(12) examined two hypervariable regions
of the mtDNA in a larger cohort constituting individuals well distributed in different geographical regions of Anatolian peninsula.
The viruses were characterized through direct sequencing of hypervariable region
of the hexon gene and phylogenetic analysis with other viruses was carried out.
The extracted RNA was used to amplify the VP2 hypervariable region
of the segment A genomic RNA sequences.
The RDP Pyro aligner does not align the hypervariable regions
while the Mothur aligner does using the Silva alignment as reference sequences.
Sheehy et al., "Comparative rates of nucleotide sequence variation in the hypervariable region
of E1/E2 and the NS5b region of hepatitis C virus in patients with a spectrum of liver disease resulting from a common source of infection," Virology, vol.
Microbialites sequences (~250 bp length) covering the V5-V6 hypervariable region
of the 16S rDNA gene were generated using a parallel massive sequencing approach as described in Centeno et al.
The encoding genes for the envelope glycoproteins (E1 and E2), are the most heterogeneous, especially the 81 nucleotides encoding hypervariable region
1 (HVR1) of E2.
The two major RSV subgroups are A (RSV-A) and B (RSV-B), which are further characterised into several genotypes, based on antigenic and genetic variability of the second hypervariable region
of the G-protein.
PCR amplification of the 16S rDNA hypervariable region
V6 was done with a pool of five degenerated forward and four degenerated reverse primers expected to target the known groups of bacteria according to Huber et al.
The hypervariable region
of hexon gene of AAV-4 was amplified by PCR.