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Introduction
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This is a tool where you can quickly get typing information by comparing your sequence to a library of consensus sequences of the (more or less) established norovirus genotypes.
The tool uses global pairwise similarity and presents the reference sequences in ascending order of similarity with the input sequence.
In this database are two sets of 30 consensus sequences, one set of polymerase sequences of 290 nt of different genotypes and subtypes. The other set are capsid sequences, 280 nt long. Of each consensus sequence the following information is presented: - the reference strain
- the number of strains used to determine the consensus sequence
- the genotype of the consensus sequence
- the reference in literature where the genotype is described
This library is of course not complete since there exist several strains which may constitute new genotypes but which have not been established yet. Changes and additions according to new insights and publications are implemented regularly. |
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How to use the quicktypingtool
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The quick typing tool consists of two sets of reference strains and is made available to the public by the FBVE next to several participants only databases. You can select region A or region C depending on the fragment you have sequenced. Region A and C are two of the most commonly used regions on the NoV genome for sequencing.  Region A 290b = set of consensus sequences using 290 nucleotides of the polymerase
Region C 280b = set of consensus sequences using 280 nucleotides of the 5’end of the capsid
If you click on the link a new window will be opened with a dialog box into which you can paste your sequence. Make sure your sequence is typed in capitals, overlaps with the corresponding fragment and is of the correct orientation. If these conditions are not met with, a nonsense result will follow. For this page the user and password are already entered so you can click the identify button as soon as the sequence is pasted or reset if you made a mistake.
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How to interpret the results
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A typical result would give you one entry with a high score (90-100) with the same genotype as your sequence, several intermediate scores (70-90), with members of the same genogroup and several low scores (50-70) with members of other genogroups. More than one high score can be obtained with the different genotype II.4 sequences because this genotype was subdivided in older and more recent variants as explained above.
If all the scores are below 50 than probably the sequence was not overlapping or in the wrong orientation; if no scores are given probably the "capitals only" warning was ignored.
The listed genotypes for capsid are according to references in literature either to the calicivirus chapter in Fields or to two journal articles indicated by their pubmed identifier (PMID), full references are given below. The listed genotypes for polymerase are in accordance with the capsid list, as far as possible, which means that there are many exceptions. For example II.2 refers to SnowMountain virus for both capsid and polymerase, II.2M in polymerase genotypes refers to Melksham virus which has a capsid that is very similar to SnowMountain virus but a polymerase that is very different from SnowMountain virus. Similar subdivisions have been made in other genotypes.
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Abbreviations used
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| I.3B | Birmingham 291 | | I.3DS | Desert Shield | | I.4M | Malta | | I.4QA | Queens Arms | | II.1W | Wortley | | II.2M | Melksham | | II.4-1 | II.4 lineage found in 2001 | | II.4-2 | II.4 lineage found in 2002 | | II.4B | Bristol | | II.4G | Grimsby | | II.4-4a | II.4 lineage found in 2004 | | II.4-4b | other II.4 lineage found in 2004 | | II.3R | Rotterdam |
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References
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Green, K. Y., A. Z. Kapikian, and R. M. Chanock. 2001. Human caliciviruses, p. 841-874. In D. M. Knipe, P. M. Howley, D. E. Griffin, et al. (ed.), Fields virology, 4th ed. Lippincott-Raven, Philadelphia, Pa Kageyama T, M. Shinohara, K. Uchida, S. Fukushi, F.B.Hoshino, S. Kojima, R. Takai, T. Oka, N. Takeda, and K. Katayama. Coexistence of multiple genotypes, including newly identified genotypes, in outbreaks of gastroenteritis due to Norovirus inJapan.J Clin Microbiol. 2004 Jul;42(7):2988-95. Vinjé J, R.A. Hamidjaja, and M.D. Sobsey. Development and application of a capsid VP1 (region D) based reverse transcription PCR assay for genotyping of genogroup I and II noroviruses, J Virol Methods. 2004 Mar 15;116(2):109-17.
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Sequencing regions
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Figure adapted from: Vinjé J, Hamidjaja RA, Sobsey MD. Development and application of a capsid VP1 (region D) based reverse transcription PCR assay for genotyping of genogroup I and II noroviruses, J Virol Methods. 2004 Mar 15;116(2):109-17. |
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