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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 (534)
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 nucleotide identity (~88%) with strains from clinically normal chickens from Germany in 2004 and Netherlands in 2019.
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 absent in most classical approaches. However, its widespread adoption in clinical settings is still pending, with...
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, are both likely to become diagnostic methods of choice in the future. tNGS is a rapid and sensitive method for p...
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 revealed that all isolates belong to sub-genotype XIII.1.1.
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 Kenya and the East and Central African regions comprehensive analysis of two novel AvCoVs designated IBV/ck/KE/192...
Avian paramyxoviruses (APMVs) belong to the recently assigned subfamily Avulavirinae of the family Paramyxoviridae and have been shown to infect a wide variety of poultry and wild bird species. Up to date there are 22 confirmed serotypes of APMV. The subfamily Avulavirinae is composed of three genera, namely, Metaavulavirus, Orthoavulavirus, and Pa...
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 distribution of this virus extends beyond Asia.
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 Ingelheim Animal Health, Brazil) and BR/1891/E2/19 (1062; Hipraviar, France) were sequenced and compared with the patho...
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 movement of viruses and the migratory routes they follow is still unclear. In this study, we performed a phylogene...
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 Kenya and the Eastern African region two novel AvCoVs, designated IBV/ck/KE/1920/A374/2017 (A374/17) and AvCoV/ck/...
Co-infections of avian species with dierent RNA viruses and pathogenic
bacteria are often misdiagnosed or incompletely characterized using targeted
diagnostic methods, which could aect the accurate management of
clinical disease. A non-targeted sequencing approach with rapid and precise
characterization of pathogens should help respiratory diseas...
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-targeted sequencing approach with rapid and precise characterization of pathogens should help respiratory dise...
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 nontargeted next-generation sequencing (NGS) of FTA card-spotted respiratory samples from commercial chickens in Mexico...
To date, the emergence of novel H5 and H7 highly pathogenic avian influenza (HPAI) viruses have been occurring through two main mechanisms: the conversion of a low pathogenic into a highly pathogenic virus and the reassortment between different genetic segments of currently circulating low and highly pathogenic viruses. The Flongle is a more access...
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 vaccine and field samples collected on FTA cards from commercial flocks in Mexico in 2019–2021. Paired-ended se...
New variants of infectious bronchitis viruses (IBVs; Coronaviridae) continuously emerge de-spite routine vaccinations. Here, we report genome sequence variations of IBVs identified by random nontargeted next generation sequencing (NGS) of vaccine and field samples collected on FTA cards from commercial flocks in Mexico in 2019-2021. Paired-ended se...
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.
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...
A low cost vaccine alternative for the early challenges with virulent Newcastle Disease Viruses
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...
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...
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...
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...
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...
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.
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...
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...
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...
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...
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.
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...
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...
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.
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...
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
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...
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...
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.
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...
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.
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...
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...
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...
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...
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...
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...
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...
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.
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...
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...
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...
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,...
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...
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...
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.
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...