Ultradeep Pyrosequencing of Hepatitis C Virus Hypervariable Region 1 in Quasispecies Analysis

<table class="table-group" id="tab1"><tr><td><table class="table"><tr><td class="thead-hr" colspan="2"><hr/></td></tr><tr><td align="left">Number of sequenced nucleotides</td><td align="center">1.37 × 10<sup>8</sup></td></tr><tr><td align="left">Number of individual sequences that passed the quality control<svg height="13.75" id="M6" style="vertical-align:-0.0pt" version="1.1" viewbox="0 0 7.7375002 13.75" width="7.7375002" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.012,-0,0,-.012,.062,5.525)"><path d="M471 153q-22 -15 -61 -13q-25 31 -45.5 49.5t-56.5 41.5q4 -71 28 -134q-17 -33 -42 -46q-24 12 -42 46q24 63 28 134q-36 -23 -56.5 -41.5t-45.5 -49.5q-36 -2 -61 13q0 28 19 59q65 10 130 43q-65 33 -130 43q-19 31 -19 59q22 15 61 13q25 -31 45.5 -49.5t56.5 -41.5
q-4 71 -28 134q17 33 42 46q24 -12 42 -46q-24 -63 -28 -134q36 23 56.5 41.5t45.5 49.5q36 2 61 -13q0 -28 -19 -59q-65 -10 -130 -43q65 -33 130 -43q19 -31 19 -59z" id="x2217"></path></g>
</svg></td><td align="center">76 332</td></tr><tr><td align="left">Number of individual sequences aligned to reference genome</td><td align="center">73 236</td></tr><tr><td align="left">Mean coverage per sequence</td><td align="center">4.6</td></tr><tr><td align="left">Identified haplotypes</td><td align="center">15 917</td></tr><tr class="table-tr"><td colspan="2"><hr class="tbody-hr"/></td></tr></table></td></tr><tr class="table-fn"><td><svg height="13.75" id="M7" style="vertical-align:-0.0pt" version="1.1" viewbox="0 0 7.7375002 13.75" width="7.7375002" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.012,-0,0,-.012,.062,5.525)"><path d="M471 153q-22 -15 -61 -13q-25 31 -45.5 49.5t-56.5 41.5q4 -71 28 -134q-17 -33 -42 -46q-24 12 -42 46q24 63 28 134q-36 -23 -56.5 -41.5t-45.5 -49.5q-36 -2 -61 13q0 28 19 59q65 10 130 43q-65 33 -130 43q-19 31 -19 59q22 15 61 13q25 -31 45.5 -49.5t56.5 -41.5
q-4 71 -28 134q17 33 42 46q24 -12 42 -46q-24 -63 -28 -134q36 23 56.5 41.5t45.5 49.5q36 2 61 -13q0 -28 -19 -59q-65 -10 -130 -43q65 -33 130 -43q19 -31 19 -59z" id="x2217"></path></g>
</svg>No undetermined bases, 100% match with primer sequences.<br/></td></tr></table>

HVR1 HCV characteristics obtained by pyrosequencing using GS Junior System (454/Roche).

BioMed Research International

tab1

Table 1

Table 1: Ultradeep Pyrosequencing of Hepatitis C Virus Hypervariable Region 1 in Quasispecies Analysis 