Claudio L Afonso

Claudio L Afonso
United States Department of Agriculture | USDA · Agricultural Research Service (ARS)

PhD

About

517
Publications
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Introduction
Prior to joining BASE₂BIO, Dr. Afonso was the Lead Scientist for Newcastle Disease at the USDA Southeast Poultry Research Laboratory from 2005 until 2019. He holds a Ph.D in Genetics, Cellular and Molecular Biology from the University of Nebraska along with post-doc training at Yale University and the Plum Island Animal Disease Center of the USDA.

Publications

Publications (517)
Presentation
Full-text available
Direct sequencing of clinical samples using next- and third-generation sequencing (NGS) platforms is suitable to conduct active surveillance of poultry farms and these technologies are mature enough to pursue development of standard operating procedures for clinical validation.
Article
Full-text available
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 obtained from 48 coronavirus disease-2019 (COVID-19) patients in five districts in Western Serbia in the period Apri...
Article
Full-text available
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 and the inability to induce full protection during the first two weeks of life. In this study, a recombinant li...
Poster
All naturally occurring highly pathogenic avian influenza (HPAI) viruses to date have been H5 and H7 subtypes resulting from mutation of the fusion cleavage site of the haemagglutinin (HA) gene. The affordable Flongle flow cell adapter for Nanopore’s MinION and GridION devices allows for cost-efficient, real-time access to smaller, frequently perfo...
Poster
Since 2012, H7N3 highly pathogenic avian influenza (HPAI) virus has been circulating in commercial chickens and backyard poultry in Mexico, possing a constant economic and animal welfare threat worldwide. Despite the control measures undertaken, cases of H7N3 HPAI in poultry, as well as reported human infection of poultry workers, have been repeate...
Article
Background There is evidence that chicken IL4 (chIL4) functions similarly to its mammalian analogue by enhancing type 2 T helper (Th2) humoral immunity and promoting protection against parasitic infections; however, no studies have been performed to assess the effect of chIL4 on the pathogenesis of Newcastle disease (ND). To assess the role of chIL...
Article
Full-text available
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 update knowledge on diversity and contribute to a better understanding of the molecular epidemiology of sicinivi...
Article
Full-text available
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 in 2004. The viral genome in this 15-year-old sample provides evidence for the circulation of the GA08-like strain at least 4 years before its first report in 2008.
Presentation
The H5 subtype of highly pathogenic avian influenza (HPAI) viruses pose a serious threat to the poultry industry worldwide. By the use of reverse genetics, we constructed a recombinant avian paramyxovirus serotype 10 vector vaccine expressing the hemagglutinin protein of AI virus H5 subtype (rA10‐H5) from the North American influenza outbreak. To e...
Conference Paper
The H5 subtype of highly pathogenic avian influenza (HPAI) viruses pose a serious threat to the poultry industry worldwide. By the use of reverse genetics, we constructed a recombinant avian paramyxovirus serotype 10 vector vaccine expressing the hemagglutinin protein of AI virus H5 subtype (rA10‐H5) from the North American influenza outbreak. To e...
Article
Full-text available
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 sequences suggest that currently circulating NDVs emerged in the 1920–1940′s from low virulence viruses by mutation at...
Article
Full-text available
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 collected from chickens, wild farm birds, and other domestic poultry species during a 2017–2018 survey conducted at 6...
Article
Full-text available
Here, we report the complete genome sequence of fowl aviadenovirus 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.
Article
Runting stunting syndrome (RSS) in commercial chickens has been reported worldwide, and although several studies have attempted to clarify the cause and describe the lesions, there are gaps in knowledge of the epidemiology, pathogenesis, and etiology. The study objective was to use commercial chicks naturally affected by RSS to describe the histolo...
Article
Full-text available
Newcastle disease (ND) is a major constraint to Kenya's poultry production, which is comprised of approximately 80% indigenous chickens (ICs; caged and free-range system) and 20% exotic chickens (intensive system). This study analyzed cases reported as suspected ND in Kenya between 2005 and 2015. Of the suspected 332 ND reported cases from the thre...
Article
Full-text available
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.
Poster
Historically, low pathogenic H5 and H7 avian influenza viruses (AIV) have the potential to mutate to become highly pathogenic and have caused costly outbreaks in poultry. The key determinant for the increase in pathogenicity is the proteolytic cleavage site of hemagglutinin (HA) gene. Even though different approaches are currently available for dir...
Method
Full-text available
This video describes the type of report produced by Base2Bio for our research team to analyze crude sequences from total RNA of clinical swab samples. The total RNA was processed and sequenced with an Illumina Myseq sequencer using our published protocols
Preprint
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 implemented to prevent virus dissemination. The infection with the highly pathogenic H7N3 virus was detected predominantly...
Article
Full-text available
Newcastle disease (ND) is a major constraint to Kenya’s poultry production, which is comprised of approximately 80% indigenous chickens (ICs; caged and free-range system) and 20% exotic chickens (intensive system). This study analyzed cases reported as suspected ND in Kenya between 2005 and 2015. Of the suspected 332 ND reported cases from the thre...
Article
Full-text available
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 broilers in the United States.
Article
Full-text available
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 genome sequence of strain GA08 of the GI-27 lineage, isolated from a fecal sample from a broiler chicken collected...
Article
Full-text available
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 revealed that all isolates belong to subgenotype VII.2 in the class II cluster.
Presentation
Hypoglycemia-spiking Mortality Syndrome (H-SMS) is a malady of broiler chicks characterized by sudden increase in mortality. The affected birds are hypoglycemic, with blood glucose levels of less than 180 mg/dl (normal = 225-300 mg/dl) and often as low as 20mg/dl. Clinical signs may include tremors, ataxia, and blindness. The etiology of H-SMS is u...
Article
Full-text available
Background Avian avulavirus (commonly known as avian paramyxovirus-1 or APMV-1) can cause disease of varying severity in both domestic and wild birds. Understanding how viruses move among hosts and geography would be useful for informing prevention and control efforts. A Bayesian statistical framework was employed to estimate the evolutionary histo...
Article
Full-text available
U.S. public health agencies have employed next-generation sequencing (NGS) as a tool to quickly identify foodborne pathogens during outbreaks. Although established short-read NGS technologies are known to provide highly accurate data, long-read sequencing is still needed to resolve highly-repetitive genomic regions and genomic arrangement, and to c...
Article
Previously, we have demonstrated that the recombinant Newcastle disease virus (NDV) expressing the infectious laryngotracheitis virus (ILTV) glycoprotein D (gD) conferred protection against both virulent NDV and ILTV challenges in chickens. In this study, we evaluated the genetic stability of the recombinant vaccine after eight serial passages in e...
Article
Full-text available
Poultry production plays an important role in the economy and livelihoods of rural households in Kenya. As part of a surveillance program, avian influenza virus (AIV)-specific real-time RT-PCR (RRT-PCR) was used to screen 282 oropharyngeal swabs collected from chickens at six live bird markets (LBMs) and 33 backyard poultry farms in Kenya and 8 pos...
Article
Full-text available
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 isolated and fully sequenced. No evidence of reassortment was detected with other avian influenza (AI) viruses, but...
Article
Full-text available
Background: Newcastle disease (ND), which is caused by infections of poultry species with virulent strains of Avian orthoavulavirus-1, also known as avian paramyxovirus 1 (APMV-1), and formerly known as Newcastle disease virus (NDV), may cause neurological signs and encephalitis. Neurological signs are often the only clinical signs observed in bir...
Article
Full-text available
Avian infectious bronchitis virus is the causative agent of a highly contagious disease that results in severe economic losses to the poultry industry worldwide. Here, we report the first coding-complete genome sequence of strain DMV/1639 of the GI-17 lineage, isolated from broiler chickens in Georgia in 2019.
Poster
Virulent strains of Newcastle disease virus (NDV) cause a devastating disease in poultry worldwide. Oropharyngeal and cloacal swabs were collected from chickens from live bird markets in four different regions of Tanzania, in 2012. Total RNA from swab-derived allantoic fluid was extracted using the QIAamp Viral RNA Mini kit. The Illumina libraries...
Poster
Hypoglycemia and spiking mortality syndrome (H-SMS) is a malady of broilers chicks characterized by sudden increase in mortality. The affected birds are hypoglycemic, with blood glucose levels of less than 180 mg/dl. Clinical signs may include tremors, ataxia, and blindness. The etiology of H-SMS is unknown; however, the successful experimental rep...
Poster
A low pathogenic avian influenza virus (LPAIV) subtype H9N2 was isolated from chickens at live bird markets in Kenya. The Kenyan H9N2 LPAIV reported here for the first time belongs to group B of the G1 lineage and is infectious and transmissible in chickens by direct contact. The presence of molecular markers for mammalian receptor specificity in t...
Article
Full-text available
Virulent Newcastle disease viruses (NDV) have been present in Mexico since 1946, and recently, multiple outbreaks have been reported in the country. Here, we characterized eleven NDV isolated from apparently healthy wild birds and backyard chickens in three different locations of Jalisco, Mexico in 2017. Total RNA from NDV was reverse-transcribed,...
Article
Full-text available
Highly virulent Newcastle disease virus (NDV) causes Newcastle disease (ND), which is a threat to poultry production worldwide. Effective disease management requires approaches to accurately determine sources of infection, which involves tracking of closely related viruses. Next-generation sequencing (NGS) has emerged as a research tool for thoroug...
Article
Full-text available
Newcastle disease virus (NDV) has a wide avian host range and a high degree of genetic variability, and virulent strains cause Newcastle disease (ND), a worldwide concern for poultry health. Although NDV has been studied in Nigeria, genetic information about the viruses involved in the endemicity of the disease and the transmission that likely occu...
Article
Full-text available
A Newcastle disease virus was isolated from a chicken from a live bird market in the Mbeya region of Tanzania. Complete genome characterization of the isolate identified it as a member of subgenotype Vd. This is the first complete genome sequence of this subgenotype.
Preprint
Newcastle disease virus (NDV) has a wide avian host range and a high degree of genetic variability, and virulent strains cause Newcastle disease (ND), a worldwide concern for poultry health. Although NDV has been studied in Nigeria, genetic information about the viruses involved in the endemicity of the disease and the transmission that likely occu...
Article
Full-text available
Newcastle disease (ND) infects wild birds and poultry species worldwide, severely impacting the economics of the poultry industry. ND is especially problematic in Latin America (Mexico, Colombia, Venezuela, and Peru) where it is either endemic or re-emerging. The disease is caused by infections with one of the different strains of virulent avian Ne...
Article
Five, class II, virulent Newcastle disease virus (vNDV) isolates of different genotypes from different host species were evaluated for their ability to infect, cause disease, and transmit to naïve chickens. Groups of five birds received a low, medium, or high dose, by the oculonasal route, of one of the following vNDV: three chicken-origin, one cor...
Article
Full-text available
Several Avian paramyxoviruses 1 (synonymous with Newcastle disease virus or NDV, used hereafter) classification systems have been proposed for strain identification and differentiation. These systems pioneered classification efforts; however, they were based on different approaches and lacked objective criteria for the differentiation of isolates....
Article
Full-text available
Our prior work has shown that live poultry vaccines have been intermittently isolated from wild birds sampled during field surveillance studies for Newcastle disease virus (NDV). Thus, we experimentally investigated the susceptibility of four native agriculturally-associated wild bird species to the NDV LaSota vaccine and evaluated the shedding dyn...
Presentation
Full-text available
BACKGROUND— Highly virulent Newcastle disease viruses (NDV), including their genetic variants (e.g., pigeon paramyxoviruses) cause Newcastle disease (ND), which is a threat to poultry production worldwide. Next-generation sequencing (NGS) has emerged as a research tool for thorough genetic characterization of infectious organisms; however, the util...
Poster
Background. The Oxford Nanopore Technologies (ONT) MinION is a relatively new sequencing technology. Not only does the MinION sequencer have a low capital cost, but it is also the most portable and fast sequencing platform among existing Next Generation Sequencing (NGS) technologies. Sequencing amplicons on the MinION is a popular method for determ...
Article
Full-text available
Our prior work has shown that live poultry vaccines have been intermittently isolated from wild birds sampled during field surveillance studies for Newcastle disease virus (NDV). Thus, we experimentally investigated the susceptibility of four native agriculturally associated wild bird species to the NDV LaSota vaccine and evaluated the shedding dyn...
Article
In May of 2018, virulent Newcastle disease virus was detected in sick, backyard, exhibition chickens in southern California. Since, the virus has affected 401 backyard and four commercial flocks, and one live bird market in California, and one backyard flock in Utah. The pathogenesis and transmission potential of this virus, along with two genetica...
Preprint
Full-text available
United States public health agencies are focusing on next-generation sequencing (NGS) to quickly identify and characterize foodborne pathogens. Here, the MinION nanopore, long-read sequencer was used to simultaneously sequence the entire chromosome and plasmids of Salmonella enterica subsp. enterica serovar Bareilly and Escherichia coli O157:H7. A...