Complete Genome Sequences of Avian Metapneumovirus Subtype B Vaccine Strains from Brazil

Kariithi, Henry M.; Volkening, Jeremy D.; Alves, Victória Veiga; Reis-Cunha, João Luís; Arantes, Letícia Cury Rocha Veloso; Fernando, Filipe Santos; Filho, Tobias Fernandes; Martins, Nélson Rodrigo da Silva; Lemière, Stéphane; Neto, Oliveiro Caetano de Freitas; Decanini, Eduardo Lucio; Afonso, Claudio L.; Suarez, David L.

doi:10.1128/mra.00235-23

Cited by 3 publications

(5 citation statements)

References 20 publications

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“…This finding was initially not anticipated, considering that only aMPV subtype C has previously been reported in the US turkey population [ 14 ]. Detection and characterization of emerging pathogens such as aMPVs can be performed rapidly using advanced NGS technologies, which can identify divergent strains that are not detected by conventional PCR and enable immediate outbreak response [ 8 , 18 , 19 , 37 ]. As a result of the early detection and confirmation of aMPV subtype B in this study, molecular and serological testing was implemented very quickly for further testing of new samples.…”

Section: Discussionmentioning

confidence: 99%

“…The L and P are non-structural proteins involved in genome replication, while the others code for nucleocapsid, matrix, and envelope structural proteins. The viral envelope is embedded with F (which promotes viral-to-cell membrane fusion), G (a major antigenic determinant involved in viral attachment), and SH (a viroporin involved in membrane permeability) proteins [ 6 , 7 , 8 ]. Proteins N, P, and L encapsulate the viral RNA to form the viral ribonucleoprotein complex (RNP), while the accessory proteins M2-2 and M2-1 are involved in viral genome replication and the 3′-leader/5′-trailer contains viral transcriptional promoters [ 7 , 8 ].…”

Section: Introductionmentioning

confidence: 99%

“…A recent phylodynamic study [ 2 ] reported that subtype B was able to spread rapidly in Western European countries, followed by Eastern countries. Whole genome sequences (WGS) of subtype B have been reported from different countries using advanced next generation sequencing (NGS) [ 8 ]. A recent study from South Korea reported six whole genomes of subtype B from chicken samples collected from live bird markets during 2019–2022.…”

Section: Introductionmentioning

confidence: 99%

“…A recent study from South Korea reported six whole genomes of subtype B from chicken samples collected from live bird markets during 2019–2022. Kariithi et al [ 8 ] reported whole genome sequence analysis of subtype B vaccine strains BR/1890/E1/19 (PL21, Nemovac; Boehringer Ingelheim Animal Health, Brazil) and BR/1891/E2/19 (1062; Hipraviar, France) along with that of the pathogenic field strain VCO3/60616. Goraichuk et al [ 23 ] reported the whole genome sequence of the subtype B strain Hungary/657/4, which was isolated from a turkey in Hungary in 1989.…”

Section: Introductionmentioning

confidence: 99%

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Geographical Expansion of Avian Metapneumovirus Subtype B: First Detection and Molecular Characterization of Avian Metapneumovirus Subtype B in US Poultry

Luqman,

Duhan,

Temeeyasen

et al. 2024

Viruses

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Avian metapneumovirus (aMPV), classified within the Pneumoviridae family, wreaks havoc on poultry health. It typically causes upper respiratory tract and reproductive tract infections, mainly in turkeys, chickens, and ducks. Four subtypes of AMPV (A, B, C, D) and two unclassified subtypes have been identified, of which subtypes A and B are widely distributed across the world. In January 2024, an outbreak of severe respiratory disease occurred on turkey and chicken farms across different states in the US. Metagenomics sequencing of selected tissue and swab samples confirmed the presence of aMPV subtype B. Subsequently, all samples were screened using an aMPV subtype A and B multiplex real-time RT-PCR kit. Of the 221 farms, 124 (56%) were found to be positive for aMPV-B. All samples were negative for subtype A. Six whole genomes were assembled, five from turkeys and one from chickens; all six assembled genomes showed 99.29 to 99.98% nucleotide identity, indicating a clonal expansion event for aMPV-B within the country. In addition, all six sequences showed 97.74 to 98.58% nucleotide identity with previously reported subtype B sequences, e.g., VCO3/60616, Hungary/657/4, and BR/1890/E1/19. In comparison to these two reference strains, the study sequences showed unique 49–62 amino acid changes across the genome, with maximum changes in glycoprotein (G). One unique AA change from T (Threonine) to I (Isoleucine) at position 153 in G protein was reported only in the chicken aMPV sequence, which differentiated it from turkey sequences. The twelve unique AA changes along with change in polarity of the G protein may indicate that these unique changes played a role in the adaptation of this virus in the US poultry. This is the first documented report of aMPV subtype B in US poultry, highlighting the need for further investigations into its genotypic characterization, pathogenesis, and evolutionary dynamics.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Geographical Expansion of Avian Metapneumovirus Subtype B: First Detection and Molecular Characterization of Avian Metapneumovirus Subtype B in US Poultry

Luqman,

Duhan,

Temeeyasen

et al. 2024

Viruses

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“…Interestingly, the study demonstrated that FTA cards could be used on field-collected clinical samples to obtain high-quality genetic information from RNAs for the untargeted discovery of avian viral agents. In [ 25 ], the Karithii team reported the detection and genome sequence analysis of avian metapneumoviruses circulating in commercial chicken flocks in Mexico by utilizing the approach of direct random sequencing of clinical samples [ 25 , 54 ]. The identification of 11 complete and 2 nearly complete genome sequences of aMPV-A from Mexico was reported.…”

Section: Short-read Sequencing On Poultry and Avian Speciesmentioning

confidence: 99%

Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples

Afonso,

Afonso

2023

Veterinary Sciences

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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 precise characterization of suspected agents. ntNGS, also known as agnostic diagnosis, does not require a hypothesis and has been used to identify unsuspected infections in clinical samples. Implemented in the form of multiplexed total DNA metagenomics or as total RNA sequencing, the approach produces comprehensive and actionable reports that allow semi-quantitative identification of most of the agents present in respiratory, cloacal, and tissue samples. The diagnostic benefits of the use of direct tNGS and ntNGS are high specificity, compatibility with different types of clinical samples (fresh, frozen, FTA cards, and paraffin-embedded), production of nearly complete infection profiles (viruses, bacteria, fungus, and parasites), production of “semi-quantitative” information, direct agent genotyping, and infectious agent mutational information. The achievements of NGS in terms of diagnosing poultry problems are described here, along with future applications. Multiplexing, development of standard operating procedures, robotics, sequencing kits, automated bioinformatics, cloud computing, and artificial intelligence (AI) are disciplines converging toward the use of this technology for active surveillance in poultry farms. Other advances in human and veterinary NGS sequencing are likely to be adaptable to avian species in the future.

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Introduction of Avian metapneumovirus subtype A to the United States: molecular insights and implications

Goraichuk,

Torchetti,

Killian

et al. 2024

Front. Microbiol.

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Avian metapneumovirus (aMPV) poses a significant threat to the poultry industry worldwide, primarily affecting turkeys and chickens. The recent detection of aMPV-A and -B subtypes in the United States marks a significant shift after a prolonged period free of aMPV following the eradication of the previously circulating subtype C. Hence, the demand for molecular diagnostic tests for aMPV has arisen due to their limited availability in the US market. In this study, we present the molecular characterization based on the complete genome sequence of aMPV subtype A, which was detected in the US for the first time. Four RT-qPCR positive samples were subjected to next-generation sequencing analysis, resulting in the assembly of one complete and one near-complete genome sequences. Phylogenetic analysis revealed that the isolated strains clustered within the aMPV-A subtype and were most closely related to recent Mexican strains. A detailed amino acid analysis identified unique mutations in the G gene of the US isolates compared to Mexican strains. Additionally, we compared the performance, cross-reactivity, and limit of detection of our revised aMPV subtype-specific RT-qPCR test with two commercial kits, demonstrating similar detection and subtyping capabilities. These findings highlight the importance of accurate diagnostic methods for disease management in the poultry industry, provide valuable insights into the epidemiology of aMPV, and underscore the need for continued vigilance and surveillance to mitigate its impact on poultry production.

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Complete Genome Sequences of Avian Metapneumovirus Subtype B Vaccine Strains from Brazil

Cited by 3 publications

References 20 publications

Geographical Expansion of Avian Metapneumovirus Subtype B: First Detection and Molecular Characterization of Avian Metapneumovirus Subtype B in US Poultry

Geographical Expansion of Avian Metapneumovirus Subtype B: First Detection and Molecular Characterization of Avian Metapneumovirus Subtype B in US Poultry

Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples

Introduction of Avian metapneumovirus subtype A to the United States: molecular insights and implications

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