Whole genomic analysis of human and bovine G8P[1] rotavirus strains isolated in Nigeria provides evidence for direct bovine-to-human interspecies transmission

Komoto, Satoshi; Adah, Mohammed I.; Ide, Tomihiko; Yoshikawa, Tetsushi; Taniguchi, Koki

doi:10.1016/j.meegid.2016.06.023

Cited by 34 publications

(24 citation statements)

References 56 publications

(95 reference statements)

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“…The extracted dsRNAs were subjected to Illumina MiSeq (Illunina Inc, San Diego, CA) sequencing as previously described . Briefly, a 200 bp fragment library ligated with bar‐coded adapters was constructed using a NEBNext Ultra RNA Library Prep Kit for Illumina v1.2 (New England Biolabs, Ipswich, MA) according to the manufacturer's instructions.…”

Section: Methodssupporting

confidence: 76%

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Persistent systemic rotavirus vaccine infection in a child with X‐linked severe combined immunodeficiency

Yoshikawa

Ihira²,

Higashimoto

et al. 2019

Journal of Medical Virology

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Objective The main aims of the present study were to elucidate the systemic group A rotavirus (RVA) infection and to clarify the genetic changes of persistent virus in the X‐linked severe combined immunodeficiency (SCID) patient. Methods RotaTeq vaccine (RV5) genotype‐specific real‐time reverse transcription polymerase chain reaction was used to monitor viral RNA load in serially collected serum and stool samples. Next‐generation sequence analysis was used to determine the genotype of the virus by sequencing 11 gene segments. Polyacrylamide gel electrophoresis (PAGE) analysis was used to identify rearrangement of viral genes. The gene rearrangement was examined in NSP5 gene by using Sanger sequence. Results A 7‐month‐old boy demonstrated chronic diarrhea following the third administration of RV5 and failure to thrive. He was diagnosed with X‐linked SCID and successfully underwent cord blood transplantation. High copy numbers of RV5 genotype G1 RNA were detected in serially collected stool and serum samples and the kinetics of viral RNA loads were correlated with the degree of clinical disease. Next‐generation sequence analysis revealed genetic reassortment at least between the strains WI79‐9/G1P7[5] and WI79‐4/G6P1A[8] in the VP7 gene and the VP4 gene among the vaccine‐derived rotavirus strains. In addition, PAGE analysis suggested genetic rearrangements in several genes, and it was confirmed in the NSP5 gene by sequence analysis. Conclusions The kinetics of RVA RNA load in serum and stool samples was consistent with the clinical course of the patient. Among five genotypes of RV5 vaccine, G1 genotype replicated well in this patient. Reassortment and rearrangements were demonstrated in persistently infected G1 genotype of RV5.

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Section: Methodssupporting

confidence: 76%

“…The extracted dsRNAs were subjected to Illumina MiSeq (Illunina Inc, San Diego, CA) sequencing as previously described. 16 Briefly, a 200 bp fragment library ligated with bar-coded adapters was constructed using a…”

Section: Next-generation Sequencing Analysis and Determination Of Rmentioning

confidence: 99%

Persistent systemic rotavirus vaccine infection in a child with X‐linked severe combined immunodeficiency

Yoshikawa

Ihira²,

Higashimoto

et al. 2019

Journal of Medical Virology

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“…Building of a cDNA library and Illumina MiSeq sequencing were performed as described previously [14, 16, 30, 33, 34]. Briefly, a 200 bp fragment library ligated with bar-coded adapters was constructed for the 14 strains using an NEBNext Ultra RNA Library Prep Kit for Illumina v1.2 (New England Biolabs), and NEBNext Multiplex Oligos for Illumina (New England Biolabs) according to the manufacturer’s instructions.…”

Section: Methodsmentioning

confidence: 99%

“…Similar DS-1-like G8P[8] strains (including strain RVN1149) were subsequently detected in Vietnam in 2014–2015 [25]. G8, like G6 and G10, is one of the common G genotypes in cattle that has been identified in humans sporadically [30]. Although human G8 strains are particularly prevalent in Africa, they have been infrequently detected elsewhere [25, 31].…”

Section: Introductionmentioning

confidence: 99%

Full Genome Characterization of Novel DS-1-Like G8P[8] Rotavirus Strains that Have Emerged in Thailand: Reassortment of Bovine and Human Rotavirus Gene Segments in Emerging DS-1-Like Intergenogroup Reassortant Strains

et al. 2016

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The emergence and rapid spread of unusual DS-1-like intergenogroup reassortant rotavirus strains have been recently reported in Asia, Australia, and Europe. During rotavirus surveillance in Thailand in 2013–2014, novel DS-1-like intergenogroup reassortant strains having G8P[8] genotypes (i.e., strains KKL-17, PCB-79, PCB-84, PCB-85, PCB-103, SKT-107, SWL-12, NP-130, PCB-656, SKT-457, SSKT-269, and SSL-55) were identified in stool samples from hospitalized children with severe diarrhea. In this study, we determined and characterized the complete genomes of these 12 strains (seven strains, KKL-17, PCB-79, PCB-84, PCB-85, PCB-103, SKT-107, and SWL-12, found in 2013 (2013 strains), and five, NP-130, PCB-656, SKT-457, SSKT-269, and SSL-55, in 2014 (2014 strains)). On full genomic analysis, all 12 strains showed a unique genotype constellation comprising a mixture of genogroup 1 and 2 genes: G8-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. With the exception of the G genotype, the unique genotype constellation of the 12 strains (P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2) was found to be shared with DS-1-like intergenogroup reassortant strains. On phylogenetic analysis, six of the 11 genes of the 2013 strains (VP4, VP2, VP3, NSP1, NSP3, and NSP5) appeared to have originated from DS-1-like intergenogroup reassortant strains, while the remaining four (VP7, VP6, VP1, and NSP2) and one (NSP4) gene appeared to be of bovine and human origin, respectively. Thus, the 2013 strains appeared to be reassortant strains as to DS-1-like intergenogroup reassortant, bovine, bovine-like human, and/or human rotaviruses. On the other hand, five of the 11 genes of the 2014 strains (VP4, VP2, VP3, NSP1, and NSP3) appeared to have originated from DS-1-like intergenogroup reassortant strains, while three (VP7, VP1, and NSP2) and one (NSP4) were assumed to be of bovine and human origin, respectively. Notably, the remaining two genes, VP6 and NSP5, of the 2014 strains appeared to have originated from locally circulating DS-1-like G2P[4] human rotaviruses. Thus, the 2014 strains were assumed to be multiple reassortment strains as to DS-1-like intergenogroup reassortant, bovine, bovine-like human, human, and/or locally circulating DS-1-like G2P[4] human rotaviruses. Overall, the great genomic diversity among the DS-1-like intergenogroup reassortant strains seemed to have been generated through additional reassortment events involving animal and human strains. Moreover, all the 11 genes of three of the 2014 strains, NP-130, PCB-656, and SSL-55, were very closely related to those of Vietnamese DS-1-like G8P[8] strains that emerged in 2014–2015, indicating the derivation of these DS-1-like G8P[8] strains from a common ancestor. To our knowledge, this is the first report on full genome-based characterization of DS-1-like G8P[8] strains that have emerged in Thailand. Our observations will add to our growing understanding of the evolutionary patterns of emerging DS-1-like intergenogroup reassortant strains.

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“…High-throughput sequencing (HTS) coupled with de novo assembly offers the possibility of recognizing viral RNA or DNA in an unbiased fashion. HTSbased screenings in both vertebrate and non-vertebrate biological specimens [1][2][3] have shown that the diversity of viruses circulating in the animal world is larger than anticipated (including potential human infections such as astroviruses, reoviruses, pseudorabies viruses, and bornaviruses [4][5][6][7][8][9]), and that many viral families are shared by the two kingdoms, raising the possibility of yet to be discovered viral infections in humans [10].…”

Section: Introductionmentioning

confidence: 99%

Detection of dicistroviruses RNA in blood of febrile Tanzanian children

Cordey

Laubscher

Hartley

et al. 2019

Emerging Microbes & Infections

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Fever is the leading cause of paediatric outpatient consultations in Sub-Saharan Africa. Although most are suspected to be of viral origin, a putative causative pathogen is not identified in over a quarter of these febrile episodes. Using a de novo assembly sequencing approach, we report the detection (15.4%) of dicistroviruses (DicV) RNA in sera collected from 692 febrile Tanzanian children. In contrast, DicV RNA was only detected in 1/77 (1.3%) plasma samples from febrile Tanzanian adults, suggesting that children could represent the primary susceptible population. Estimated viral load by specific quantitative real-time RT–PCR assay ranged from < 1.32E3 to 1.44E7 viral RNA copies/mL serum. Three DicV full-length genomes were obtained, and a phylogenetic analyse on the capsid region showed the presence of two clusters representing tentative novel genus. Although DicV-positive cases were detected throughout the year, a significantly higher positivity rate was observed during the rainy season. This study reveals that novel DicV RNA is frequently detected in the blood of Tanzanian children, paving the way for further investigations to determine if DicV possibly represent a new agent in humans.

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Whole genomic analysis of human and bovine G8P[1] rotavirus strains isolated in Nigeria provides evidence for direct bovine-to-human interspecies transmission

Cited by 34 publications

References 56 publications

Persistent systemic rotavirus vaccine infection in a child with X‐linked severe combined immunodeficiency

Persistent systemic rotavirus vaccine infection in a child with X‐linked severe combined immunodeficiency

Full Genome Characterization of Novel DS-1-Like G8P[8] Rotavirus Strains that Have Emerged in Thailand: Reassortment of Bovine and Human Rotavirus Gene Segments in Emerging DS-1-Like Intergenogroup Reassortant Strains

Detection of dicistroviruses RNA in blood of febrile Tanzanian children

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