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Intergenogroup recombination in sapoviruses.

Hansman GS, Takeda N, Oka T, Oseto M, Hedlund KO, Katayama K - Emerging Infect. Dis. (2005)

Bottom Line: Analyses of the complete genome sequences led us to identify the first sapovirus intergenogroup recombinant strain.We found that a recombination event occurred at the polymerase and capsid junction.This is the first report of intergenogroup recombination for any calicivirus and highlights a possible route of zoonoses because sapovirus strains that infect pig species belong to genogroup III.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Infectious Diseases, Tokyo, Japan.

ABSTRACT
Sapovirus, a member of the family Caliciviridae, is an etiologic agent of gastroenteritis in humans and pigs. Analyses of the complete genome sequences led us to identify the first sapovirus intergenogroup recombinant strain. Phylogenetic analysis of the nonstructural region (i.e., genome start to capsid start) grouped this strain into genogroup II, whereas the structural region (i.e., capsid start to genome end) grouped this strain into genogroup IV. We found that a recombination event occurred at the polymerase and capsid junction. This is the first report of intergenogroup recombination for any calicivirus and highlights a possible route of zoonoses because sapovirus strains that infect pig species belong to genogroup III.

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A) SimPlot analysis of 7 sapovirus (SaV) complete genome sequences. The Mc10 genome sequence was compared to C12, Bristol, Mc2, SK15, SW278, and Ehime1107 by using a window size of 100 bp with an increment of 20 bp. All gaps were removed. The recombination site is suspected to be located between the polymerase and capsid gene, as shown by the arrows. B) Genomic organization of the SaV SW278 and Ehime1107 strains.
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Figure 2: A) SimPlot analysis of 7 sapovirus (SaV) complete genome sequences. The Mc10 genome sequence was compared to C12, Bristol, Mc2, SK15, SW278, and Ehime1107 by using a window size of 100 bp with an increment of 20 bp. All gaps were removed. The recombination site is suspected to be located between the polymerase and capsid gene, as shown by the arrows. B) Genomic organization of the SaV SW278 and Ehime1107 strains.

Mentions: We next used SimPlot (available from http://sray.med.som.jhmi.edu/SCRoftware/simplot/) with a window size of 100 and an increment of 20 bp (11) to further analyze these novel recombinant SW278 and Ehime1107 strains. We analyzed 7 complete genome SaV sequences. The Mc10 genome sequence was compared to C12, Bristol, Mc2, SK15, SW278, and Ehime1107. We observed a sudden drop in nucleotide similarity after the polymerase region for SW278 and Ehime1107 (Figure 2A). Nucleotide sequence analysis of the nonstructural region showed that SW278 and Ehime1107 shared between 74.0% to 77.6% nucleotide identity to the Mc2, C12, Mc10, and SK15 sequences, whereas analysis of the structural region showed that SW278 and Ehime1107 had only 54.0%–55.2% nucleotide identity to the Mc2, C12, Mc10, and SK15 sequences (Table); i.e., the nonstructural and structural regions of SW278 and Ehime1107 were ≈20% different. A similar result was observed with the nonstructural and structural regions of the already-established recombinant Mc10 and C12 strains, which had an 18.6% difference (3). When we analyzed the nonstructural and structural regions of Mc2 and SK15, we found only a 1.5% difference. Likewise, all other SaV strains generally maintained their nucleotide identities over the complete genome (Table). This result can be best explained as a recombination event at the polymerase and capsid junction for the SW278 and Ehime1107 strains, i.e., the nonstructural region originated from a GII strain, and the structural region originated from a strain belonging to another genogroup. The SaV GI, GIV, and GV genomes are predicted to encode an ORF3, whereas the SaV GII and GIII genomes have 2 main ORFs. We found that SW278 and Ehime1107 each had an ORF3, which is predicted to encode a yet-unknown protein of 161 amino acids. Notably, the structural region–based grouping showed that GI, GIV, and GV grouped in 1 major branch, while GII and GIII represented 2 other branches. These data provide further evidence of the intergenogroup recombination for SW278 and Ehime1107 strains.


Intergenogroup recombination in sapoviruses.

Hansman GS, Takeda N, Oka T, Oseto M, Hedlund KO, Katayama K - Emerging Infect. Dis. (2005)

A) SimPlot analysis of 7 sapovirus (SaV) complete genome sequences. The Mc10 genome sequence was compared to C12, Bristol, Mc2, SK15, SW278, and Ehime1107 by using a window size of 100 bp with an increment of 20 bp. All gaps were removed. The recombination site is suspected to be located between the polymerase and capsid gene, as shown by the arrows. B) Genomic organization of the SaV SW278 and Ehime1107 strains.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3367643&req=5

Figure 2: A) SimPlot analysis of 7 sapovirus (SaV) complete genome sequences. The Mc10 genome sequence was compared to C12, Bristol, Mc2, SK15, SW278, and Ehime1107 by using a window size of 100 bp with an increment of 20 bp. All gaps were removed. The recombination site is suspected to be located between the polymerase and capsid gene, as shown by the arrows. B) Genomic organization of the SaV SW278 and Ehime1107 strains.
Mentions: We next used SimPlot (available from http://sray.med.som.jhmi.edu/SCRoftware/simplot/) with a window size of 100 and an increment of 20 bp (11) to further analyze these novel recombinant SW278 and Ehime1107 strains. We analyzed 7 complete genome SaV sequences. The Mc10 genome sequence was compared to C12, Bristol, Mc2, SK15, SW278, and Ehime1107. We observed a sudden drop in nucleotide similarity after the polymerase region for SW278 and Ehime1107 (Figure 2A). Nucleotide sequence analysis of the nonstructural region showed that SW278 and Ehime1107 shared between 74.0% to 77.6% nucleotide identity to the Mc2, C12, Mc10, and SK15 sequences, whereas analysis of the structural region showed that SW278 and Ehime1107 had only 54.0%–55.2% nucleotide identity to the Mc2, C12, Mc10, and SK15 sequences (Table); i.e., the nonstructural and structural regions of SW278 and Ehime1107 were ≈20% different. A similar result was observed with the nonstructural and structural regions of the already-established recombinant Mc10 and C12 strains, which had an 18.6% difference (3). When we analyzed the nonstructural and structural regions of Mc2 and SK15, we found only a 1.5% difference. Likewise, all other SaV strains generally maintained their nucleotide identities over the complete genome (Table). This result can be best explained as a recombination event at the polymerase and capsid junction for the SW278 and Ehime1107 strains, i.e., the nonstructural region originated from a GII strain, and the structural region originated from a strain belonging to another genogroup. The SaV GI, GIV, and GV genomes are predicted to encode an ORF3, whereas the SaV GII and GIII genomes have 2 main ORFs. We found that SW278 and Ehime1107 each had an ORF3, which is predicted to encode a yet-unknown protein of 161 amino acids. Notably, the structural region–based grouping showed that GI, GIV, and GV grouped in 1 major branch, while GII and GIII represented 2 other branches. These data provide further evidence of the intergenogroup recombination for SW278 and Ehime1107 strains.

Bottom Line: Analyses of the complete genome sequences led us to identify the first sapovirus intergenogroup recombinant strain.We found that a recombination event occurred at the polymerase and capsid junction.This is the first report of intergenogroup recombination for any calicivirus and highlights a possible route of zoonoses because sapovirus strains that infect pig species belong to genogroup III.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Infectious Diseases, Tokyo, Japan.

ABSTRACT
Sapovirus, a member of the family Caliciviridae, is an etiologic agent of gastroenteritis in humans and pigs. Analyses of the complete genome sequences led us to identify the first sapovirus intergenogroup recombinant strain. Phylogenetic analysis of the nonstructural region (i.e., genome start to capsid start) grouped this strain into genogroup II, whereas the structural region (i.e., capsid start to genome end) grouped this strain into genogroup IV. We found that a recombination event occurred at the polymerase and capsid junction. This is the first report of intergenogroup recombination for any calicivirus and highlights a possible route of zoonoses because sapovirus strains that infect pig species belong to genogroup III.

Show MeSH
Related in: MedlinePlus