Molecular analysis of a fragment of gene E1B 19K of canine adenovirus 2 (CAV-2) isolated from dogs with symptoms of cough

AbstractThe aim of this study was to perform molecular analysis of canine adenovirus 2 (CAV-2) E1B 19K gene fragment isolated from 20 dogs of various breeds (12 males and 8 females aged 1-9 years), with clinical symptoms of upper respiratory tract infections, from the Lubelszczyzna region. Nasal swabs were taken from dogs. DNA of CAV-2 was detected using the PCR method in 16 swabs. All PCR products were sequenced, and the obtained sequences were compared with each other and with the sequence of the E1B 19K gene of the CAV-2 strain from an online database of NCBI GenBank: AC 000003. Based on analysis of the obtained sequences, three polymorphic variants of CAV-2 (No.1-3) with homology of 78 - 100% were distinguished. The nucleotide and amino acid sequences of the most frequently represented polymorphic variant, No. 1, differed from the sequences of polymorphic variant No. 2 with one substitution. The nucleotide and amino acid sequence of the E1B 19K gene of CAV-2 AC 000003 differed from the analogous sequences of representatives of variant No. 1 with 44 nucleotide and 19 amino acid substitutions. The small number of nucleotide differences in the E1B 19K CAV-2 gene among the examined own isolates, compared with AC 000003, suggest that the infections in dogs were caused by a relatively genetically stable virus which occurs in eastern Poland.

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Molecular characterization of Prunus necrotic ringspot virus isolated from rose in Brazil

Ciência Rural ◽

10.1590/0103-8478cr20141810 ◽

2015 ◽

Vol 45 (12) ◽

pp. 2197-2200 ◽

Cited By ~ 2

Author(s):

Thor Vinícius Martins Fajardo ◽

Monique Bezerra Nascimento ◽

Marcelo Eiras ◽

Osmar Nickel ◽

Gilvan Pio-Ribeiro

Keyword(s):

Amino Acid ◽

Molecular Characterization ◽

Molecular Analysis ◽

Nucleotide Sequences ◽

Amino Acid Sequences ◽

Causal Agent ◽

Ringspot Virus ◽

Prunus Necrotic Ringspot Virus ◽

First Time

ABSTRACT: There is no molecular characterization of Brazilian isolates of Prunus necrotic ringspot virus (PNRSV), except for those infecting peach. In this research, the causal agent of rose mosaic was determined and the movement (MP) and coat (CP) protein genes of a PNRSV isolate from rose were molecularly characterized for the first time in Brazil. The nucleotide and deduced amino acid sequences of MP and CP complete genes were aligned and compared with other isolates. Molecular analysis of the MP and CP nucleotide sequences of a Brazilian PNRSV isolate from rose and others from this same host showed highest identities of 96.7% and 98.6%, respectively, and Rose-Br isolate was classified in PV32 group.

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Evolution and Adaptation of the Avian H7N9 Virus into the Human Host

Microorganisms ◽

10.3390/microorganisms8050778 ◽

2020 ◽

Vol 8 (5) ◽

pp. 778

Author(s):

Andrew T. Bisset ◽

Gerard F. Hoyne

Keyword(s):

Amino Acid ◽

Avian Influenza ◽

Influenza A ◽

Amino Acid Sequences ◽

Influenza Viruses ◽

Amino Acid Substitutions ◽

Upper Respiratory Tract ◽

Viral Polymerase ◽

Evolutionary Changes ◽

Avian Origin

Influenza viruses arise from animal reservoirs, and have the potential to cause pandemics. In 2013, low pathogenic novel avian influenza A(H7N9) viruses emerged in China, resulting from the reassortment of avian-origin viruses. Following evolutionary changes, highly pathogenic strains of avian influenza A(H7N9) viruses emerged in late 2016. Changes in pathogenicity and virulence of H7N9 viruses have been linked to potential mutations in the viral glycoproteins hemagglutinin (HA) and neuraminidase (NA), as well as the viral polymerase basic protein 2 (PB2). Recognizing that effective viral transmission of the influenza A virus (IAV) between humans requires efficient attachment to the upper respiratory tract and replication through the viral polymerase complex, experimental evidence demonstrates the potential H7N9 has for increased binding affinity and replication, following specific amino acid substitutions in HA and PB2. Additionally, the deletion of extended amino acid sequences in the NA stalk length was shown to produce a significant increase in pathogenicity in mice. Research shows that significant changes in transmissibility, pathogenicity and virulence are possible after one or a few amino acid substitutions. This review aims to summarise key findings from that research. To date, all strains of H7N9 viruses remain restricted to avian reservoirs, with no evidence of sustained human-to-human transmission, although mutations in specific viral proteins reveal the efficacy with which these viruses could evolve into a highly virulent and infectious, human-to-human transmitted virus.

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Human Rhinovirus Molecular Epidemiology and Genotyping in Iranian Military Trainees with Acute Respiratory Symptoms

Journal of Archives in Military Medicine ◽

10.5812/jamm.111224 ◽

2021 ◽

Vol 8 (4) ◽

Author(s):

Fahimeh Safarnezhad Tameshkel ◽

Ali Salimi Jeda ◽

Ahmad Tavakoli ◽

Mohammad Hadi Karbalaie Niya ◽

Morteza Izadi ◽

...

Keyword(s):

Molecular Epidemiology ◽

Clinical Symptoms ◽

Respiratory Infections ◽

Direct Sequencing ◽

Human Rhinovirus ◽

P Value ◽

Rt Pcr ◽

Respiratory Problems ◽

Pcr Products ◽

Tract Infections

Background: Human rhinovirus (HRV) is still the most prevalent viral infection in humans and a significant cause of acute respiratory tract infections (ARTIs) in many communities, including military personnel undergoing basic training. Objectives: In this research, we assessed the molecular epidemiology, genotyping, and phylogenetic classification of HRVs in Iranian military trainees with respiratory infections (RI). Methods: For HRV identification and genotyping, respiratory specimens were obtained, and RT-PCR was conducted for genotyping and phylogenetic analysis of HRV utilizing primers for the 5-UTR region. Results: Among 400 Iranian military trainees (average age of 21 ± 4 years, the range of 18 - 57 years) with respiratory infections, HRV was detected in 29 patients (7%) using RT-PCR. The direct sequencing of PCR products from 10 specimens showed that the incidence of type A (n = 5, 50%) was higher than that of type B (n = 4, 40%) and type C (n = 1, 10%). There were no significant associations between HRV and respiratory and clinical symptoms, blood group, and indoor or outdoor conditions (P-value > 0.05). Conclusions: This research was the first to record HRV as a significant cause of respiratory problems among military trainees in Iran, with a frequency of 7%. The most prevalent genotype was HRV-A, which may be applicable in epidemiological and clinical studies, as well as vaccination plans.

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Cefotaxime-Resistant EnterobacteriaceaeIsolates from a Hospital in Warsaw, Poland: Identification of a New CTX-M-3 Cefotaxime-Hydrolyzing β-Lactamase That Is Closely Related to the CTX-M-1/MEN-1 Enzyme

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.42.4.827 ◽

1998 ◽

Vol 42 (4) ◽

pp. 827-832 ◽

Cited By ~ 122

Author(s):

Marek Gniadkowski ◽

Ines Schneider ◽

Andrzej Pal/ucha ◽

Renate Jungwirth ◽

Barbara Mikiewicz ◽

...

Keyword(s):

Amino Acid ◽

Clinical Laboratory ◽

Amino Acid Sequences ◽

Hospital Environment ◽

M Gene ◽

E Coli ◽

Men 1 ◽

Long Time ◽

Dna Restriction ◽

Tract Infections

ABSTRACT A group of cefotaxime-resistant Citrobacter freundiiand Escherichia coli isolates were collected by a clinical laboratory in a hospital in Warsaw, Poland, in July 1996. Detailed analysis has shown that all of these produced a β-lactamase (pI, 8.4) belonging to the CTX-M family, one of the minor extended-spectrum β-lactamase families with a strong cefotaxime-hydrolyzing activity. Sequencing has revealed that C. freundii isolates produced a new CTX-M-3 enzyme which is very closely related to the CTX-M-1/MEN-1 β-lactamase, sporadically identified in Europe over a period of 6 years. Amino acid sequences of these two β-lactamases differ at four positions: Val77Ala, Asp114Asn, Ser140Ala, and Asn288Asp (the first amino acid of each pair refers to CTX-M-1/MEN-1 and second refers to CTX-M-3). The partial sequence of the E. coli CTX-M gene was identical to the corresponding region ofbla CTX-M-3, but a transconjugant of theE. coli isolate expressed higher levels of resistance to β-lactams than did C. freundii transconjugants. These resistance differences correlated with differences in plasmid DNA restriction patterns. Our results suggest that CTX-M genes have been spread among different species of the familyEnterobacteriaceae in the hospital and that the CTX-M-3-expressing C. freundii strain causing routine urinary tract infections has been maintained for a relatively long time in the hospital environment.

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Nontypeable Haemophilus influenzae isolates from the lower respiratory tract in Western Sichuan, China: MIC value of ofloxacin and Mutation characteristics of Quinolones Resistance determining region gene

10.21203/rs.3.rs-19694/v1 ◽

2020 ◽

Author(s):

Wang Xiaolei ◽

Xie Jiang ◽

Guo YuanBiao ◽

Shao ZhuJun ◽

Zhu BingQing ◽

...

Keyword(s):

Amino Acid ◽

Respiratory Tract ◽

Haemophilus Influenzae ◽

Lower Respiratory Tract ◽

Amino Acid Sequences ◽

Quinolone Resistance ◽

Nontypeable Haemophilus Influenzae ◽

Western Sichuan ◽

Tract Infections ◽

Mic Value

Abstract Background: Fluoroquinolones are one of the most widely used antibiotics in the treatment of respiratory tract infections, and the mechanism of resistance to fluoroquinolones is considered to be related to the amino acid substitution of gyrA, gyrB, parC, and parE, the Quinolone Resistance-Determining Regions (QRDRs) of DNA cyclase type II topoisomerase and IV topoisomerase. The purpose of this study was to explore the molecular mechanism of quinolone resistance of Nontypeable Haemophilus influenzae(NTHi ) isolates and analyze the mutation law of the QRDRs gene. Results: MIC value of ofloxacin of 280 NTHi isolates from lower respiratory tract secretions in children group during 2003~2004 and in whole age group during 2013~2014 in Western Sichuan, China were monitored and the amino acid sequences of gyrA, gyrB, parC and parE gene in QRDRs were detected. The resistance rate of ofloxacin in adult group was 1.92% (n=52), while the NTHi strains with ofloxacin MIC value≥0.5 showed an upward trend in all age groups. No ofloxacin-resistant strains were found in 57 NTHi strains isolated from the children patient. Four amino acid substitutions were found in GyrA genes, four in GyrB, three in parC and nine in parE genes. The results showed that different amino acid replacement patterns of the gyrA , gyrB, parC and parE gene had different effects on ofloxacin MIC values. Conclusions: Ser-84-leu and asp-88-tyr/asn mutation of the gyrA, ser-84-lys/ile and ser -133-ala mutations of the parC and ala-400-val variation of the gyrB were the main factors leading to the increase of MIC value of ofloxacin of NTHi strains in Western Sichuan, China. It can be predicted that with the increase of quinolones exposure, the susceptibility of isolates from children to quinolones will be further reduced.

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Investigation of Two Evolutionarily Unrelated Halocarboxylic Acid Dehalogenase Gene Families

Journal of Bacteriology ◽

10.1128/jb.181.8.2535-2547.1999 ◽

1999 ◽

Vol 181 (8) ◽

pp. 2535-2547 ◽

Cited By ~ 72

Author(s):

Katja E. Hill ◽

Julian R. Marchesi ◽

Andrew J. Weightman

Keyword(s):

Amino Acid ◽

Molecular Analysis ◽

Phylogenetic Trees ◽

Gene Families ◽

Amino Acid Sequences ◽

Group I ◽

Silent Genes ◽

Degrading Bacteria ◽

Group Ii ◽

Almost All

ABSTRACT Dehalogenases are key enzymes in the metabolism of halo-organic compounds. This paper describes a systematic approach to the isolation and molecular analysis of two families of bacterial α-halocarboxylic acid (αHA) dehalogenase genes, called group I and group II deh genes. The two families are evolutionarily unrelated and together represent almost all of the αHAdeh genes described to date. We report the design and evaluation of degenerate PCR primer pairs for the separate amplification and isolation of group I and II dehgenes. Amino acid sequences derived from 10 of 11 group Ideh partial gene products of new and previously reported bacterial isolates showed conservation of five residues previously identified as essential for activity. The exception, DehD from a Rhizobium sp., had only two of these five residues. Group II deh gene sequences were amplified from 54 newly isolated strains, and seven of these sequences were cloned and fully characterized. Group II dehalogenases were stereoselective, dechlorinating l- but not d-2-chloropropionic acid, and derived amino acid sequences for all of the genes exceptdehII°P11 showed conservation of previously identified essential residues. Molecular analysis of the twodeh families highlighted four subdivisions in each, which were supported by high bootstrap values in phylogenetic trees and by enzyme structure-function considerations. Group Ideh genes included two putative cryptic or silent genes, dehI°PP3 anddehI°17a, produced by different organisms. Group II deh genes included two cryptic genes and an active gene, dehII PP3, that can be switched off and on. All αHA-degrading bacteria so far described were Proteobacteria, a result that may be explained by limitations either in the host range fordeh genes or in isolation methods.

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Patterns of Human Respiratory Viruses and Lack of MERS-Coronavirus in Patients with Acute Upper Respiratory Tract Infections in Southwestern Province of Saudi Arabia

Advances in Virology ◽

10.1155/2017/4247853 ◽

2017 ◽

Vol 2017 ◽

pp. 1-7 ◽

Cited By ~ 8

Author(s):

Ahmed A. Abdulhaq ◽

Vinod Kumar Basode ◽

Anwar M. Hashem ◽

Ahmed S. Alshrari ◽

Nassrin A. Badroon ◽

...

Keyword(s):

Saudi Arabia ◽

Respiratory Viruses ◽

Surveillance Systems ◽

Upper Respiratory Tract ◽

Nasal Swabs ◽

Syncytial Virus ◽

Human Coronaviruses ◽

Winter Time ◽

Tract Infections ◽

Dual Infections

We undertook enhanced surveillance of those presenting with respiratory symptoms at five healthcare centers by testing all symptomatic outpatients between November 2013 and January 2014 (winter time). Nasal swabs were collected from 182 patients and screened for MERS-CoV as well as other respiratory viruses using RT-PCR and multiplex microarray. A total of 75 (41.2%) of these patients had positive viral infection. MERS-CoV was not detected in any of the samples. Human rhinovirus (hRV) was the most detected pathogen (40.9%) followed by non-MERS-CoV human coronaviruses (19.3%), influenza (Flu) viruses (15.9%), and human respiratory syncytial virus (hRSV) (13.6%). Viruses differed markedly depending on age in which hRV, Flu A, and hCoV-OC43 were more prevalent in adults and RSV, hCoV-HKU1, and hCoV-NL63 were mostly restricted to children under the age of 15. Moreover, coinfection was not uncommon in this study, in which 17.3% of the infected patients had dual infections due to several combinations of viruses. Dual infections decreased with age and completely disappeared in people older than 45 years. Our study confirms that MERS-CoV is not common in the southwestern region of Saudi Arabia and shows high diversity and prevalence of other common respiratory viruses. This study also highlights the importance and contribution of enhanced surveillance systems for better infection control.

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Ciliary Ultrastructure and Mucociliary Transport in Upper Respiratory Tract Infections

American Journal of Rhinology ◽

10.2500/105065894782537307 ◽

1994 ◽

Vol 8 (5) ◽

pp. 211-216 ◽

Cited By ~ 3

Author(s):

Tommi Torkkeli ◽

Markus Rautiainen ◽

Juhani Nuutinen

Keyword(s):

Respiratory Tract ◽

Respiratory Tract Infections ◽

Clinical Symptoms ◽

Upper Respiratory Tract Infections ◽

Mucociliary Transport ◽

Upper Respiratory Tract ◽

Severe Infections ◽

Upper Respiratory ◽

Tract Infections ◽

Ciliary Ultrastructure

The ciliary ultrastructure in transmission electron microscopy and nasal mucociliary transport rate (MTR) by a radioisotopic method were studied in 50 patients with longstanding upper respiratory tract infections. The clinical symptoms correlated well with MTR. The symptoms in patients with MTR 3 mm/min or better were mild, but the patients with poor MTR (less than 3 mm/min) suffered from recurrent or severe infections. The completely normal ultrastructural findings were found only in patients with MTR better than 3 mm/min. All the patients with poor MTR had pathological ciliary ultrastructure, with numerous tubular anomalies and disorientation of ciliary beat direction. The outer dynein arms were found to be short in 16% of cases with poor MTR.

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Study of Effect of Household Parental Smoking on Development of Acute Otitis Media in Children Under 12 Years

Global Journal of Health Science ◽

10.5539/gjhs.v8n5p81 ◽

2015 ◽

Vol 8 (5) ◽

pp. 81 ◽

Cited By ~ 8

Author(s):

Soroush Amani ◽

Parastoo Yarmohammadi

Keyword(s):

Otitis Media ◽

Clinical Symptoms ◽

Demographic Data ◽

Acute Otitis Media ◽

Parental Smoking ◽

Upper Respiratory Tract ◽

Respiratory Problems ◽

Significant Difference ◽

Group 2 ◽

Tract Infections

BACKGROUND & AIM: High prevalence of acute otitis media (AOM) in children represents a combination of the factors developing eustachian tube dysfunction and higher susceptibility to upper respiratory tract infections in children. This disease is relatively prevalent in Iran and much cost is spent annually to treat it. This study investigated the effect of household parental smoking on development of AOM in children under 12 years. METHODS: In this case-control study all patients under the age of 12 years with AOM referring an ENT clinic in Shahrekord, southwest Iran between April 2014 and August 2014 were enrolled by convenience sampling. This study included two groups. Group 1 (G1) was exposed to parental smoking at home and group 2 (G2) was not. For the patients, a questionnaire of demographic data such as age and gender, the disease symptoms, parents' education level, history of respiratory diseases, allergy, surgery (adenoidectomy, tonsillectomy, and tympanostomy), and household smoking was filled out by a specialist through interview. RESULTS: In this study, 250 children 1-12 years with AOM, 145 in G1 and 105 in G2, were investigated. Clinical symptoms including fever (p=0.001) and hearing loss (p=0.014) were significantly more frequent in the children of G1 than G2, and otalgia, discharge, and tinnitus were similarly frequent in the two groups (p>0.05). Also, eardrum inflammation was more frequent in G1 than G2, with no significant difference (p>0.05). AOM was reported 70.3% in G1, which was higher than 26.7% reported in G2 (p=0.001). Also, asthma, recurrent ear pain, enlargement of the tonsils, and respiratory problems were more frequent in G1 than G2 (p<0.05). CONCLUSIONS: Parental smoking was a risk factor for AOM and respiratory problems and therefore the parents are recommended to avoid smoking near children to reduce the likelihood of AOM development and exacerbation in children.

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Cloning and Sequencing of Hydroxylase Genes Involved in Taxol Biosynthesis

Zeitschrift für Naturforschung C ◽

10.1515/znc-2004-7-820 ◽

2004 ◽

Vol 59 (7-8) ◽

pp. 561-564 ◽

Cited By ~ 2

Author(s):

Jun Tu ◽

Ping Zhu ◽

Ke-di Cheng ◽

Chao Meng

Keyword(s):

Amino Acid ◽

Cdna Library ◽

Amino Acid Sequences ◽

Full Length ◽

Taxus Chinensis ◽

Specific Primer ◽

Cloning And Sequencing ◽

Taxol Biosynthesis ◽

New Genes ◽

Pcr Method

AbstractTwo full-length cDNAs (TCH1 and TCH2) were obtained from a cDNA library of Taxus chinensis mainly by the single specific-primer PCR (SSP-PCR) method. Compared with other reported enzymes from Taxus species, the deduced amino acid sequences of TCH1 and TCH2 exhibit significant homologies to hydroxylases that are involved in taxol biosynthesis. These findings imply that the two new genes are closely related to the biosynthesis of taxol/taxoids.

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