Classification scheme for human astroviruses

Schermata 2016-01-15 alle 11.50.37

Genome of astroviruses: location of the diagnostic regions A to C

 

Lineage classification scheme

Canonical human astroviruses (HAstVs) are important enteric pathogens and can be classified genetically and antigenically into eight types. Sequence analysis of small diagnostic regions at either the 5’ or 3’ end of ORF2 (capsid precursor) is a good proxy for prediction of HAstV types and for distinction of intra-typic genetic lineages (sub-types). Upon sequence and phylogenetic analysis of the full-length ORF2 of nearli 95 HAstV strains selected from the databases and/or sequenced ex novo, a detailed classification of HAstV types 1 to 6 into lineages has been proposed and updated (Martella et al., 2014; Medici et al., 2015). The classification scheme was integrated in a novel nomenclature system suitable for designation of HAstV strains.

Table: Reference strains proposed for each lineage according to a lineage classification scheme based on the analysis of the full-length ORF2.

Reference strain Lineage Accession
GBR/1993/Oxford-1 1a L23513
CHN/2008/SH1 1b FJ375759
DEU/2004/Dresden 1d AY720892
GBR/1993/Oxford-AS8811 2a AB000289
GBR/1993/Oxford-H2 2b L13745
ITA/2002/PA65R 2c JX087963
ITA/2009/PR5142 2d JX087964
DEU/1999/Berlin 3a AF141381
CHN/2007/WH1859 3b DQ630763
ITA/2012/PR1365 3c KF668570
DEU/2004/Dresden 4a AY720891
BRA/1995/Goiania/GO/12 4b DQ070852
CHN/2005/Guangzhou 4c DQ344027
BRA/1994/Goiania-12 5a DQ028633
JPN/1993/O-1 5b AB000298
CHN/2010/DL030 5c JQ403108
CHN/2007/192-BJ07 6a GQ495608
JPN/2010/Katano 6b HM237363
GBR/1991/Oxford-7 7* AF248738
MEX/2000/Yuc-8 8* AF260508

*For types 7 and 8 no lineages were determined.

 

Nomenclature for ORF2 lineages

In the attempt to be consistent with HAstV literature, nomenclature for ORF2 lineages followed the schemes used in previous studies, i.e. HAstV type-xy, where x is a romanic number indicating the (sero)type assignment and y is a lower-case letter, indicating the genetic lineage (sub-type). Examples of this nomenclature system are herewith indicated

 

ITA/2009/PR5142/type-2d, a type-2 strain of lineage d

DEU/2004/Dresden/type-1a, a type-1 strain of lineage a

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