Genetic characterisation and analysis of infectious bronchitis virus isolated from Brazilian flocks between 2010 and 2015. 2017

Claudia Carranza, and Claudete S Astolfi-Ferreira, and Silvana H Santander Parra, and Luis F N Nuñez, and Zoltan Penzes, and Jorge L Chacón, and Luiz Sesti, and Ruy D Chacón, and Antonio J Piantino Ferreira
a Department of Pathology, School of Veterinary Medicine , University of São Paulo , São Paulo , Brazil.

1. Infectious bronchitis virus (IBV) variants in Brazil were isolated during 2010-2015 for epidemiological and molecular analysis to characterise the different variants and perform a bioinformatic analysis to compare with sequences of variants collected over the previous 40 years. 2. Of the 453 samples examined, 61.4% were positive for IBV and 75.9% of these were considered to have the BR-I genotype and were detected in birds of all ages distributed in all five Brazilian regions. 3. The ratio of non-synonymous substitutions per non-synonymous site (dN) to synonymous substitutions per synonymous site (dS), i.e. dN/dS, revealed a predominance of codons with non-synonymous substitutions in the first third of the S1 gene and a dN/dS ratio of 0.67. Additionally, prediction of N-glycosylation sites showed that most of the BR-I variants (from 2003 to early 2014) had an extra site at amino acid position 20, whereas the newest variants lacked this extra site. 4. These results suggest that Brazilian IBV variants probably underwent drastic mutations at various points between 1983 and 2003 and that the selection processes became silent after achieving a sufficiently effective antigenic structure for invasion and replication in their hosts. Brazilian IBV genotype BR-I is currently the predominant genotype circulating in Brazil and South America.

UI MeSH Term Description Entries
D010802 Phylogeny The relationships of groups of organisms as reflected by their genetic makeup. Community Phylogenetics,Molecular Phylogenetics,Phylogenetic Analyses,Phylogenetic Analysis,Phylogenetic Clustering,Phylogenetic Comparative Analysis,Phylogenetic Comparative Methods,Phylogenetic Distance,Phylogenetic Generalized Least Squares,Phylogenetic Groups,Phylogenetic Incongruence,Phylogenetic Inference,Phylogenetic Networks,Phylogenetic Reconstruction,Phylogenetic Relatedness,Phylogenetic Relationships,Phylogenetic Signal,Phylogenetic Structure,Phylogenetic Tree,Phylogenetic Trees,Phylogenomics,Analyse, Phylogenetic,Analysis, Phylogenetic,Analysis, Phylogenetic Comparative,Clustering, Phylogenetic,Community Phylogenetic,Comparative Analysis, Phylogenetic,Comparative Method, Phylogenetic,Distance, Phylogenetic,Group, Phylogenetic,Incongruence, Phylogenetic,Inference, Phylogenetic,Method, Phylogenetic Comparative,Molecular Phylogenetic,Network, Phylogenetic,Phylogenetic Analyse,Phylogenetic Clusterings,Phylogenetic Comparative Analyses,Phylogenetic Comparative Method,Phylogenetic Distances,Phylogenetic Group,Phylogenetic Incongruences,Phylogenetic Inferences,Phylogenetic Network,Phylogenetic Reconstructions,Phylogenetic Relatednesses,Phylogenetic Relationship,Phylogenetic Signals,Phylogenetic Structures,Phylogenetic, Community,Phylogenetic, Molecular,Phylogenies,Phylogenomic,Reconstruction, Phylogenetic,Relatedness, Phylogenetic,Relationship, Phylogenetic,Signal, Phylogenetic,Structure, Phylogenetic,Tree, Phylogenetic
D011201 Poultry Diseases Diseases of birds which are raised as a source of meat or eggs for human consumption and are usually found in barnyards, hatcheries, etc. The concept is differentiated from BIRD DISEASES which is for diseases of birds not considered poultry and usually found in zoos, parks, and the wild. Disease, Poultry,Diseases, Poultry,Poultry Disease
D001938 Brazil A country located on the eastern coast of South America, located between Colombia and Peru, that borders the Atlantic Ocean. It is bordered on the north by Venezuela, Guyana, Suriname, and French Guiana, on the south by Uruguay, and on the west by Argentina. The capital is Brasilia.
D002645 Chickens Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA. Gallus gallus,Gallus domesticus,Gallus gallus domesticus,Chicken
D005838 Genotype The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS. Genogroup,Genogroups,Genotypes
D000818 Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA. Animal,Metazoa,Animalia
D001351 Infectious bronchitis virus A species of CORONAVIRUS causing infections in chickens and possibly pheasants. Chicks up to four weeks old are the most severely affected. Avian Infectious Bronchitis Virus,Infectious Bronchitis Virus, Avian,Infectious bronchitis viruses,bronchitis viruses, Infectious
D017423 Sequence Analysis, RNA A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE. RNA Sequence Analysis,Sequence Determination, RNA,Analysis, RNA Sequence,Determination, RNA Sequence,Determinations, RNA Sequence,RNA Sequence Determination,RNA Sequence Determinations,RNA Sequencing,Sequence Determinations, RNA,Analyses, RNA Sequence,RNA Sequence Analyses,Sequence Analyses, RNA,Sequencing, RNA
D018352 Coronavirus Infections Virus diseases caused by the CORONAVIRUS genus. Some specifics include transmissible enteritis of turkeys (ENTERITIS, TRANSMISSIBLE, OF TURKEYS); FELINE INFECTIOUS PERITONITIS; and transmissible gastroenteritis of swine (GASTROENTERITIS, TRANSMISSIBLE, OF SWINE). Infections, Coronavirus,MERS (Middle East Respiratory Syndrome),Middle East Respiratory Syndrome,Coronavirus Infection,Infection, Coronavirus

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