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  1. Article: Editorial: Sequencing and phylogenetic analysis as a tool in molecular epidemiology of veterinary infectious diseases.

    Leyson, Christina M / Alkhamis, Moh A / Goraichuk, Iryna V

    Frontiers in veterinary science

    2023  Volume 10, Page(s) 1236155

    Language English
    Publishing date 2023-07-13
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2834243-4
    ISSN 2297-1769
    ISSN 2297-1769
    DOI 10.3389/fvets.2023.1236155
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: The 28S rRNA RT-qPCR assay for host depletion evaluation to enhance avian virus detection in Illumina and Nanopore sequencing.

    Goraichuk, Iryna V / Harden, Mark / Spackman, Erica / Suarez, David L

    Frontiers in microbiology

    2024  Volume 15, Page(s) 1328987

    Abstract: Abundant host and bacterial sequences can obscure the detection of less prevalent viruses in untargeted next-generation sequencing (NGS). Efficient removal of these non-targeted sequences is vital for accurate viral detection. This study presents a novel ...

    Abstract Abundant host and bacterial sequences can obscure the detection of less prevalent viruses in untargeted next-generation sequencing (NGS). Efficient removal of these non-targeted sequences is vital for accurate viral detection. This study presents a novel 28S ribosomal RNA (rRNA) RT-qPCR assay designed to assess the efficiency of avian rRNA depletion before conducting costly NGS for the detection of avian RNA viruses. The comprehensive evaluation of this 28S-test focuses on substituting DNase I with alternative DNases in our established depletion protocols and finetuning essential parameters for reliable host rRNA depletion. To validate the effectiveness of the 28S-test, we compared its performance with NGS results obtained from both Illumina and Nanopore sequencing platforms. This evaluation utilized swab samples from chickens infected with highly pathogenic avian influenza virus, subjected to established and modified depletion protocols. Both methods significantly reduced host rRNA levels, but using the alternative DNase had superior performance. Additionally, utilizing the 28S-test, we explored cost- and time-effective strategies, such as reduced probe concentrations and other alternative DNase usage, assessed the impact of filtration pre-treatment, and evaluated various experimental parameters to further optimize the depletion protocol. Our findings underscore the value of the 28S-test in optimizing depletion methods for advancing improvements in avian disease research through NGS.
    Language English
    Publishing date 2024-01-31
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2024.1328987
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Editorial

    Christina M. Leyson / Moh A. Alkhamis / Iryna V. Goraichuk

    Frontiers in Veterinary Science, Vol

    Sequencing and phylogenetic analysis as a tool in molecular epidemiology of veterinary infectious diseases

    2023  Volume 10

    Keywords genome sequencing ; next-generation sequencing ; sanger sequencing ; phylogenetic analysis ; metagenomics ; molecular surveillance ; Veterinary medicine ; SF600-1100
    Language English
    Publishing date 2023-07-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Complete genome sequence of seven virulent Newcastle disease virus isolates of sub-genotype XIII.1.1 from Tanzania.

    Goraichuk, Iryna V / Msoffe, Peter L M / Chiwanga, Gaspar H / Dimitrov, Kiril M / Afonso, Claudio L / Suarez, David L

    Microbiology resource announcements

    2023  Volume 12, Issue 10, Page(s) e0040523

    Abstract: 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 ... ...

    Abstract 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.
    Language English
    Publishing date 2023-09-26
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.00405-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Virulent Newcastle disease virus genotypes V.3, VII.2, and XIII.1.1 and their coinfections with infectious bronchitis viruses and other avian pathogens in backyard chickens in Tanzania.

    Kariithi, Henry M / Volkening, Jeremy D / Chiwanga, Gaspar H / Goraichuk, Iryna V / Olivier, Tim L / Msoffe, Peter L M / Suarez, David L

    Frontiers in veterinary science

    2023  Volume 10, Page(s) 1272402

    Abstract: Oropharyngeal (OP) and cloacal (CL) swabs from 2049 adult backyard chickens collected at 12 live bird markets, two each in Arusha, Dar es Salaam, Iringa, Mbeya, Morogoro and Tanga regions of Tanzania were screened for Newcastle disease virus (NDV) using ... ...

    Abstract Oropharyngeal (OP) and cloacal (CL) swabs from 2049 adult backyard chickens collected at 12 live bird markets, two each in Arusha, Dar es Salaam, Iringa, Mbeya, Morogoro and Tanga regions of Tanzania were screened for Newcastle disease virus (NDV) using reverse transcription real-time PCR (rRT-PCR). The virus was confirmed in 25.23% of the birds (
    Language English
    Publishing date 2023-10-19
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2834243-4
    ISSN 2297-1769
    ISSN 2297-1769
    DOI 10.3389/fvets.2023.1272402
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Molecular Characterization of Complete Genome Sequence of an Avian Coronavirus Identified in a Backyard Chicken from Tanzania.

    Kariithi, Henry M / Volkening, Jeremy D / Chiwanga, Gaspar H / Goraichuk, Iryna V / Msoffe, Peter L M / Suarez, David L

    Genes

    2023  Volume 14, Issue 10

    Abstract: 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. ... ...

    Abstract 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 (
    MeSH term(s) Animals ; Chickens/genetics ; Gammacoronavirus/genetics ; Tanzania/epidemiology ; Genome, Viral ; Coronavirus Infections/epidemiology ; Coronavirus Infections/veterinary ; Coronavirus Infections/genetics ; Infectious bronchitis virus/genetics
    Language English
    Publishing date 2023-09-23
    Publishing country Switzerland
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes14101852
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Whole-Genome Sequence of

    Goraichuk, Iryna V / Davis, James F / Kulkarni, Arun B / Afonso, Claudio L / Suarez, David L

    Microbiology resource announcements

    2021  Volume 10, Issue 15

    Abstract: Here, we report the complete genome sequence of ... ...

    Abstract Here, we report the complete genome sequence of an
    Language English
    Publishing date 2021-04-15
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.01460-20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Zoonotic and Reverse Zoonotic Transmissibility of SARS-CoV-2.

    Goraichuk, Iryna V / Arefiev, Vasiliy / Stegniy, Borys T / Gerilovych, Anton P

    Virus research

    2021  Volume 302, Page(s) 198473

    Abstract: The Coronavirus Disease 2019 (COVID-19) is the first known pandemic caused by a coronavirus. Its causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), appears to be capable of infecting different mammalian species. Recent ... ...

    Abstract The Coronavirus Disease 2019 (COVID-19) is the first known pandemic caused by a coronavirus. Its causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), appears to be capable of infecting different mammalian species. Recent detections of this virus in pet, zoo, wild, and farm animals have compelled inquiry regarding the zoonotic (animal-to-human) and reverse zoonotic (human-to-animal) transmissibility of SARS-CoV-2 with the potential of COVID-19 pandemic evolving into a panzootic. It is important to monitor the global spread of disease and to assess the significance of genomic changes to support prevention and control efforts during a pandemic. An understanding of the SARS-CoV-2 epidemiology provides opportunities to prevent the risk of repeated re-infection of humans and requires a robust One Health-based investigation. This review paper describes the known properties and the existing gaps in scientific knowledge about the zoonotic and reverse zoonotic transmissibility of the novel virus SARS-CoV-2 and the COVID-19 disease it causes.
    MeSH term(s) Animals ; COVID-19/epidemiology ; COVID-19/prevention & control ; COVID-19/transmission ; COVID-19/virology ; Humans ; One Health ; Pandemics ; SARS-CoV-2/genetics ; SARS-CoV-2/physiology ; Zoonoses
    Language English
    Publishing date 2021-06-09
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 605780-9
    ISSN 1872-7492 ; 0168-1702
    ISSN (online) 1872-7492
    ISSN 0168-1702
    DOI 10.1016/j.virusres.2021.198473
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1965: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  9. Article ; Online: Complete Genome Sequence of an

    Goraichuk, Iryna V / Kapczynski, Darrell R / Seal, Bruce S / Suarez, David L

    Microbiology resource announcements

    2020  Volume 9, Issue 19

    Abstract: Avian metapneumoviruses (aMPVs), which have been reported in many countries, cause acute upper respiratory tract disease in chickens and turkeys. Using next-generation sequencing, we report here the complete genome sequence of an aMPV subtype B strain ... ...

    Abstract Avian metapneumoviruses (aMPVs), which have been reported in many countries, cause acute upper respiratory tract disease in chickens and turkeys. Using next-generation sequencing, we report here the complete genome sequence of an aMPV subtype B strain that was isolated from a turkey in Hungary in 1989.
    Language English
    Publishing date 2020-05-07
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.00177-20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Complete Coding Sequences of Three Chicken Parvovirus Isolates from the United States.

    Goraichuk, Iryna V / Davis, James F / Afonso, Claudio L / Suarez, David L

    Microbiology resource announcements

    2020  Volume 9, Issue 39

    Abstract: 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. ...

    Abstract 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.
    Language English
    Publishing date 2020-09-24
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.00735-20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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