The sequence containing the first and second stem loops, nt 5923-5977, and that containing the third and fourth stem loops, nt 5992-6046, were nearly identical, suggesting that duplication of this sequence segment had occurred in the 3′ NCR of PeVYV, as has been observed for flaviviruses [ 5].
The duplication of large DNA segments has occurred repeatedly throughout evolution (see [21]).
Since the THOV genome is segmented, a portion of each of the 6 genome segments from each isolate was sequenced and compared with available sequence from other THOV isolates to determine if reassortment of virus genome segments had occurred.
The detection of essentially the same Seg-3 in isolates belonging to different serotypes (i.e with divergent Seg-2 sequences), indicates that genome segment reassortment has occurred during the evolution of these strains, as analysed by Nomikou et al (manuscript in preparation).
A positive value indicates that a better segmental stabilisation has occurred on the absolute vertical or horizontal axis than on the underlying segment, whereas a negative value indicates that better segmental stabilisation has occurred on the underlying segment.
Historical events that occurred before seismometers were operating in the region were the large to very large events of 1840, 1867, and 1875, but unlike the northwestern Sumatra segment, no megathrust earthquake has occurred on the Java segment of the Sunda Trench in the last 300 years.
In rare instances, however, mistaking a polymorphic variant for a fixed one can lead to misidentification of the exact segment where the substitution has occurred.
Samples from co-infected hosts will have RNA present from multiple viruses [31], and culture and PCR amplification may result in specific segment sub-regions being amplified from different viruses, giving the appearance of homologous intra-segment recombination where none has occurred.
It indicates that the fluorene unit has been completely quenched, and an efficient energy transfer from the PFO segments to the DBT units has occurred.
First, fragments can be produced from circularized templates where nick translation has occurred in a segment that does not contain a biotinylated adaptor (Supplementary Fig. S1) presumably the selection stages are sometimes ineffective.
