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Use of S1 nuclease in deep sequencing for detection of double-stranded RNA viruses.

Shimada S, Nagai M, Moriyama H, Fukuhara T, Koyama S, Omatsu T, Furuya T, Shirai J, Mizutani T - J. Vet. Med. Sci. (2015)

Bottom Line: However, in many cases, majority of the detected sequences originate from the host genome and bacterial flora in the gut.Moreover, increasing coverage of mapping to reference sequences allowed for sufficient genotyping using analytical software.These results suggest that library construction using S1 nuclease is useful for deep sequencing in the detection of dsRNA viruses.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Epizootiology, Cooperative Department of Veterinary Medicine Faculty and Agriculture, Tokyo University of Agriculture and Technology, Saiwai, Fuchu, Tokyo 183-8509, Japan.

ABSTRACT
Metagenomic approach using next-generation DNA sequencing has facilitated the detection of many pathogenic viruses from fecal samples. However, in many cases, majority of the detected sequences originate from the host genome and bacterial flora in the gut. Here, to improve efficiency of the detection of double-stranded (ds) RNA viruses from samples, we evaluated the applicability of S1 nuclease on deep sequencing. Treating total RNA with S1 nuclease resulted in 1.5-28.4- and 10.1-208.9-fold increases in sequence reads of group A rotavirus in fecal and viral culture samples, respectively. Moreover, increasing coverage of mapping to reference sequences allowed for sufficient genotyping using analytical software. These results suggest that library construction using S1 nuclease is useful for deep sequencing in the detection of dsRNA viruses.

No MeSH data available.


Related in: MedlinePlus

Mapping of RVA sequence reads of non-treated and S1 treated samples of calf No.1 andswine No.1 against bovine reference sequences of (A) VP4 and (B) swine reference of VP7.Positional sequence coverage and sequencing depth of VP4 (P[1], P[5], P[11] and P[14])and VP7 (G2, G4, G5, G9 and G11) of calf No.1 and swine No.1, based on referenceassembly to P[1]: NCDV Lincoln (AB119636), P[5]: WC3 (AY05071), P[11]: B223 (D13394),P[14]: RVA/Cow-wt/JPN/Tottori-SG/2013/G15P[14] (AB853893), G2:RVA/Vaccine/USA/RotaTeq-SC2-9/G2P7 [5] (GU565068), G4:RVA/Vaccine/USA/RotaTeq-BrB-9/1996/G4P7[5] (GU565090), G5:RVA/Pig-tc/ESP/OSU-C5111/2010/G5P[7] (KJ450849), G9: JP3-6 (AB176678) and G11: HLJhg7(JX498964).
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fig_001: Mapping of RVA sequence reads of non-treated and S1 treated samples of calf No.1 andswine No.1 against bovine reference sequences of (A) VP4 and (B) swine reference of VP7.Positional sequence coverage and sequencing depth of VP4 (P[1], P[5], P[11] and P[14])and VP7 (G2, G4, G5, G9 and G11) of calf No.1 and swine No.1, based on referenceassembly to P[1]: NCDV Lincoln (AB119636), P[5]: WC3 (AY05071), P[11]: B223 (D13394),P[14]: RVA/Cow-wt/JPN/Tottori-SG/2013/G15P[14] (AB853893), G2:RVA/Vaccine/USA/RotaTeq-SC2-9/G2P7 [5] (GU565068), G4:RVA/Vaccine/USA/RotaTeq-BrB-9/1996/G4P7[5] (GU565090), G5:RVA/Pig-tc/ESP/OSU-C5111/2010/G5P[7] (KJ450849), G9: JP3-6 (AB176678) and G11: HLJhg7(JX498964).

Mentions: Furthermore, RVA genotyping was performed by mapping the reads of the samples to the RVAreference sequences by using CLC[9]. Figure 1Fig. 1.


Use of S1 nuclease in deep sequencing for detection of double-stranded RNA viruses.

Shimada S, Nagai M, Moriyama H, Fukuhara T, Koyama S, Omatsu T, Furuya T, Shirai J, Mizutani T - J. Vet. Med. Sci. (2015)

Mapping of RVA sequence reads of non-treated and S1 treated samples of calf No.1 andswine No.1 against bovine reference sequences of (A) VP4 and (B) swine reference of VP7.Positional sequence coverage and sequencing depth of VP4 (P[1], P[5], P[11] and P[14])and VP7 (G2, G4, G5, G9 and G11) of calf No.1 and swine No.1, based on referenceassembly to P[1]: NCDV Lincoln (AB119636), P[5]: WC3 (AY05071), P[11]: B223 (D13394),P[14]: RVA/Cow-wt/JPN/Tottori-SG/2013/G15P[14] (AB853893), G2:RVA/Vaccine/USA/RotaTeq-SC2-9/G2P7 [5] (GU565068), G4:RVA/Vaccine/USA/RotaTeq-BrB-9/1996/G4P7[5] (GU565090), G5:RVA/Pig-tc/ESP/OSU-C5111/2010/G5P[7] (KJ450849), G9: JP3-6 (AB176678) and G11: HLJhg7(JX498964).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4591160&req=5

fig_001: Mapping of RVA sequence reads of non-treated and S1 treated samples of calf No.1 andswine No.1 against bovine reference sequences of (A) VP4 and (B) swine reference of VP7.Positional sequence coverage and sequencing depth of VP4 (P[1], P[5], P[11] and P[14])and VP7 (G2, G4, G5, G9 and G11) of calf No.1 and swine No.1, based on referenceassembly to P[1]: NCDV Lincoln (AB119636), P[5]: WC3 (AY05071), P[11]: B223 (D13394),P[14]: RVA/Cow-wt/JPN/Tottori-SG/2013/G15P[14] (AB853893), G2:RVA/Vaccine/USA/RotaTeq-SC2-9/G2P7 [5] (GU565068), G4:RVA/Vaccine/USA/RotaTeq-BrB-9/1996/G4P7[5] (GU565090), G5:RVA/Pig-tc/ESP/OSU-C5111/2010/G5P[7] (KJ450849), G9: JP3-6 (AB176678) and G11: HLJhg7(JX498964).
Mentions: Furthermore, RVA genotyping was performed by mapping the reads of the samples to the RVAreference sequences by using CLC[9]. Figure 1Fig. 1.

Bottom Line: However, in many cases, majority of the detected sequences originate from the host genome and bacterial flora in the gut.Moreover, increasing coverage of mapping to reference sequences allowed for sufficient genotyping using analytical software.These results suggest that library construction using S1 nuclease is useful for deep sequencing in the detection of dsRNA viruses.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Epizootiology, Cooperative Department of Veterinary Medicine Faculty and Agriculture, Tokyo University of Agriculture and Technology, Saiwai, Fuchu, Tokyo 183-8509, Japan.

ABSTRACT
Metagenomic approach using next-generation DNA sequencing has facilitated the detection of many pathogenic viruses from fecal samples. However, in many cases, majority of the detected sequences originate from the host genome and bacterial flora in the gut. Here, to improve efficiency of the detection of double-stranded (ds) RNA viruses from samples, we evaluated the applicability of S1 nuclease on deep sequencing. Treating total RNA with S1 nuclease resulted in 1.5-28.4- and 10.1-208.9-fold increases in sequence reads of group A rotavirus in fecal and viral culture samples, respectively. Moreover, increasing coverage of mapping to reference sequences allowed for sufficient genotyping using analytical software. These results suggest that library construction using S1 nuclease is useful for deep sequencing in the detection of dsRNA viruses.

No MeSH data available.


Related in: MedlinePlus