Rediscovery and genomic characterization of bovine astroviruses

The genus Mamastrovirus belongs to the family Astroviridae and consists of at least six members infecting different mammalian hosts, including humans, cattle and pigs. In recent years, novel astroviruses have been identified in other mammalian species like roe deer, bats and sea lions. While the bovine astrovirus was one of the earliest astroviruses to have been studied, no further research has been performed recently and its genome sequence remains uncharacterized. In this report, we describe the detection and genomic characterization of astroviruses in bovine faecal specimens obtained in Hong Kong. Five of 209 specimens were found to be positive for astrovirus by RT-PCR. Two of the positive specimens were found to contain sequences from two different astrovirus strains. Complete genome sequences of approximately 6.3 kb in length were obtained for four strains, which showed similar organization of the genome compared to other astroviruses. Phylogenetic analysis confirmed their identities as members of the genus Mamastrovirus, and showed them to be most closely related to the Capreolus capreolus astrovirus. Based on the pairwise genetic distances among their full-length ORF2 sequences, these bovine astroviruses may be assigned into at least three different genotype species. Sequence analysis revealed evidence of potential recombination in ORF2. In summary, we report the first genome sequences of bovine astroviruses and clearly establish the species status of the virus. Additionally, our study is among the first to report co-infection by different astrovirus genotypes in the same host, which is an essential step for recombination to occur.

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Characterization of Rhodococcus equi isolates from submaxillary lymph nodes of wild boars (Sus scrofa), red deer (Cervus elaphus) and roe deer (Capreolus capreolus)

Veterinary Microbiology ◽

10.1016/j.vetmic.2014.04.020 ◽

2014 ◽

Vol 172 (1-2) ◽

pp. 272-278 ◽

Cited By ~ 9

Author(s):

Magdalena Rzewuska ◽

Lucjan Witkowski ◽

Agata A. Cisek ◽

Ilona Stefańska ◽

Dorota Chrobak ◽

...

Keyword(s):

Lymph Nodes ◽

Cervus Elaphus ◽

Sus Scrofa ◽

Red Deer ◽

Roe Deer ◽

Capreolus Capreolus ◽

Rhodococcus Equi ◽

Wild Boars

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Genomic characterization of 99 viruses from the bunyavirus families Nairoviridae, Peribunyaviridae, and Phenuiviridae, including 35 previously unsequenced viruses

PLoS Pathogens ◽

10.1371/journal.ppat.1009315 ◽

2021 ◽

Vol 17 (3) ◽

pp. e1009315

Author(s):

Marylee L. Kapuscinski ◽

Nicholas A. Bergren ◽

Brandy J. Russell ◽

Justin S. Lee ◽

Erin M. Borland ◽

...

Keyword(s):

Plant Pathogens ◽

Reference Sequence ◽

Large Sample Size ◽

Emerging Pathogens ◽

Genome Sequences ◽

Pathogenic Potential ◽

Genomic Characterization ◽

Response Decisions ◽

Rapid Characterization

Bunyaviruses (Negarnaviricota: Bunyavirales) are a large and diverse group of viruses that include important human, veterinary, and plant pathogens. The rapid characterization of known and new emerging pathogens depends on the availability of comprehensive reference sequence databases that can be used to match unknowns, infer evolutionary and pathogenic potential, and make response decisions in an evidence-based manner. In this study, we determined the coding-complete genome sequences of 99 bunyaviruses in the Centers for Disease Control and Prevention’s Arbovirus Reference Collection, focusing on orthonairoviruses (family Nairoviridae), orthobunyaviruses (Peribunyaviridae), and phleboviruses (Phenuiviridae) that either completely or partially lacked genome sequences. These viruses had been collected over 66 years from 27 countries from vertebrates and arthropods representing 37 genera. Many of the viruses had been characterized serologically and through experimental infection of animals but were isolated in the pre-sequencing era. We took advantage of our unusually large sample size to systematically evaluate genomic characteristics of these viruses, including reassortment, and co-infection. We corroborated our findings using several independent molecular and virologic approaches, including Sanger sequencing of 197 genome segments, and plaque isolation of viruses from putative co-infected virus stocks. This study contributes to the described genetic diversity of bunyaviruses and will enhance the capacity to characterize emerging human pathogenic bunyaviruses.

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Complete Genomic Characterization of Two Beet Soil-Borne Virus Isolates from Turkey: Implications of Comparative Analysis of Genome Sequences

The Plant Pathology Journal ◽

10.5423/ppj.oa.12.2020.0223 ◽

2021 ◽

Vol 37 (2) ◽

pp. 152-161

Author(s):

Zohreh Moradi ◽

Hossein Maghdoori ◽

Ehsan Nazifi ◽

Mohsen Mehrvar

Keyword(s):

Comparative Analysis ◽

Genome Sequences ◽

Genomic Characterization ◽

Virus Isolates ◽

Complete Genomic

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Genomic characterization of novel marine vesiviruses from Steller sea lions (Eumetopias jubatus) from Alaska

Virus Research ◽

10.1016/j.virusres.2008.08.002 ◽

2008 ◽

Vol 138 (1-2) ◽

pp. 26-35 ◽

Cited By ~ 8

Author(s):

Shasta D. McClenahan ◽

Kathy A. Burek ◽

Kimberlee B. Beckmen ◽

Nick J. Knowles ◽

John D. Neill ◽

...

Keyword(s):

Eumetopias Jubatus ◽

Steller Sea Lions ◽

Sea Lions ◽

Genomic Characterization

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Progestogen Profiling Over the Course of Diapause and Resumption of Embryo Development in the European Roe Deer

SciMedicine Journal ◽

10.28991/scimedj-2019-0104-1 ◽

2019 ◽

Vol 1 (4) ◽

pp. 158-167 ◽

Cited By ~ 1

Author(s):

Vera A. Van der Weijden ◽

Anna-Katharina Hankele ◽

Anna B. Rüegg ◽

Marion Schmicke ◽

Karoline Rehm ◽

...

Keyword(s):

Embryo Development ◽

Luteal Phase ◽

Roe Deer ◽

Binding Capacity ◽

Mammalian Species ◽

Capreolus Capreolus ◽

Corpora Lutea ◽

Embryonic Diapause ◽

Weak Correlation ◽

Species Specific

Progesterone (P4) plays a pivotal role in maintenance of pregnancy in many mammalian species. Species-specific P4 metabolites have been shown to function as primary acting progestogen and the receptor binding capacity varies between species. The European roe deer (Capreolus capreolus) displays a 4-5 month period of embryonic diapause, which decouples fertilization from implantation. The majority of roe deer have two corpora lutea that secrete P4. No changes in P4 concentrations have been observed during pre-implantation embryo development. As 5α-DHP is known to play a major role during pregnancy in elephants and horses, we hypothesized that 5α-DHP functions as additional progestogen facilitating embryo reactivation. The profile of 11 progestogens was quantified in roe deer plasma over the course of diapause and resumption of embryo development including P4, 3α- and 3β-DHP, 20α- and 20β-DHP, 5α- and 5β-DHP, 3α,5α- and 3α,5β-THP, as well as 3β,5α- and 3β,5β-THP. While P4 was most abundant during diapause and resumption of development, 20α-DHP was the most abundant P4 metabolite. This is different than in pregnant elephants, where 5α-DHP was most abundant, and the luteal phase in cattle, where 3α,5α-THP was most abundant. With the exception of a weak correlation of 3β,5α-THP, none of the progestogens significantly correlated with embryonic development in the roe deer. Thus, plasma 5α-DHP does not seem to play a role in embryo reactivation. We propose that progestogens might contribute to priming the endometrium for supporting embryo development and preparation for implantation.

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One year of SARS-CoV-2: Genomic characterization of COVID-19 outbreak in Qatar

10.1101/2021.05.19.21257433 ◽

2021 ◽

Author(s):

Fatiha M. Benslimane ◽

Hebah A. AlKhatib ◽

Ola Al-Jamal ◽

Dana Albatesh ◽

Sonia Boughattas ◽

...

Keyword(s):

International Travel ◽

Genomic Diversity ◽

Whole Genome ◽

Genome Sequences ◽

Short Period ◽

National Response ◽

Genomic Characterization ◽

One Year ◽

Local Transmission

The state of Qatar has emerged as a major transit hub connecting all parts of the globe, making it as a hotspot for infectious disease introduction and providing an ideal setting to monitor the emergence and spread of variants. In this study, we report on 2634 SARS-CoV-2 whole-genome sequences from infected patients in Qatar between March-2020 and March-2021, representing 1.5% of all positive cases in this period. Despite the restrictions on international travel, the viruses sampled from the populace of Qatar mirrored nearly the entire global population's genomic diversity with nine predominant viral lineages that were sustained by local transmission chains and the emergence of mutations that are likely to have originated in Qatar. We reported an increased number in the mutations and deletions in B.1.1.7 and B.1.351 lineages in a short period. This raises the imperative need to continue the ongoing genomic surveillance that has been an integral part of the national response to monitor SARS-CoV-2 profile and re-emergence in Qatar.

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Draft Genome Sequences of 29 Helicobacter pylori Strains Isolated from Colombia

Microbiology Resource Announcements ◽

10.1128/mra.00218-21 ◽

2021 ◽

Vol 10 (19) ◽

Author(s):

Angela B. Muñoz ◽

Johanna Stepanian ◽

Carmen Acosta ◽

Juan S. Solano-Gutierrez ◽

Filipa F. Vale ◽

...

Keyword(s):

Helicobacter Pylori ◽

Chronic Gastritis ◽

Draft Genome ◽

Genetic Composition ◽

Genome Sequences ◽

Content Type ◽

Genomic Characterization ◽

H Pylori

ABSTRACT Here, we present the draft genome sequences of 29 Colombian Helicobacter pylori strains. These strains were isolated in Bogotá, Colombia, from patients diagnosed with chronic gastritis. The genomic characterization of these strains will provide more information on the genetic composition of H. pylori strains from Colombia.

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