I. Greiser-wilke et al., Application of a computer program for genetic typing of classical swine fever virus isolates from Germany, J VIROL MET, 75(2), 1998, pp. 141-150
The commercial software program HLA SequiTyper (Amersham Pharmacia Biotech)
, designed originally for human leukocyte antigen typing, was adapted for r
apid typing of classical swine fever (CSF) virus isolates. The program comp
ares new sequence data with those stored in a database file and calculates
the most probable assignment. For generating the CSF virus sequence databas
e, 150 bp of the 5' nontranslated genomic region (5'-NTR) from 88 German cl
assical swine fever virus isolates from outbreaks between 1984 and 1997 wer
e solid-phase sequenced directly after RT-PCR amplification. Sequence align
ments showed that they all belonged to the previously defined genetic group
2. Within this group, six different subgroups could be distinguished, and
were designated according to the geographic location where they are either
still endemic or where they appeared most commonly. The advantage of using
the HLA SequiTyper program is that it reads directly the sequence files as
generated by the ALF sequencer (Amersham Pharmacia Biotech), making any man
ipulations unnecessary. In addition, a constant quality control of the raw
sequence data can be achieved, as more than one sequence from the same isol
ate can be evaluated at once. Using this approach, new CSF isolates can be
typed within 2 days. (C) 1998 Elsevier Science B.V. All rights reserved.