Evolutionary analysis of Tembusu virus: Evidence for the emergence of a dominant genotype

Dai, Li-Shang; Li, Zejun

doi:10.1016/j.meegid.2015.03.004

Cited by 24 publications

(34 citation statements)

References 47 publications

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“…Our time‐scaled phylogenetic analysis based on the largest number of the polyprotein gene sequences of DTMUV identified during 2007–2015 showed that DTMUV might have emerged since 1960. In contrast with a previous report using a different set of DTMUV data collected only from China between 2010 and 2013 to establish the clusters of DTMUVs into four clusters (I, II‐a, II‐b and II‐c) (Dai et al., ), three clusters of DTMUVs (1, 2.1 and 2.2) were established in this study using sequences of DTMUV identified in China and South‐East Asia during 2007–2015. It is noted that all of the DTMUV sequences in cluster I, II‐a, II‐b and II‐c described in Dai et al.…”

Section: Discussionmentioning

confidence: 69%

“…To determine the evolution of DTMUV, the time‐scaled phylogenetic analysis was performed as previously described (Dai, Li, & Tao, ; Moureau et al., ; Yu et al., ). The polyprotein gene sequences of the 2007 Thai DTMUV and the previously reported Chinese, Malaysian and Thai DTMUVs, identified during 2010‐2015, were aligned using Muscle v.3.6 (Edgar, ).…”

Section: Methodsmentioning

confidence: 99%

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The presence of duck Tembusu virus in Thailand since 2007: A retrospective study

Ninvilai

Nonthabenjawan

Limcharoen

et al. 2018

Transbound Emerg Dis

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Duck Tembusu virus (DTMUV), a newly emerging virus in ducks, was first reported in China in 2010. However, an unknown severe contagious disease associated with severe neurological signs and egg production losses in ducks, resembling to DTMUV infection, was observed in Thailand since 2007. To determine the presence of DTMUV in 2007, the clinical samples from affected ducks collected in 2007 were tested for DTMUV using pathological and virological analyses. Gross and histopathological lesions of affected ducks were mostly restricted to the ovary, brain and spinal cord, and correlated with the presence of flavivirus antigen in the brain and spinal cord samples. Subsequently, DTMUV was identified by RT-PCR and nucleotide sequencing of the polyprotein gene. Phylogenetic analysis of the polyprotein gene sequence revealed that the 2007 Thai DTMUV was a unique virus, belonged within DTMUV cluster 1, but distinctively separated from the Malaysian DTMUV, which was the most closely related DTMUV. It is interesting to note that the 2007 Thai DTMUV was genetically different from the currently circulating Thai and Chinese DTMUVs, which belonged to cluster 2. Our findings indicated that the 2007 Thai DTMUV emerged earlier from a common ancestor with the recently reported DTMUVs; however, it was genetically distinctive to any of the currently circulating DTMUVs. In conclusion, our data demonstrated the presence of DTMUV in the Thai ducks since 2007, prior to the first report of DTMUV in China in 2010. This study indicates that DTMUV may have circulated in the region long before 2010 and highlights high genetic diversity of DTMUVs in Asia.

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Section: Discussionmentioning

confidence: 69%

Section: Methodsmentioning

confidence: 99%

The presence of duck Tembusu virus in Thailand since 2007: A retrospective study

Ninvilai

Nonthabenjawan

Limcharoen

et al. 2018

Transbound Emerg Dis

View full text Add to dashboard Cite

show abstract

“…Thus, to develop a universal TMUV detection assay, identifying conserved regions in the TMUV genome sequence is a critical step in RT-LAMP primer design. Recently, Dai et al 36. provided evidence of natural recombination in TMUV and genetic divergence between various TMUV strains isolated in different years.…”

Section: Discussionmentioning

confidence: 99%

“…These strains represent all different TMUV genotyping groups/subgroups described in a recent TMUV evolutionary analysis study36. The alignment of complete ORFs was conducted using the mVISTA online program (http://genome.lbl.gov/vista/mvista/submit.shtml) and the pairwise comparison of the selected conserved region was performed using the ClustalW method in Genomic Workbench V7.5 software (QIAGEN, Boston, MA, USA).…”

Section: Methodsmentioning

confidence: 99%

Advanced uracil DNA glycosylase-supplemented real-time reverse transcription loop-mediated isothermal amplification (UDG-rRT-LAMP) method for universal and specific detection of Tembusu virus

Tang

Chen

Diao

2016

Sci Rep

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Tembusu virus (TMUV) is a mosquito-borne flavivirus which threatens both poultry production and public health. In this study we developed a complete open reading frame alignment-based rRT-LAMP method for the universal detection of TUMV. To prevent false-positive results, the reaction was supplemented with uracil DNA glycosylase (UDG) to eliminate carryover contamination. The detection limit of the newly developed UDG-rRT-LAMP for TMUV was as low as 100 copies/reaction of viral RNA and 1 × 100.89 − 1 × 101.55 tissue culture infectious dose/100 μL of viruses. There were no cross-reactions with other viruses, and the reproducibility of the assay was confirmed by intra- and inter-assay tests with variability ranging from 0.22–3.33%. The new UDG-rRT-LAMP method for TMUV produced the same results as viral isolation combined with RT-PCR as the “gold standard” in 96.88% of cases for 81 clinical samples from subjects with suspected TMUV infection. The addition of UDG can eliminate as much as 1 × 10−16 g/reaction of contaminants, which can significantly reduce the likelihood of false-positive results during the rRT-LAMP reaction. Our result indicated that our UDG-rRT-LAMP is a rapid, sensitive, specific, and reliable method that can effectively prevent carryover contamination in the detection of TMUV.

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“…To date, DTMUV-related studies have focused on pathogenicity [21,22], detection methods [23,24], vaccines [10,25,26], transmission routes [27], genetic evolution and epidemiology [1,28,29], and molecular structure [30,31]. Unfortunately, the immune mechanisms of DTMUV invasion and infection in host cells remain poorly understood.…”

Section: Introductionmentioning

confidence: 99%

Comparative Transcriptomic Analysis of Immune-Related Gene Expression in Duck Embryo Fibroblasts Following Duck Tembusu Virus Infection

Lin

Tang

et al. 2018

IJMS

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Duck is a major waterfowl species in China, providing high-economic benefit with a population of up to 20–30 billion per year. Ducks are commonly affected by severe diseases, including egg-drop syndrome caused by duck Tembusu virus (DTMUV). The immune mechanisms against DTMUV invasion and infection remain poorly understood. In this study, duck embryo fibroblasts (DEFs) were infected with DTMUV and harvested at 12 and 24 h post-infection (hpi), and their genomes were sequenced. In total, 911 (764 upregulated and 147 downregulated genes) and 3008 (1791 upregulated and 1217 downregulated) differentially expressed genes (DEGs) were identified at 12 and 24 hpi, respectively. Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that DEGs were considerably enriched in immune-relevant pathways, including Toll-like receptor signaling pathway, Cytosolic DNA-sensing pathway, RIG-I-like receptor signaling pathway, Chemokine signaling pathway, NOD-like receptor signaling pathway, and Hematopoietic cell lineage at both time points. The key DEGs in immune system included those of the cytokines (IFN α2, IL-6, IL-8L, IL-12B, CCR7, CCL19, and CCL20), transcription factors or signaling molecules (IRF7, NF-κB, STAT1, TMEM173, and TNFAIP3), pattern recognition receptors (RIG-I and MDA5), and antigen-presenting proteins (CD44 and CD70). This suggests DTMUV infection induces strong proinflammatory/antiviral effects with enormous production of cytokines. However, these cytokines could not protect DEFs against viral attack. Our data revealed valuable transcriptional information regarding DTMUV-infected DEFs, thereby broadening our understanding of the immune response against DTMUV infection; this information might contribute in developing strategies for controlling the prevalence of DTMUV infection.

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Evolutionary analysis of Tembusu virus: Evidence for the emergence of a dominant genotype

Cited by 24 publications

References 47 publications

The presence of duck Tembusu virus in Thailand since 2007: A retrospective study

The presence of duck Tembusu virus in Thailand since 2007: A retrospective study

Advanced uracil DNA glycosylase-supplemented real-time reverse transcription loop-mediated isothermal amplification (UDG-rRT-LAMP) method for universal and specific detection of Tembusu virus

Comparative Transcriptomic Analysis of Immune-Related Gene Expression in Duck Embryo Fibroblasts Following Duck Tembusu Virus Infection

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