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  1. Article: Gene editing of pigs to control influenza A virus infections.

    Kwon, Taeyong / Artiaga, Bianca L / McDowell, Chester D / Whitworth, Kristin M / Wells, Kevin D / Prather, Randall S / Delhon, Gustavo / Cigan, Mark / White, Stephen N / Retallick, Jamie / Gaudreault, Natasha N / Morozov, Igor / Richt, Juergen A

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Proteolytic activation of the hemagglutinin (HA) glycoprotein by host cellular proteases is pivotal for influenza A virus (IAV) infectivity. Highly pathogenic avian influenza viruses possess the multibasic cleavage site of the HA which is cleaved by ... ...

    Abstract Proteolytic activation of the hemagglutinin (HA) glycoprotein by host cellular proteases is pivotal for influenza A virus (IAV) infectivity. Highly pathogenic avian influenza viruses possess the multibasic cleavage site of the HA which is cleaved by ubiquitous proteases, such as furin; in contrast, the monobasic HA motif is recognized and activated by trypsin-like proteases, such as the transmembrane serine protease 2 (TMPRSS2). Here, we aimed to determine the effects of TMPRSS2 on the replication of pandemic H1N1 and H3N2 subtype IAVs in the natural host, the pig. The use of the CRISPR/Cas 9 system led to the establishment of homozygous gene edited (GE)
    Language English
    Publishing date 2024-01-16
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.01.15.575771
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Molecular detection of SARS-CoV-2 strains and differentiation of Delta variant strains.

    Hamill, Vaughn / Noll, Lance / Lu, Nanyan / Tsui, Wai Ning Tiffany / Porter, Elizabeth Poulsen / Gray, Mark / Sebhatu, Tesfaalem / Goerl, Kyle / Brown, Susan / Palinski, Rachel / Thomason, Sasha / Almes, Kelli / Retallick, Jamie / Bai, Jianfa

    Transboundary and emerging diseases

    2022  Volume 69, Issue 5, Page(s) 2879–2889

    Abstract: The Delta variant of SARS-CoV-2 has now become the predominant strain in the global COVID-19 pandemic. Strain coverage of some detection assays developed during the early pandemic stages has declined due to periodic mutations in the viral genome. We have ...

    Abstract The Delta variant of SARS-CoV-2 has now become the predominant strain in the global COVID-19 pandemic. Strain coverage of some detection assays developed during the early pandemic stages has declined due to periodic mutations in the viral genome. We have developed a real-time RT-PCR (RT-qPCR) for SARS-CoV-2 detection that provides nearly 100% strain coverage, and differentiation of highly transmissible Delta variant strains. All full or nearly full (≥28 kb) SARS-CoV-2 genomes (n = 403,812), including 6422 Delta and 280 Omicron variant strains, were collected from public databases at the time of analysis and used for assay design. The two amino acid deletions in the spike gene (S-gene, Δ156-157) that is characteristic of the Delta variant were targeted during the assay design. Although strain coverage for the Delta variant was very high (99.7%), detection coverage for non-Delta wild-type strains was 93.9%, mainly due to the confined region of design. To increase strain coverage of the assay, the design for CDC N1 target was added to the assay. In silico analysis of 403,812 genomes indicated a 95.4% strain coverage for the CDC N1 target, however, in combination with our new non-Delta S-gene target, total coverage for non-Delta wild-type strains increased to 99.8%. A human 18S rRNA gene was also analyzed and used as an internal control. The final four-plex RT-qPCR assay generated PCR amplification efficiencies between 95.4% and 102.0% with correlation coefficients (R
    MeSH term(s) Amino Acids ; Animals ; COVID-19/diagnosis ; COVID-19/veterinary ; Humans ; Pandemics ; RNA, Viral/genetics ; SARS-CoV-2/genetics
    Chemical Substances Amino Acids ; RNA, Viral
    Language English
    Publishing date 2022-01-05
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2414822-2
    ISSN 1865-1682 ; 1865-1674
    ISSN (online) 1865-1682
    ISSN 1865-1674
    DOI 10.1111/tbed.14443
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Molecular detection of SARS-CoV-2 and differentiation of Omicron and Delta variant strains.

    Tsui, Wai Ning Tiffany / Hamill, Vaughn / Noll, Lance / Lu, Nanyan / Porter, Elizabeth Poulsen / Harbidge, Donald / Cox, Emily / Richardson, Claire / Gray, Mark / Sebhatu, Tesfaalem / Goerl, Kyle / Brown, Susan / Hanzlicek, Gregg / Retallick, Jamie / Bai, Jianfa

    Transboundary and emerging diseases

    2022  Volume 69, Issue 5, Page(s) e1618–e1631

    Abstract: The SARS-CoV-2 virus is the causative agent of COVID-19 and has undergone continuous mutations throughout the pandemic. The more transmissible Omicron variant has quickly spread and is replacing the Delta variant as the most prevalent strain globally, ... ...

    Abstract The SARS-CoV-2 virus is the causative agent of COVID-19 and has undergone continuous mutations throughout the pandemic. The more transmissible Omicron variant has quickly spread and is replacing the Delta variant as the most prevalent strain globally, including in the United States. A new molecular assay that can detect and differentiate both the Delta and Omicron variants was developed. A collection of 660,035 SARS-CoV-2 full- or near-full genomes, including 169,454 Delta variant and 24,202 Omicron variant strains, were used for primer and probe designs. In silico data analysis predicted an assay coverage of >99% of all strains, including >99% of the Delta and >99% of Omicron strains. The Omicron variant differential test was designed based on the Δ31-33 aa deletion in the N-gene, which is present in the original B.1.1.529 main genotype, BA.1, as well as in BA.2 and BA.3 subtypes. Therefore, the assay should detect the majority of all Omicron variant strains. Standard curves generated with human clinical samples indicated that the PCR amplification efficiencies were 104%, 90.7% and 90.4% for the Omicron, Delta, and non-Delta/non-Omicron wild-type genotypes, respectively. Correlation coefficients of the standard curves were all >0.99. The detection limit of the assay was 14.3, 32.0, and 21.5 copies per PCR reaction for Omicron, Delta, and wild-type genotypes, respectively. The assay was designed to specifically detect SAR-CoV-2 strains. Selected samples with Omicron, Delta and wild-type genotypes identified by the RT-qPCR assay were also confirmed by sequencing. The assay did not detect any animal coronavirus-positive samples that were tested. Human nasal swab samples that previously tested positive (n = 182) or negative (n = 42) for SARS-CoV-2 by the ThermoFisher TaqPath COVID-19 Combo Kit, produced the same result with the new assay. Among positive samples, 55.5% (101/182), 23.1% (42/182), and 21.4% (39/182) were identified as Omicron, Delta, and non-Omicron/non-Delta wild-type genotypes, respectively.
    MeSH term(s) Animals ; COVID-19/diagnosis ; COVID-19/veterinary ; Humans ; Nucleic Acid Amplification Techniques/veterinary ; RNA, Viral/genetics ; SARS-CoV-2/genetics
    Chemical Substances RNA, Viral
    Language English
    Publishing date 2022-03-13
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2414822-2
    ISSN 1865-1682 ; 1865-1674
    ISSN (online) 1865-1682
    ISSN 1865-1674
    DOI 10.1111/tbed.14497
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

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  4. Article: Molecular detection of SARS‐CoV‐2 strains and differentiation of Delta variant strains

    Hamill, Vaughn / Noll, Lance / Lu, Nanyan / Tsui, Wai Ning Tiffany / Porter, Elizabeth Poulsen / Gray, Mark / Sebhatu, Tesfaalem / Goerl, Kyle / Brown, Susan / Palinski, Rachel / Thomason, Sasha / Almes, Kelli / Retallick, Jamie / Bai, Jianfa

    Transboundary and emerging diseases. 2022 Sept., v. 69, no. 5

    2022  

    Abstract: The Delta variant of SARS‐CoV‐2 has now become the predominant strain in the global COVID‐19 pandemic. Strain coverage of some detection assays developed during the early pandemic stages has declined due to periodic mutations in the viral genome. We have ...

    Abstract The Delta variant of SARS‐CoV‐2 has now become the predominant strain in the global COVID‐19 pandemic. Strain coverage of some detection assays developed during the early pandemic stages has declined due to periodic mutations in the viral genome. We have developed a real‐time RT‐PCR (RT‐qPCR) for SARS‐CoV‐2 detection that provides nearly 100% strain coverage, and differentiation of highly transmissible Delta variant strains. All full or nearly full (≥28 kb) SARS‐CoV‐2 genomes (n = 403,812), including 6422 Delta and 280 Omicron variant strains, were collected from public databases at the time of analysis and used for assay design. The two amino acid deletions in the spike gene (S‐gene, Δ156‐157) that is characteristic of the Delta variant were targeted during the assay design. Although strain coverage for the Delta variant was very high (99.7%), detection coverage for non‐Delta wild‐type strains was 93.9%, mainly due to the confined region of design. To increase strain coverage of the assay, the design for CDC N1 target was added to the assay. In silico analysis of 403,812 genomes indicated a 95.4% strain coverage for the CDC N1 target, however, in combination with our new non‐Delta S‐gene target, total coverage for non‐Delta wild‐type strains increased to 99.8%. A human 18S rRNA gene was also analyzed and used as an internal control. The final four‐plex RT‐qPCR assay generated PCR amplification efficiencies between 95.4% and 102.0% with correlation coefficients (R²) of >0.99 for cloned positive controls; Delta and non‐Delta human clinical samples generated PCR efficiencies of 93.4%–97.0% and R² > 0.99. The assay also detects 98.6% of 280 Omicron sequences. Assay primers and probes have no match to other closely related human coronaviruses, and did not produce a signal from samples positive to selected animal coronaviruses. Genotypes of selected clinical samples identified by the RT‐qPCR were confirmed by Sanger sequencing.
    Keywords COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; amino acids ; computer simulation ; genes ; humans ; pandemic ; viral genome
    Language English
    Dates of publication 2022-09
    Size p. 2879-2889.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 2414822-2
    ISSN 1865-1682 ; 1865-1674
    ISSN (online) 1865-1682
    ISSN 1865-1674
    DOI 10.1111/tbed.14443
    Database NAL-Catalogue (AGRICOLA)

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  5. Article: Molecular detection of SARS‐CoV‐2 and differentiation of Omicron and Delta variant strains

    Tsui, Wai Ning Tiffany / Hamill, Vaughn / Noll, Lance / Lu, Nanyan / Porter, Elizabeth Poulsen / Harbidge, Donald / Cox, Emily / Richardson, Claire / Gray, Mark / Sebhatu, Tesfaalem / Goerl, Kyle / Brown, Susan / Hanzlicek, Gregg / Retallick, Jamie / Bai, Jianfa

    Transboundary and emerging diseases. 2022 Sept., v. 69, no. 5

    2022  

    Abstract: The SARS‐CoV‐2 virus is the causative agent of COVID‐19 and has undergone continuous mutations throughout the pandemic. The more transmissible Omicron variant has quickly spread and is replacing the Delta variant as the most prevalent strain globally, ... ...

    Abstract The SARS‐CoV‐2 virus is the causative agent of COVID‐19 and has undergone continuous mutations throughout the pandemic. The more transmissible Omicron variant has quickly spread and is replacing the Delta variant as the most prevalent strain globally, including in the United States. A new molecular assay that can detect and differentiate both the Delta and Omicron variants was developed. A collection of 660,035 SARS‐CoV‐2 full‐ or near‐full genomes, including 169,454 Delta variant and 24,202 Omicron variant strains, were used for primer and probe designs. In silico data analysis predicted an assay coverage of >99% of all strains, including >99% of the Delta and >99% of Omicron strains. The Omicron variant differential test was designed based on the Δ31‐33 aa deletion in the N‐gene, which is present in the original B.1.1.529 main genotype, BA.1, as well as in BA.2 and BA.3 subtypes. Therefore, the assay should detect the majority of all Omicron variant strains. Standard curves generated with human clinical samples indicated that the PCR amplification efficiencies were 104%, 90.7% and 90.4% for the Omicron, Delta, and non‐Delta/non‐Omicron wild‐type genotypes, respectively. Correlation coefficients of the standard curves were all >0.99. The detection limit of the assay was 14.3, 32.0, and 21.5 copies per PCR reaction for Omicron, Delta, and wild‐type genotypes, respectively. The assay was designed to specifically detect SAR‐CoV‐2 strains. Selected samples with Omicron, Delta and wild‐type genotypes identified by the RT‐qPCR assay were also confirmed by sequencing. The assay did not detect any animal coronavirus‐positive samples that were tested. Human nasal swab samples that previously tested positive (n = 182) or negative (n = 42) for SARS‐CoV‐2 by the ThermoFisher TaqPath COVID‐19 Combo Kit, produced the same result with the new assay. Among positive samples, 55.5% (101/182), 23.1% (42/182), and 21.4% (39/182) were identified as Omicron, Delta, and non‐Omicron/non‐Delta wild‐type genotypes, respectively.
    Keywords COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; computer simulation ; detection limit ; etiological agents ; genome ; genotype ; humans ; nose ; pandemic ; viruses
    Language English
    Dates of publication 2022-09
    Size p. e1618-e1631.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 2414822-2
    ISSN 1865-1682 ; 1865-1674
    ISSN (online) 1865-1682
    ISSN 1865-1674
    DOI 10.1111/tbed.14497
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: Experimental Infection of Domestic Pigs with African Swine Fever Virus Isolated in 2019 in Mongolia.

    McDowell, Chester D / Bold, Dashzeveg / Trujillo, Jessie D / Meekins, David A / Keating, Cassidy / Cool, Konner / Kwon, Taeyong / Madden, Daniel W / Artiaga, Bianca L / Balaraman, Velmurugan / Ankhanbaatar, Ulaankhuu / Zayat, Batsukh / Retallick, Jamie / Dodd, Kimberly / Chung, Chungwon J / Morozov, Igor / Gaudreault, Natasha N / Souza-Neto, Jayme A / Richt, Jürgen A

    Viruses

    2022  Volume 14, Issue 12

    Abstract: African swine fever (ASF) is an infectious viral disease caused by African swine fever virus (ASFV), that causes high mortality in domestic swine and wild boar ( ...

    Abstract African swine fever (ASF) is an infectious viral disease caused by African swine fever virus (ASFV), that causes high mortality in domestic swine and wild boar (
    MeSH term(s) Swine ; Animals ; African Swine Fever Virus ; African Swine Fever/epidemiology ; Mongolia/epidemiology ; Virulence ; Viremia/veterinary ; Sus scrofa
    Language English
    Publishing date 2022-12-01
    Publishing country Switzerland
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v14122698
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Preliminary Study on the Efficacy of a Recombinant, Subunit SARS-CoV-2 Animal Vaccine against Virulent SARS-CoV-2 Challenge in Cats.

    Morozov, Igor / Gaudreault, Natasha N / Trujillo, Jessie D / Indran, Sabarish V / Cool, Konner / Kwon, Taeyong / Meekins, David A / Balaraman, Velmurugan / Artiaga, Bianca Libanori / Madden, Daniel W / McDowell, Chester / Njaa, Bradley / Retallick, Jamie / Hainer, Nicole / Millership, Jason / Wilson, William C / Tkalcevic, George / Vander Horst, Hanne / Burakova, Yulia /
    King, Vickie / Hutchinson, Kendra / Hardham, John M / Schwahn, Denise J / Kumar, Mahesh / Richt, Juergen A

    Vaccines

    2023  Volume 11, Issue 12

    Abstract: The objective of this work was to evaluate the safety and efficacy of a recombinant, subunit SARS-CoV-2 animal vaccine in cats against virulent SARS-CoV-2 challenge. Two groups of cats were immunized with two doses of either a recombinant SARS-CoV-2 ... ...

    Abstract The objective of this work was to evaluate the safety and efficacy of a recombinant, subunit SARS-CoV-2 animal vaccine in cats against virulent SARS-CoV-2 challenge. Two groups of cats were immunized with two doses of either a recombinant SARS-CoV-2 spike protein vaccine or a placebo, administered three weeks apart. Seven weeks after the second vaccination, both groups of cats were challenged with SARS-CoV-2 via the intranasal and oral routes simultaneously. Animals were monitored for 14 days post-infection for clinical signs and viral shedding before being humanely euthanized and evaluated for macroscopic and microscopic lesions. The recombinant SARS-CoV-2 spike protein subunit vaccine induced strong serologic responses post-vaccination and significantly increased neutralizing antibody responses post-challenge. A significant difference in nasal and oral viral shedding, with significantly reduced virus load (detected using RT-qPCR) was observed in vaccinates compared to mock-vaccinated controls. Duration of nasal, oral, and rectal viral shedding was also significantly reduced in vaccinates compared to controls. No differences in histopathological lesion scores were noted between the two groups. Our findings support the safety and efficacy of the recombinant spike protein-based SARS-CoV-2 vaccine which induced high levels of neutralizing antibodies and reduced nasal, oral, and rectal viral shedding, indicating that this vaccine will be efficacious as a COVID-19 vaccine for domestic cats.
    Language English
    Publishing date 2023-12-08
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2703319-3
    ISSN 2076-393X
    ISSN 2076-393X
    DOI 10.3390/vaccines11121831
    Database MEDical Literature Analysis and Retrieval System OnLINE

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