Unique Variants of Avian Coronaviruses from Indigenous Chickens in Kenya

Kariithi, Henry M.; Volkening, Jeremy D.; Goraichuk, Iryna V.; Ateya, Leonard O.; Williams-Coplin, Dawn; Olivier, Tim L.; Binepal, Yatinder S.; Afonso, Claudio L.; Suarez, David L.

doi:10.3390/v15020264

Cited by 10 publications

(17 citation statements)

References 68 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…IBV and rotavirus were therefore the most prevalent in chickens while retroviruses were predominantly detected in ducks. This is consistent with previous studies that were done in other countries that identified these viruses as major pathogens in poultry [37][38][39]. It is noteworthy that most of the chickens sold in Nairobi are transported from Western Kenya, especially Trans Nzoia, and the coastal region, including Kilifi and Kwale counties.…”

Section: Discussionsupporting

confidence: 92%

Metagenomic characterization reveals virus coinfections associated with Newcastle disease virus among poultry in Kenya

Panyako,

Ommeh,

Kuria

et al. 2023

J Basic Microbiol

View full text Add to dashboard Cite

Newcastle disease (ND) is an endemic viral disease affecting poultry and causing massive economic losses. This cross‐sectional purposive study detected coinfections that are associated with the Newcastle disease virus among poultry from selected regions in Kenya. Cloacal (n = 599) and oral–pharyngeal (n = 435) swab samples were collected and pooled into 17 and 15 samples, respectively. A total of 17,034,948 and 7,751,974 paired‐end reads with an average of 200 nucleotides were generated from the cloacal and oral–pharyngeal swab samples, respectively. Analysis of the de novo assembled contigs identified 177 and 18 cloacal and oral–pharyngeal contigs, respectively with hits to viral sequences, as determined by BLASTx and BLASTn analyses. Several known and unknown representatives of Coronaviridae, Picobirnaviridae, Reoviridae, Retroviridae, and unclassified Deltavirus were identified in the cloacal swab samples. However, no Newcastle disease virus (family Paramyxoviridae) was detected in the cloacal swabs, although they were detected in the oropharyngeal swabs of chickens sampled in Nairobi, Busia, and Trans Nzoia. Additionally, sequences representative of Paramyxoviridae, Coronaviridae, and Retroviridae were identified in the oral–pharyngeal swab samples. Infectious bronchitis virus and rotavirus were chickens' most prevalent coinfections associated with the Newcastle disease virus. The detection of these coinfections suggests that these viruses are significant threats to the control of Newcastle disease as the Newcastle disease virus vaccines are known to fail because of these coinfections. Therefore, this study provides important information that will help improve disease diagnosis and vaccine development for coinfections associated with the Newcastle disease virus.

show abstract

Section: Discussionsupporting

confidence: 92%

Metagenomic characterization reveals virus coinfections associated with Newcastle disease virus among poultry in Kenya

Panyako,

Ommeh,

Kuria

et al. 2023

J Basic Microbiol

View full text Add to dashboard Cite

show abstract

“…Then, samples from 20 birds containing high amounts of NDV RNAs by the rRT-PCT tests (cycle threshold (C T ) cutoff of below 30) were randomly selected for the NGS. Sequencing libraries were prepared from the selected samples using sequence-independent, single-primer amplification [27] and Illumina Nextera TM Flex protocols, followed by paired-end sequencing (600-cycle MiSeq Reagent Kit v3) on an Illumina MiSeq instrument, as previously described [18].…”

Section: Total Rna Extraction and Next-generation Sequencingmentioning

confidence: 99%

“…A recently described Sanger sequencing protocol [18] was used to determine missing bases in ORF1a of the assembled consensus genome sequence (n = 8 nt at position 11,064-11,071) with primers specifically designed for the gap, i.e., IBV-10886F (5 -CTC CTA TGC GGA GTA CGA A-3 ) and IBV-11529R (5 -CAC TGC AGC GTA GAG TCT-3 ).…”

Section: Sanger Sequencingmentioning

confidence: 99%

“…The spike protein is the largest of the structural proteins and is post-translationally cleaved by cellular proteases into subunits S1 and S2; S1 harbors serotype-specific antigenic epitopes associated with the hypervariable regions (HVRs) [16]. For IBVs, the S1 heterogeneity, which results from mutations and/or recombination events, distinguishes at least 32 distinct lineages within eight genotypes (GI to G-VIII), and dozens of unique variants (UVs) and inter-lineage recombinants that do not classify with the established lineages [17,18]. However, this system, which relies on the full-length S1 sequence, is limited because the vast majority of strains only have partial S1 sequences.…”

Section: Introductionmentioning

confidence: 99%

“…Currently, only eight GI lineages (GI-1, GI-12, GI-13, GI-14, GI-16, GI-19, GI-23 and GI-26) and several UVs have been reported in Africa [18], but little is known about their impacts on the poultry industry in the continent. The current study reports the complete genome sequence of a recombinant TCoV-like strain we identified using nontargeted nextgeneration sequencing (NGS) of clinical samples collected during a Newcastle disease viruses (NDVs) surveillance study in backyard chickens presented for sale at live bird markets (LBMs) in Tanzania.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Molecular Characterization of Complete Genome Sequence of an Avian Coronavirus Identified in a Backyard Chicken from Tanzania

Kariithi,

Volkening,

Chiwanga

et al. 2023

Genes

Self Cite

View full text Add to dashboard Cite

A complete genome sequence of an avian coronavirus (AvCoV; 27,663 bp excluding 3′ poly(A) tail) was determined using nontargeted next-generation sequencing (NGS) of an oropharyngeal swab from a backyard chicken in a live bird market in Arusha, Tanzania. The open reading frames (ORFs) of the Tanzanian strain TZ/CA127/19 are organized as typical of gammaCoVs (Coronaviridae family): 5′UTR-[ORFs 1a/1b encoding replicase complex (Rep1ab) non-structural peptides nsp2-16]-[spike (S) protein]-[ORFs 3a/3b]-[small envelop (E) protein]-[membrane (M) protein]-[ORFs 4a/4c]-[ORFs 5a/5b]-[nucleocapsid (N) protein]-[ORF6b]-3′UTR. The structural (S, E, M and N) and Rep1ab proteins of TZ/CA127/19 contain features typically conserved in AvCoVs, including the cleavage sites and functional motifs in Rep1ab and S. Its genome backbone (non-spike region) is closest to Asian GI-7 and GI-19 infectious bronchitis viruses (IBVs) with 87.2–89.7% nucleotide (nt) identities, but it has a S gene closest (98.9% nt identity) to the recombinant strain ck/CN/ahysx-1/16. Its 3a, 3b E and 4c sequences are closest to the duck CoV strain DK/GD/27/14 at 99.43%, 100%, 99.65% and 99.38% nt identities, respectively. Whereas its S gene phylogenetically cluster with North American TCoVs and French guineafowl COVs, all other viral genes group monophyletically with Eurasian GI-7/GI-19 IBVs and Chinese recombinant AvCoVs. Detection of a 4445 nt-long recombinant fragment with breakpoints at positions 19,961 and 24,405 (C- and N-terminus of nsp16 and E, respectively) strongly suggested that TZ/CA127/19 acquired its genome backbone from an LX4-type (GI-19) field strain via recombination with an unknown AvCoV. This is the first report of AvCoV in Tanzania and leaves unanswered the questions of its emergence and the biological significance.

show abstract

Global Emergence of Infectious Bronchitis Virus Variants: Evolution, Immunity, and Vaccination Challenges

Abozeid

2023

Transboundary and Emerging Diseases

View full text Add to dashboard Cite

Infectious bronchitis is an acute, extremely contagious viral disease affecting chickens of all ages, leading to devastating economic losses in the poultry industry worldwide. Affected chickens show respiratory distress and/or nephritis, in addition to decrease of egg production and quality in layers. The avian coronavirus, infectious bronchitis virus (IBV), is a rapidly evolving virus due to the high frequency of mutations and recombination events that are common in coronaviruses. This leads to the continual emergence of novel genotypes that show variable or poor crossprotection. The immune response against IBV is complex. Passive, innate and adaptive humoral and cellular immunity play distinct roles in protection against IBV. Despite intensive vaccination using the currently available live-attenuated and inactivated IBV vaccines, IBV continues to circulate, evolve, and trigger outbreaks worldwide, indicating the urgent need to update the current vaccines to control the emerging variants. Different approaches for preparation of IBV vaccines, including DNA, subunit, peptides, virus-like particles, vectored and recombinant vaccines, have been tested in many studies to combat the disease. This review focuses on several key aspects related to IBV, including its clinical significance, the functional structure of the virus, the factors that contribute to its evolution and diversity, the types of immune responses against IBV, and the characteristics of both current and emerging IBV vaccines. The goal is to provide a comprehensive understanding of IBV and explore the emergence of variants, their dissemination around the world, and the challenges to define the efficient vaccination strategies.

show abstract

Unique Variants of Avian Coronaviruses from Indigenous Chickens in Kenya

Cited by 10 publications

References 68 publications

Metagenomic characterization reveals virus coinfections associated with Newcastle disease virus among poultry in Kenya

Metagenomic characterization reveals virus coinfections associated with Newcastle disease virus among poultry in Kenya

Molecular Characterization of Complete Genome Sequence of an Avian Coronavirus Identified in a Backyard Chicken from Tanzania

Global Emergence of Infectious Bronchitis Virus Variants: Evolution, Immunity, and Vaccination Challenges

Contact Info

Product

Resources

About