Claudio L. Afonso
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View article: Coding-complete genome sequence of a GI-13 infectious bronchitis virus from commercial chicken in India
Coding-complete genome sequence of a GI-13 infectious bronchitis virus from commercial chicken in India Open
Infectious bronchitis virus (IBV) causes a highly contagious, acute upper respiratory disease in chickens characterized by nasal discharge, coughing, and rales. Here, the complete genome sequence of a recombinant GI-13 IBV strain ck/IN/A23…
View article: Sequencing of historic samples provides complete coding sequences of chicken calicivirus from the United States
Sequencing of historic samples provides complete coding sequences of chicken calicivirus from the United States Open
Here, we report the coding-complete genomic sequences of two chicken caliciviruses from US poultry flocks in 2003 and 2004. They show the same genomic organization as that of other members of the Bavovirus genus and have the highest nucleo…
View article: Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases
Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases Open
Metagenomics offers the potential to replace and simplify classical methods used in the clinical diagnosis of human and veterinary infectious diseases. Metagenomics boasts a high pathogen discovery rate and high specificity, advantages abs…
View article: Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples
Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples Open
Direct-targeted next-generation sequencing (tNGS), with its undoubtedly superior diagnostic capacity over real-time PCR (RT-PCR), and direct-non-targeted NGS (ntNGS), with its higher capacity to identify and characterize multiple agents, a…
View article: Complete genome sequence of seven virulent Newcastle disease virus isolates of sub-genotype XIII.1.1 from Tanzania
Complete genome sequence of seven virulent Newcastle disease virus isolates of sub-genotype XIII.1.1 from Tanzania Open
We report the complete genome sequences of seven virulent Newcastle disease viruses (NDVs) that were isolated from chickens from live bird markets in the Arusha, Iringa, Mbeya, and Tanga regions of Tanzania in 2012. Phylogenetic analysis r…
View article: Complete Genome Sequence of an Avian Orthoavulavirus 13 Strain Detected in Ukraine
Complete Genome Sequence of an Avian Orthoavulavirus 13 Strain Detected in Ukraine Open
We report the complete genome sequence of an avian orthoavulavirus 13 strain, isolated from a white-fronted goose in the Odesa region of Ukraine in 2013. The detection of avian orthoavulavirus 13 in Ukraine confirms that the geographic dis…
View article: Complete Genome Sequences of Avian Metapneumovirus Subtype B Vaccine Strains from Brazil
Complete Genome Sequences of Avian Metapneumovirus Subtype B Vaccine Strains from Brazil Open
Avian metapneumovirus (aMPV) causes a highly contagious upper respiratory and reproductive disease in chickens, turkeys, and ducks. Here, complete genome sequences of aMPV-B vaccine strains BR/1890/E1/19 (PL21, Nemovac; Boehringer Ingelhei…
View article: Genetic diversity of Newcastle disease viruses circulating in wild and synanthropic birds in Ukraine between 2006 and 2015
Genetic diversity of Newcastle disease viruses circulating in wild and synanthropic birds in Ukraine between 2006 and 2015 Open
Newcastle disease virus (NDV) infects a wide range of bird species worldwide and is of importance to the poultry industry. Although certain virus genotypes are clearly associated with wild bird species, the role of those species in the mov…
View article: Unique Variants of Avian Coronaviruses from Indigenous Chickens in Kenya
Unique Variants of Avian Coronaviruses from Indigenous Chickens in Kenya Open
The avian gamma-coronavirus infectious bronchitis virus (AvCoV, IBV; Coronaviridae family) causes upper respiratory disease associated with severe economic losses in the poultry industry worldwide. Here, we report for the first time in Ken…
View article: Comparable outcomes from long and short read random sequencing of total RNA for detection of pathogens in chicken respiratory samples
Comparable outcomes from long and short read random sequencing of total RNA for detection of pathogens in chicken respiratory samples Open
Co-infections of avian species with different RNA viruses and pathogenic bacteria are often misdiagnosed or incompletely characterized using targeted diagnostic methods, which could affect the accurate management of clinical disease. A non…
View article: Detection and Genome Sequence Analysis of Avian Metapneumovirus Subtype A Viruses Circulating in Commercial Chicken Flocks in Mexico
Detection and Genome Sequence Analysis of Avian Metapneumovirus Subtype A Viruses Circulating in Commercial Chicken Flocks in Mexico Open
Avian metapneumoviruses (aMPV subtypes A-D) are respiratory and reproductive pathogens of poultry. Since aMPV-A was initially reported in Mexico in 2014, there have been no additional reports of its detection in the country. Using nontarge…
View article: Genome Sequence Variations of Infectious Bronchitis Virus Serotypes From Commercial Chickens in Mexico
Genome Sequence Variations of Infectious Bronchitis Virus Serotypes From Commercial Chickens in Mexico Open
New variants of infectious bronchitis viruses (IBVs; Coronaviridae ) continuously emerge despite routine vaccinations. Here, we report genome sequence variations of IBVs identified by random non-targeted next generation sequencing (NGS) of…
View article: Novel Recombinant Newcastle Disease Virus-Based In Ovo Vaccines Bypass Maternal Immunity to Provide Full Protection from Early Virulent Challenge
Novel Recombinant Newcastle Disease Virus-Based In Ovo Vaccines Bypass Maternal Immunity to Provide Full Protection from Early Virulent Challenge Open
Newcastle disease (ND) is one of the most economically important poultry diseases. Despite intensive efforts with current vaccination programs, this disease still occurs worldwide, causing significant mortality even in vaccinated flocks. T…
View article: A Novel Recombinant Newcastle Disease Vaccine Improves Post- In Ovo Vaccination Survival with Sustained Protection against Virulent Challenge
A Novel Recombinant Newcastle Disease Vaccine Improves Post- In Ovo Vaccination Survival with Sustained Protection against Virulent Challenge Open
In ovo vaccination has been employed by the poultry industry for over 20 years to control numerous avian diseases. Unfortunately, in ovo live vaccines against Newcastle disease have significant limitations, including high embryo mortality …
View article: Near-Complete Genome Sequences of Five Siciniviruses from North America
Near-Complete Genome Sequences of Five Siciniviruses from North America Open
Here, we report near-complete genome sequences of Sicinivirus from U.S. poultry flocks in 2003 to 2005 and Mexico in 2019. They show highest nucleotide identity (84.5 to 85.5%) with other members of the Sicinivirus genus. These sequences u…
View article: Whole-Genome Sequence of <i>Avian coronavirus</i> from a 15-Year-Old Sample Confirms Evidence of GA08-like Strain Circulation 4 Years Prior to Its First Reported Outbreak
Whole-Genome Sequence of <i>Avian coronavirus</i> from a 15-Year-Old Sample Confirms Evidence of GA08-like Strain Circulation 4 Years Prior to Its First Reported Outbreak Open
Here, we report the complete genome sequence of an Avian coronavirus strain GA08-like isolate from a fecal sample from a broiler chicken collected in Georgia, USA, in 2004. The viral genome in this 15-year-old sample provides evidence for …
View article: Virulence during Newcastle Disease Viruses Cross Species Adaptation
Virulence during Newcastle Disease Viruses Cross Species Adaptation Open
The hypothesis that host adaptation in virulent Newcastle disease viruses (NDV) has been accompanied by virulence modulation is reviewed here. Historical records, experimental data, and phylogenetic analyses from available GenBank sequence…
View article: Surveillance and Genetic Characterization of Virulent Newcastle Disease Virus Subgenotype V.3 in Indigenous Chickens from Backyard Poultry Farms and Live Bird Markets in Kenya
Surveillance and Genetic Characterization of Virulent Newcastle Disease Virus Subgenotype V.3 in Indigenous Chickens from Backyard Poultry Farms and Live Bird Markets in Kenya Open
Kenyan poultry consists of ~80% free-range indigenous chickens kept in small flocks (~30 birds) on backyard poultry farms (BPFs) and they are traded via live bird markets (LBMs). Newcastle disease virus (NDV) was detected in samples collec…
View article: A 24-Year-Old Sample Contributes the Complete Genome Sequence of Fowl Aviadenovirus D from the United States
A 24-Year-Old Sample Contributes the Complete Genome Sequence of Fowl Aviadenovirus D from the United States Open
Here, we report the complete genome sequence of fowl adenovirus D (FAdV-D) isolated from a preserved 24-year-old pancreas sample of a broiler chicken embryo. The results of the sequence showed that the viral genome is 44,079 bp long.
View article: First whole-genome analysis of the novel coronavirus (SARS-CoV-2) obtained from COVID-19 patients from five districts in Western Serbia
First whole-genome analysis of the novel coronavirus (SARS-CoV-2) obtained from COVID-19 patients from five districts in Western Serbia Open
This study was endeavoured to contribute in furthering our understanding of the molecular epidemiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by sequencing and analysing the first full-length genome sequences obtai…
View article: Complete Coding Sequences of Three Chicken Parvovirus Isolates from the United States
Complete Coding Sequences of Three Chicken Parvovirus Isolates from the United States Open
Parvoviruses are commonly found in U.S. poultry and are associated with clinical disease. Here, we report the complete coding sequences of three chicken parvoviruses from broiler chickens from commercial farms in the state of Georgia.
View article: Epizootic of highly pathogenic H7N3 Avian Influenza in an ecologic reserve in Mexico
Epizootic of highly pathogenic H7N3 Avian Influenza in an ecologic reserve in Mexico Open
Summary This report includes a 2015 epizootic of highly pathogenic H7N3 avian influenza virus among captive and wild birds at “El Zapotal” ecologic reserve, located in the state of Chiapas, Mexico. Epidemiological control measures were imp…
View article: Complete Genome Sequence of <i>Avian Coronavirus</i> Strain GA08 (GI-27 Lineage)
Complete Genome Sequence of <i>Avian Coronavirus</i> Strain GA08 (GI-27 Lineage) Open
Avian coronavirus , also known as infectious bronchitis virus, is a highly contagious respiratory pathogen of chickens that is responsible for major economic losses to the poultry industry around the globe. Here, we report the complete gen…
View article: A 25-Year-Old Sample Contributes the Complete Genome Sequence of <i>Avian Coronavirus</i> Vaccine Strain ArkDPI, Reisolated from Commercial Broilers in the United States
A 25-Year-Old Sample Contributes the Complete Genome Sequence of <i>Avian Coronavirus</i> Vaccine Strain ArkDPI, Reisolated from Commercial Broilers in the United States Open
Here, we report the complete genome sequence of Avian coronavirus strain ArkDPI of the GI-9 lineage, isolated from broiler chickens in North Georgia in 1994. This is the complete genome sequence of this vaccine strain, reisolated from broi…
View article: Complete Genome Sequences of 11 Newcastle Disease Virus Isolates of Subgenotype VII.2 from Indonesia
Complete Genome Sequences of 11 Newcastle Disease Virus Isolates of Subgenotype VII.2 from Indonesia Open
We report the complete genome sequences of 11 virulent Newcastle disease viruses. The isolates were obtained from vaccinated broiler and layer chickens in three different provinces of Indonesia in 2013 and 2014. Phylogenetic analysis revea…
View article: Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology
Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology Open
View article: Genetic characterization and pathogenesis of the first H9N2 low pathogenic avian influenza viruses isolated from chickens in Kenyan live bird markets
Genetic characterization and pathogenesis of the first H9N2 low pathogenic avian influenza viruses isolated from chickens in Kenyan live bird markets Open
View article: Rapid evolution of Mexican H7N3 highly pathogenic avian influenza viruses in poultry
Rapid evolution of Mexican H7N3 highly pathogenic avian influenza viruses in poultry Open
Highly pathogenic avian influenza (HPAI) virus subtype H7N3 has been circulating in poultry in Mexico since 2012 and vaccination has been used to control the disease. In this study, eight Mexican H7N3 HPAI viruses from 2015-2017 were isola…
View article: A retrospective study of Newcastle disease in Kenya
A retrospective study of Newcastle disease in Kenya Open
View article: Tropism of Newcastle disease virus strains for chicken neurons, astrocytes, oligodendrocytes, and microglia
Tropism of Newcastle disease virus strains for chicken neurons, astrocytes, oligodendrocytes, and microglia Open