detailed comprehensive surveillance of RSV and other viruses in community and hospital settings is required. Information on the molecular characterization of currently circulating strains of RSV will contribute towards better understanding of the epidemiology and evolutionary dynamics of this viral pathogen. Moreover, the determination of the genetic composition of circulating RSV strains will be important during evaluation of initial vaccine trials.

scholarly journals Description of respiratory syncytial virus genotypes circulating in Colombia

2018 ◽  
Vol 12 (12) ◽  
pp. 1112-1118
Author(s):  
Viviana Avila ◽  
Eliana Calvo ◽  
Juliana Barbosa ◽  
Myriam L Velandia-Romero ◽  
Jaime E. Castellanos
Keyword(s):  
Respiratory Syncytial Virus ◽  
Respiratory Infections ◽  
Circulation Pattern ◽  
Older Children ◽  
Seasonal Behavior ◽  
Nucleotide Variability ◽  
Subtype B ◽  
Virus Genotypes ◽  
Syncytial Virus ◽  
Subtype A

Introduction: Respiratory syncytial virus (RSV) is the most common cause of acute respiratory infections in children younger than two years but also produces infection in older children and even reinfection in people of any age, a characteristic related to the existence of different infecting subtypes and genotypes. Although Colombia has established the surveillance of classical respiratory viruses, there is no information about the RSV genotypes circulating in Colombian patients. Methodology: A subgroup of 227 previously RSV positive respiratory secretion samples were taken from a nationwide surveillance study, amplified and sequenced to define the circulation pattern of RSV subtypes and genotypes during 2000-2009 period in Colombia. Results. RSV exhibited seasonal behavior with an A subtype more prevalent. Both RSV subtypes had low nucleotide variability. During the study period, the GA2 and GA5 genotypes from RSV subtype A and the BA genotype from RSV subtype B were found. Conclusion. In this report, for the first time RSV genotypes circulating in Colombia were described, this information adds valuable information about virus epidemiology helping to understand the RSV epidemic and prepare our country for the introduction of new vaccines.

scholarly journals Molecular epidemiology of human respiratory syncytial virus with severe acute respiratory infection in Huzhou from 2016 to 2019

2021 ◽  
Author(s):  
Deshun Xu ◽  
Lei Ji ◽  
Xiaofang Wu ◽  
Wei Yan ◽  
Liping Chen
Keyword(s):  
Phylogenetic Analysis ◽  
Respiratory Syncytial Virus ◽  
Nucleic Acid ◽  
G Protein ◽  
Respiratory Infection ◽  
Detection Rate ◽  
Human Respiratory Syncytial Virus ◽  
Age Group ◽  
Severe Acute Respiratory Infection ◽  
Syncytial Virus

AbstractBackgroundHuman respiratory syncytial virus (HRSV) is one of the major cause of acute lower respiratory infection in infants, the elderly and people with low immunity worldwide. Based on antigenic and genetic variations, Human respiratory syncytial virus is divided into two subgroups (A and B). Each of the subgroups is further categorized into genotypes based on the phylogenetic analyses of the sequences of the second hypervariable region.MethodsNasopharyngeal swabs (NPSs) were collected from patients of the First People’s Hospital in Huzhou from January 2016 to December 2019. Real-time RT-PCR (qPCR) was performed using double nucleic acid detection kit for respiratory syncytial virus (A\B) (Shenzhen shengkeyuan) with the ABI Q7 (Applied Biosystems). For genotyping, the primer set A-F/A-R was used to amplify the G protein of HRSV-A. Primer set B-F/B-R was used to amplify the G protein of HRSV-B. The phylogenetic analysis was constructed using the neighbor-joining algorithm with the Kimura two-parameter model and supported statistically by bootstrapping with 1000 replicates with MEGA software (version 7.0) with 1000 bootstrap replicates.ResultsA total of 973 nasopharyngeal swab samples were collected from January 2016 to December 2019, and 63 samples were positive for RSV nucleic acid, with the detection rate of 6.47%. Of the positive specimens, 28 were belonged to HRSV-A, and 35 were belonged to HRSV-B. Infection with RSV was found in all age groups tested, with the 0-1 year age group having the highest detection rate 15.2%. The detection rate was high from November to next March. Phylogenetic analysis clustered HRSV-A strains identified in Huzhou into ON1genotype. All 17 of the HRSV-B strains belonged to BA9 genotype.ConclusionsWe analyzed the HRSV strains circulation in Huzhou from January 2016 to December 2019 in Huzhou, China. This is the first molecular analysis on HRSV in Huzhou. We found Subgroup A and B of RSV were co-circulating and the 0-1 year age group having the highest infection rate.

Sign in / Sign up

Export Citation Format

Share Document