<?xml version="1.0" standalone="yes"?>
<?xml-stylesheet type="text/xsl" href="http://hivdb.stanford.edu/dr/xsl/hivTransform.xsl"?>
<Stanford_Algorithm_Interpretation>
    <algorithmVersion>java-beta-0.9.3</algorithmVersion>
    <webServiceVersion>beta-0.9.4</webServiceVersion>

    <success>
        <sequence>CCTCAAATCACTCTTTGGCAACGACCCATCGTCACAATAAAGATAGGGGGGCAGCTAARGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGATATAAATTTGCCAGGAAGATGGACACCAAAAATKATAGTGGGAATTGGAGGTTTTACCAAAGTAAGACAGTATGATCAGATACCTGTAGAAATTTGTGGACATAAAGCTATAGGTACAGTRTTAGTAGGACCTACACCTGCCAACATAATTGGAAGAAATCTGTTGACYCAGATTGGTTGCACTTTAAATTTTCCCATTAGTCCTATTGACACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTGCAGAATTGGAASAGGACGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAGAACAGYGATAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGGAGGGTTAAAAAAGAACAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCARTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGACTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAGAATCTTAGAACCTTTTAGAAAACAGAATCCAGACATAGTTATCTGTCAATAYGTGGATGATTTGTATGTAGGATCTGACTTAGAAATAGAGMAGCATAGAACAAAAGTAGAGGAACTGAGACAACATTTGTGGAAGTGGGGNTTTTACACACCAGACAAMAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACA</sequence>
        <summary>
            <PR>
                <present>true</present>
                <consensus>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF</consensus>
                <alignedNASequence>CCTCAAATCACTCTTTGGCAACGACCCATCGTCACAATAAAGATAGGGGGGCAGCTAARGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGATATAAATTTGCCAGGAAGATGGACACCAAAAATKATAGTGGGAATTGGAGGTTTTACCAAAGTAAGACAGTATGATCAGATACCTGTAGAAATTTGTGGACATAAAGCTATAGGTACAGTRTTAGTAGGACCTACACCTGCCAACATAATTGGAAGAAATCTGTTGACYCAGATTGGTTGCACTTTAAATTTT</alignedNASequence>
                <alignedAASequence>PQITLWQRPIVTIKIGGQLREALLDTGADDTVLEDINLPGRWTPKIIVGIGGFTKVRQYDQIPVEICGHKAIGTVLVGPTPANIIGRNLLTQIGCTLNF</alignedAASequence>
                <firstAA>1</firstAA>
                <lastAA>99</lastAA>
                <subtype type="B" percentSimilarity="93.6"/>
            </PR>
            <RT>
                <present>true</present>
                <consensus>PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDKDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGFTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYAGIKVKQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKIATESIVIWGKTPKFKLPIQKETWEAWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTDRGRQKVVSLTDTTNQKTELQAIHLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVSQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKVL</consensus>
                <alignedNASequence>CCCATTAGTCCTATTGACACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTGCAGAATTGGAASAGGACGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAGAACAGYGATAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGGAGGGTTAAAAAAGAACAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCARTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGACTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAGAATCTTAGAACCTTTTAGAAAACAGAATCCAGACATAGTTATCTGTCAATAYGTGGATGATTTGTATGTAGGATCTGACTTAGAAATAGAGMAGCATAGAACAAAAGTAGAGGAACTGAGACAACATTTGTGGAAGTGGGGNTTTTACACACCAGACAAMAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACA</alignedNASequence>
                <alignedAASequence>PISPIDTVPVKLKPGMDGPKVKQWPLTEEKIKALVEICAELEQDGKISKIGPENPYNTPVFAIKKKNSDKWRKLVDFRELNKRTQDFWEVQLGIPHPGGLKKNKSVTVLDVGDAYFSIPLDEDFRKYTAFTIPSINNETPGTRYQYNVLPQGWKGSPAIFQSSMTRILEPFRKQNPDIVICQYVDDLYVGSDLEIEKHRTKVEELRQHLWKWGFYTPDNKHQKEPPFLWMGYELHPDKWT</alignedAASequence>
                <firstAA>1</firstAA>
                <lastAA>240</lastAA>
                <subtype type="B" percentSimilarity="95.3"/>
            </RT>
        </summary>

        <PR_mutations>
            <mutation classification="PI_MINOR">L10I</mutation>
            <mutation classification="PI_MINOR">K20KR</mutation>
            <mutation classification="OTHER">E35D</mutation>
            <mutation classification="PI_MINOR">M36I</mutation>
            <mutation classification="OTHER">K43T</mutation>
            <mutation classification="PI_MAJOR">M46IM</mutation>
            <mutation classification="PI_MAJOR">G48V</mutation>
            <mutation classification="PI_MAJOR">I54T</mutation>
            <mutation classification="PI_MINOR">L63P</mutation>
            <mutation classification="OTHER">I64V</mutation>
            <mutation classification="PI_MAJOR">V82A</mutation>
        </PR_mutations>

        <RT_mutations>
            <mutation classification="OTHER">E6D</mutation>
            <mutation classification="OTHER">T39A</mutation>
            <mutation classification="NRTI">M41L</mutation>
            <mutation classification="OTHER">K43EQ</mutation>
            <mutation classification="NRTI">E44D</mutation>
            <mutation classification="NRTI">D67N</mutation>
            <mutation classification="NRTI">T69D</mutation>
            <mutation classification="NNRTI">A98G</mutation>
            <mutation classification="NNRTI">K103N</mutation>
            <mutation classification="NRTI">V118IV</mutation>
            <mutation classification="OTHER">K122E</mutation>
            <mutation classification="OTHER">I142T</mutation>
            <mutation classification="OTHER">K166R</mutation>
            <mutation classification="NNRTI">Y181C</mutation>
            <mutation classification="NRTI">M184V</mutation>
            <mutation classification="OTHER">G196E</mutation>
            <mutation classification="OTHER">Q197KQ</mutation>
            <mutation classification="OTHER">I202V</mutation>
            <mutation classification="NRTI">L210W</mutation>
            <mutation classification="OTHER">R211K</mutation>
            <mutation classification="NRTI">T215Y</mutation>
            <mutation classification="NRTI">K219KN</mutation>
        </RT_mutations>

        <drugScores>
            <drug code="3TC" type="NRTI" score="87" levelStanford="5" levelSIR="R" >
                <partialScore mutation="K219KN" score="0"/>
                <partialScore mutation="E44D" score="5"/>
                <partialScore mutation="T215Y" score="4"/>
                <partialScore mutation="V118IV" score="5"/>
                <partialScore mutation="T69D" score="5"/>
                <partialScore mutation="M41L" score="4"/>
                <partialScore mutation="L210W" score="4"/>
                <partialScore mutation="Y181C" score="0"/>
                <partialScore mutation="D67N" score="0"/>
                <partialScore mutation="M184V" score="60"/>
            </drug>
            <drug code="ABC" type="NRTI" score="73" levelStanford="5" levelSIR="R" >
                <partialScore mutation="K219KN" score="0"/>
                <partialScore mutation="E44D" score="2"/>
                <partialScore mutation="T215Y" score="20"/>
                <partialScore mutation="V118IV" score="2"/>
                <partialScore mutation="T69D" score="5"/>
                <partialScore mutation="M41L" score="12"/>
                <partialScore mutation="L210W" score="12"/>
                <partialScore mutation="Y181C" score="0"/>
                <partialScore mutation="D67N" score="8"/>
                <partialScore mutation="M184V" score="12"/>
            </drug>
            <drug code="ATV" type="PI" score="55" levelStanford="4" levelSIR="I" >
                <partialScore mutation="V82A" score="15"/>
                <partialScore mutation="G48V" score="10"/>
                <partialScore mutation="L63P" score="1"/>
                <partialScore mutation="M36I" score="0"/>
                <partialScore mutation="I54T" score="10"/>
                <partialScore mutation="K20KR" score="2"/>
                <partialScore mutation="L10I" score="2"/>
                <partialScore mutation="M46IM" score="15"/>
            </drug>
            <drug code="AZT" type="NRTI" score="92" levelStanford="5" levelSIR="R" >
                <partialScore mutation="K219KN" score="15"/>
                <partialScore mutation="E44D" score="2"/>
                <partialScore mutation="T215Y" score="35"/>
                <partialScore mutation="V118IV" score="2"/>
                <partialScore mutation="T69D" score="5"/>
                <partialScore mutation="M41L" score="15"/>
                <partialScore mutation="L210W" score="15"/>
                <partialScore mutation="Y181C" score="-4"/>
                <partialScore mutation="D67N" score="15"/>
                <partialScore mutation="M184V" score="-8"/>
            </drug>
            <drug code="D4T" type="NRTI" score="91" levelStanford="5" levelSIR="R" >
                <partialScore mutation="K219KN" score="10"/>
                <partialScore mutation="E44D" score="2"/>
                <partialScore mutation="T215Y" score="30"/>
                <partialScore mutation="V118IV" score="2"/>
                <partialScore mutation="T69D" score="10"/>
                <partialScore mutation="M41L" score="15"/>
                <partialScore mutation="L210W" score="15"/>
                <partialScore mutation="Y181C" score="0"/>
                <partialScore mutation="D67N" score="12"/>
                <partialScore mutation="M184V" score="-5"/>
            </drug>
            <drug code="DDI" type="NRTI" score="81" levelStanford="5" levelSIR="R" >
                <partialScore mutation="K219KN" score="0"/>
                <partialScore mutation="E44D" score="2"/>
                <partialScore mutation="T215Y" score="20"/>
                <partialScore mutation="V118IV" score="2"/>
                <partialScore mutation="T69D" score="20"/>
                <partialScore mutation="M41L" score="12"/>
                <partialScore mutation="L210W" score="12"/>
                <partialScore mutation="Y181C" score="0"/>
                <partialScore mutation="D67N" score="8"/>
                <partialScore mutation="M184V" score="5"/>
            </drug>
            <drug code="DLV" type="NNRTI" score="125" levelStanford="5" levelSIR="R" >
                <partialScore mutation="K103N" score="60"/>
                <partialScore mutation="Y181C" score="60"/>
                <partialScore mutation="A98G" score="5"/>
            </drug>
            <drug code="EFV" type="NNRTI" score="85" levelStanford="5" levelSIR="R" >
                <partialScore mutation="K103N" score="60"/>
                <partialScore mutation="Y181C" score="20"/>
                <partialScore mutation="A98G" score="5"/>
            </drug>
            <drug code="FTC" type="NRTI" score="87" levelStanford="5" levelSIR="R" >
                <partialScore mutation="K219KN" score="0"/>
                <partialScore mutation="E44D" score="5"/>
                <partialScore mutation="T215Y" score="4"/>
                <partialScore mutation="V118IV" score="5"/>
                <partialScore mutation="T69D" score="5"/>
                <partialScore mutation="M41L" score="4"/>
                <partialScore mutation="L210W" score="4"/>
                <partialScore mutation="Y181C" score="0"/>
                <partialScore mutation="D67N" score="0"/>
                <partialScore mutation="M184V" score="60"/>
            </drug>
            <drug code="IDV" type="PI" score="72" levelStanford="5" levelSIR="R" >
                <partialScore mutation="V82A" score="35"/>
                <partialScore mutation="G48V" score="10"/>
                <partialScore mutation="L63P" score="1"/>
                <partialScore mutation="M36I" score="0"/>
                <partialScore mutation="I54T" score="10"/>
                <partialScore mutation="K20KR" score="2"/>
                <partialScore mutation="L10I" score="2"/>
                <partialScore mutation="M46IM" score="12"/>
            </drug>
            <drug code="LPV" type="PI" score="57" levelStanford="4" levelSIR="I" >
                <partialScore mutation="V82A" score="20"/>
                <partialScore mutation="G48V" score="10"/>
                <partialScore mutation="L63P" score="1"/>
                <partialScore mutation="M36I" score="0"/>
                <partialScore mutation="I54T" score="10"/>
                <partialScore mutation="K20KR" score="2"/>
                <partialScore mutation="L10I" score="2"/>
                <partialScore mutation="M46IM" score="12"/>
            </drug>
            <drug code="NFV" type="PI" score="105" levelStanford="5" levelSIR="R" >
                <partialScore mutation="V82A" score="35"/>
                <partialScore mutation="G48V" score="25"/>
                <partialScore mutation="L63P" score="1"/>
                <partialScore mutation="M36I" score="0"/>
                <partialScore mutation="I54T" score="15"/>
                <partialScore mutation="K20KR" score="2"/>
                <partialScore mutation="L10I" score="2"/>
                <partialScore mutation="M46IM" score="25"/>
            </drug>
            <drug code="NVP" type="NNRTI" score="140" levelStanford="5" levelSIR="R" >
                <partialScore mutation="K103N" score="70"/>
                <partialScore mutation="Y181C" score="60"/>
                <partialScore mutation="A98G" score="10"/>
            </drug>
            <drug code="SQV" type="PI" score="80" levelStanford="5" levelSIR="R" >
                <partialScore mutation="V82A" score="10"/>
                <partialScore mutation="G48V" score="50"/>
                <partialScore mutation="L63P" score="1"/>
                <partialScore mutation="M36I" score="0"/>
                <partialScore mutation="I54T" score="10"/>
                <partialScore mutation="K20KR" score="2"/>
                <partialScore mutation="L10I" score="2"/>
                <partialScore mutation="M46IM" score="5"/>
            </drug>
            <drug code="TDF" type="NRTI" score="46" levelStanford="4" levelSIR="I" >
                <partialScore mutation="K219KN" score="0"/>
                <partialScore mutation="E44D" score="2"/>
                <partialScore mutation="T215Y" score="20"/>
                <partialScore mutation="V118IV" score="2"/>
                <partialScore mutation="T69D" score="5"/>
                <partialScore mutation="M41L" score="12"/>
                <partialScore mutation="L210W" score="12"/>
                <partialScore mutation="Y181C" score="-4"/>
                <partialScore mutation="D67N" score="5"/>
                <partialScore mutation="M184V" score="-8"/>
            </drug>
            <drug code="TMC114" type="PI" score="23" levelStanford="3" levelSIR="I" >
                <partialScore mutation="V82A" score="6"/>
                <partialScore mutation="G48V" score="0"/>
                <partialScore mutation="L63P" score="1"/>
                <partialScore mutation="M36I" score="0"/>
                <partialScore mutation="I54T" score="6"/>
                <partialScore mutation="K20KR" score="2"/>
                <partialScore mutation="L10I" score="2"/>
                <partialScore mutation="M46IM" score="6"/>
            </drug>
            <drug code="TPV" type="PI" score="28" levelStanford="3" levelSIR="I" >
                <partialScore mutation="V82A" score="10"/>
                <partialScore mutation="G48V" score="0"/>
                <partialScore mutation="L63P" score="1"/>
                <partialScore mutation="M36I" score="0"/>
                <partialScore mutation="I54T" score="5"/>
                <partialScore mutation="K20KR" score="2"/>
                <partialScore mutation="L10I" score="2"/>
                <partialScore mutation="M46IM" score="8"/>
            </drug>
            <drug code="fAPV" type="PI" score="42" levelStanford="4" levelSIR="I" >
                <partialScore mutation="V82A" score="10"/>
                <partialScore mutation="G48V" score="5"/>
                <partialScore mutation="L63P" score="1"/>
                <partialScore mutation="M36I" score="0"/>
                <partialScore mutation="I54T" score="10"/>
                <partialScore mutation="K20KR" score="2"/>
                <partialScore mutation="L10I" score="2"/>
                <partialScore mutation="M46IM" score="12"/>
            </drug>
        </drugScores>

        <comments>
            <comment id="PR2">The following 3 of the 21 tipranavir RESIST study mutations were present: K20KR, M36I, K43T (Baxter J et al J Virology 2006). </comment>
            <comment id="PR_POS10">L10I/V/F/R are associated with resistance to each of the PIs when present with other mutations. L10F may be more significant because it rarely occurs in the absence of PI therapy. </comment>
            <comment id="PR_POS20">K20R/M/I/T are weakly associated with resistance to each of the PIs when present with other mutations. Many variants at this position occur commonly in non-subtype B viruses. </comment>
            <comment id="PR_POS36">M36I/V are weakly associated with PI resistance when present with other mutations. M36I occurs commonly in certain non-subtype B viruses. M36L/T are rare variants of uncertain significance. </comment>
            <comment id="PR_POS46">M46I/L decreases susceptibility to IDV, RTV, NFV, APV, LPV, ATV, TPV, and possibly SQV when present with other mutations. M46V is a rare mutation at this position of uncertain significance. The effect of mutations at this position on TMC114 is not known. </comment>
            <comment id="PR_POS48">G48V causes resistance to SQV and low-level cross-resistance to NFV, IDV, and RTV. It also appears to contribute to resistance to LPV and ATV. G48M occurs in heavily treated persons but its effect on phenotype and clinical outcome has not been reported. </comment>
            <comment id="PR_POS54">I54V contributes resistance to each of the PIs when present with other mutations. I54M/L occur in patients receiving APV and TMC114 and reduces susceptibility to these drugs and LPV. I54A is a two-base pair mutation that is common in heavily treated persons. I54T/S are also selected by PIs. Like I54A, their precise effect on drug susceptibility is not known. </comment>
            <comment id="PR_POS63">L63P is a common polymorphism that becomes even more common in persons receiving PIs. </comment>
            <comment id="PR_POS82">V82A/T/F/S reduce susceptibility to IDV, RTV, and LPV. When present with other mutations, V82A/T/F/S also reduce susceptibility to APV, NFV, SQV, ATV, and TPV. The effect of mutations at this position on TMC114 is likely to be low but is not known with certainty. V82L emerges during TPV therapy and reduces susceptibility to this PI. V82I is a polymorphism that is common in some non-B subtypes; it has little if any effect on PI susceptibility. V82M is particularly common in subtype G isolates and also reduces IDV susceptibility. </comment>
            <comment id="RT_POS41">M41L usually occurs with T215Y. Together these mutations confer intermediate-to-high level resistance to AZT and d4T and a lower level of resistance to ddI, ABC, and TDF. </comment>
            <comment id="RT_POS44">E44A/D occur in patients receiving multiple NRTIs. E44D causes low-level resistance to 3TC and probably to each of the other NRTIs when present with V118I or one or more TAMs. </comment>
            <comment id="RT_POS67NEG">D67N contributes some degree of resistance to each of the NRTIs except 3TC and FTC. It usually occurs with mutations at positions 70 or 215. D67E/G occur in heavily treated patients and probably have a similar effect as D67N. </comment>
            <comment id="RT_POS69DNASIG">T69D contributes resistance to ddI, d4T, and ABC when present with multiple TAMs. T69N/S/A/I are additional NRTI-related mutations but their effect on NRTI susceptibility is not known. T69G occurs in isolates with a deletion at position 67. </comment>
            <comment id="RT_POS98">A98G causes low-level (about 2-fold) decreased NVP susceptibility. It occurs in about 1% of NNRTI-naive persons and may not compromise drug activity. A98S is a common polymorphism that does not reduce NNRTI susceptibility. </comment>
            <comment id="RT_POS103">K103N causes high-level resistance to NVP (50-fold), DLV (50-fold), and EFV (25-fold). K103S causes intermediate resistance to DLV and EFV and high-level resistance to NVP. K103R occurs in about 1%-2% of untreated persons and by itself has no effect on NNRTI susceptibility. The combination of K103R + V179D, however, reduces susceptibility to each of the NNRTIs about 15-fold. K103Q/T are rare mutations at this position. Preliminary data suggest that K103Q causes minimal resistance whereas K103T causes intermediate resistance to each NNRTI. </comment>
            <comment id="RT_POS118">V118I occurs in ~2% of untreated persons and with increased frequency in persons receiving multiple NRTIs. It causes low-level resistance to 3TC and possibly to other NRTIs when present with E44A/D and/or one or more TAMs. </comment>
            <comment id="RT_POS181">Y181C/I/V cause high-level resistance to NVP and DLV and low-level resistance to EFV. Y181C increases susceptibility to AZT and TDF. </comment>
            <comment id="RT_POS184">M184V/I cause high-level resistance to 3TC and FTC. It causes low-level in vitro resistance to ddI and ABC. However, it has not been shown to limit the effectiveness of ddI and it has been shown to limit the effectiveness of ABC only when it occurs in combination with multiple TAMs. M184V partially reverses T215Y-mediated resistance to AZT, TDF, and d4T. </comment>
            <comment id="RT_POS210">L210W contributes resistance to each of the NRTIs except 3TC and probably FTC. It usually occurs with the mutations M41L and T215Y. L210F/S occur rarely and are of unknown significance. </comment>
            <comment id="RT_POS215">T215Y/F cause AZT and D4T resistance and limits the effectiveness of ABC, ddI, and TDF particularly when it occurs in combination with M41L and L210W. 215S/C/D/E/I/V represent transitions between wild type and the mutations Y and F. Most of these have do not decrease drug susceptibility. But their presence suggests that a resistant virus that harbors T215Y or F may have been transmitted. </comment>
            <comment id="RT_POS219">K219Q/E increase AZT and probably d4T resistance when present with K70R or T215Y/F but may not have any effect on the remaining NRTIs. K219N/R occur commonly in heavily NRTI-treated patients. </comment>
            <comment id="RT3">Y181C partially reverse(s) AZT resistance caused by other mutations. </comment>
            <comment id="RT4">M184V partially reverses AZT, d4T, and TDF resistance caused by other TAMs. </comment>
        </comments>
    </success>

    <success>
        <sequence>CCTCAGATCACTCTTTGGCAACGACCCATCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAGGAAATGGATTTGCCAGGAAGATGGAGACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAACAGATACCCATAGAAATCTGTGGACATAAAGTTATAACTACAGTATTAATAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGATGACTCAGCTTGGNTGCACCTTAAATTTTCCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGTCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAATTGGAACAGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAGAAAAACAGTAATAGATGGAGAAAAWTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCTGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATACCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTTCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGAGATGGTTATCTATCAGTACATGGATGATTTGTACGTAGGATCTGAYTTAGAAATAGAGCAGCATAGAACAAAAATAGATGAACTGAGAAAACATCTGTTGGCGTGGGGGTTTTTCACACCAGACCAAAAACATCAGAAAGAGCCGCCATTCCATTGGATGGGGTATGAACTMCATCCTGATAAATGGMCAGTACAGCCTATAGTGCTGCCAGAA</sequence>
        <summary>
            <PR>
                <present>true</present>
                <consensus>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF</consensus>
                <alignedNASequence>CCTCAGATCACTCTTTGGCAACGACCCATCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAGGAAATGGATTTGCCAGGAAGATGGAGACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAACAGATACCCATAGAAATCTGTGGACATAAAGTTATAACTACAGTATTAATAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGATGACTCAGCTTGGNTGCACCTTAAATTTT</alignedNASequence>
                <alignedAASequence>PQITLWQRPIVTIKIGGQLKEALLDTGADDTVLEEMDLPGRWRPKMIGGIGGFIKVRQYEQIPIEICGHKVITTVLIGPTPVNIIGRNLMTQLGCTLNF</alignedAASequence>
                <firstAA>1</firstAA>
                <lastAA>99</lastAA>
                <subtype type="B" percentSimilarity="94.6"/>
            </PR>
            <RT>
                <present>true</present>
                <consensus>PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDKDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGFTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYAGIKVKQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKIATESIVIWGKTPKFKLPIQKETWEAWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTDRGRQKVVSLTDTTNQKTELQAIHLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVSQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKVL</consensus>
                <alignedNASequence>CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGTCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAATTGGAACAGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAGAAAAACAGTAATAGATGGAGAAAAWTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCTGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATACCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTTCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGAGATGGTTATCTATCAGTACATGGATGATTTGTACGTAGGATCTGAYTTAGAAATAGAGCAGCATAGAACAAAAATAGATGAACTGAGAAAACATCTGTTGGCGTGGGGGTTTTTCACACCAGACCAAAAACATCAGAAAGAGCCGCCATTCCATTGGATGGGGTATGAACTMCATCCTGATAAATGGMCAGTACAGCCTATAGTGCTGCCAGAA</alignedNASequence>
                <alignedAASequence>PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTELEQEGKISKIGPENPYNTPVFAIKKKNSNRWRKIVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPEMVIYQYMDDLYVGSDLEIEQHRTKIDELRKHLLAWGFFTPDQKHQKEPPFHWMGYELHPDKWPVQPIVLPE</alignedAASequence>
                <firstAA>1</firstAA>
                <lastAA>248</lastAA>
                <subtype type="B" percentSimilarity="95.0"/>
            </RT>
        </summary>

        <PR_mutations>
            <mutation classification="PI_MINOR">L10I</mutation>
            <mutation classification="OTHER">N37D</mutation>
            <mutation classification="OTHER">K43R</mutation>
            <mutation classification="OTHER">D60E</mutation>
            <mutation classification="PI_MINOR">L63P</mutation>
            <mutation classification="PI_MINOR">A71V</mutation>
            <mutation classification="PI_MAJOR">G73T</mutation>
            <mutation classification="PI_MINOR">V77I</mutation>
            <mutation classification="PI_MAJOR">L90M</mutation>
            <mutation classification="PI_MINOR">I93L</mutation>
        </PR_mutations>

        <RT_mutations>
            <mutation classification="NRTI">M41L</mutation>
            <mutation classification="OTHER">K43Q</mutation>
            <mutation classification="NRTI">D67N</mutation>
            <mutation classification="NRTI">T69N</mutation>
            <mutation classification="NRTI">K70R</mutation>
            <mutation classification="NRTI">L74IL</mutation>
            <mutation classification="OTHER">K122E</mutation>
            <mutation classification="OTHER">D177E</mutation>
            <mutation classification="OTHER">I178M</mutation>
            <mutation classification="OTHER">G196E</mutation>
            <mutation classification="OTHER">E203D</mutation>
            <mutation classification="OTHER">Q207K</mutation>
            <mutation classification="OTHER">R211A</mutation>
            <mutation classification="NRTI">T215F</mutation>
            <mutation classification="NRTI">K219Q</mutation>
            <mutation classification="OTHER">L228H</mutation>
            <mutation classification="OTHER">T240PT</mutation>
        </RT_mutations>

        <SequenceQA>
            <PR>
                <atypical>60</atypical>
            </PR>
            <RT>
                <atypical>240</atypical>
            </RT>
        </SequenceQA>

        <drugScores>
            <drug code="3TC" type="NRTI" score="13" levelStanford="2" levelSIR="S" >
                <partialScore mutation="L74IL" score="0"/>
                <partialScore mutation="D67N" score="0"/>
                <partialScore mutation="M41L" score="4"/>
                <partialScore mutation="T69N" score="5"/>
                <partialScore mutation="K219Q" score="0"/>
                <partialScore mutation="T215F" score="4"/>
                <partialScore mutation="K70R" score="0"/>
            </drug>
            <drug code="ABC" type="NRTI" score="65" levelStanford="5" levelSIR="R" >
                <partialScore mutation="L74IL" score="20"/>
                <partialScore mutation="D67N" score="8"/>
                <partialScore mutation="M41L" score="12"/>
                <partialScore mutation="T69N" score="5"/>
                <partialScore mutation="K219Q" score="0"/>
                <partialScore mutation="T215F" score="20"/>
                <partialScore mutation="K70R" score="0"/>
            </drug>
            <drug code="ATV" type="PI" score="31" levelStanford="4" levelSIR="I" >
                <partialScore mutation="L63P" score="1"/>
                <partialScore mutation="I93L" score="0"/>
                <partialScore mutation="G73T" score="5"/>
                <partialScore mutation="A71V" score="3"/>
                <partialScore mutation="V77I" score="0"/>
                <partialScore mutation="L10I" score="2"/>
                <partialScore mutation="L90M" score="20"/>
            </drug>
            <drug code="AZT" type="NRTI" score="103" levelStanford="5" levelSIR="R" >
                <partialScore mutation="L74IL" score="0"/>
                <partialScore mutation="D67N" score="15"/>
                <partialScore mutation="M41L" score="15"/>
                <partialScore mutation="T69N" score="5"/>
                <partialScore mutation="K219Q" score="15"/>
                <partialScore mutation="T215F" score="35"/>
                <partialScore mutation="K70R" score="18"/>
            </drug>
            <drug code="D4T" type="NRTI" score="87" levelStanford="5" levelSIR="R" >
                <partialScore mutation="L74IL" score="0"/>
                <partialScore mutation="D67N" score="12"/>
                <partialScore mutation="M41L" score="15"/>
                <partialScore mutation="T69N" score="10"/>
                <partialScore mutation="K219Q" score="10"/>
                <partialScore mutation="T215F" score="30"/>
                <partialScore mutation="K70R" score="10"/>
            </drug>
            <drug code="DDI" type="NRTI" score="80" levelStanford="5" levelSIR="R" >
                <partialScore mutation="L74IL" score="30"/>
                <partialScore mutation="D67N" score="8"/>
                <partialScore mutation="M41L" score="12"/>
                <partialScore mutation="T69N" score="10"/>
                <partialScore mutation="K219Q" score="0"/>
                <partialScore mutation="T215F" score="20"/>
                <partialScore mutation="K70R" score="0"/>
            </drug>
            <drug code="DLV" type="NNRTI" score="0" levelStanford="1" levelSIR="S" >
            </drug>
            <drug code="EFV" type="NNRTI" score="0" levelStanford="1" levelSIR="S" >
            </drug>
            <drug code="FTC" type="NRTI" score="13" levelStanford="2" levelSIR="S" >
                <partialScore mutation="L74IL" score="0"/>
                <partialScore mutation="D67N" score="0"/>
                <partialScore mutation="M41L" score="4"/>
                <partialScore mutation="T69N" score="5"/>
                <partialScore mutation="K219Q" score="0"/>
                <partialScore mutation="T215F" score="4"/>
                <partialScore mutation="K70R" score="0"/>
            </drug>
            <drug code="IDV" type="PI" score="31" levelStanford="4" levelSIR="I" >
                <partialScore mutation="L63P" score="1"/>
                <partialScore mutation="I93L" score="0"/>
                <partialScore mutation="G73T" score="5"/>
                <partialScore mutation="A71V" score="3"/>
                <partialScore mutation="V77I" score="0"/>
                <partialScore mutation="L10I" score="2"/>
                <partialScore mutation="L90M" score="20"/>
            </drug>
            <drug code="LPV" type="PI" score="18" levelStanford="3" levelSIR="I" >
                <partialScore mutation="L63P" score="1"/>
                <partialScore mutation="I93L" score="0"/>
                <partialScore mutation="G73T" score="2"/>
                <partialScore mutation="A71V" score="3"/>
                <partialScore mutation="V77I" score="0"/>
                <partialScore mutation="L10I" score="2"/>
                <partialScore mutation="L90M" score="10"/>
            </drug>
            <drug code="NFV" type="PI" score="63" levelStanford="5" levelSIR="R" >
                <partialScore mutation="L63P" score="1"/>
                <partialScore mutation="I93L" score="0"/>
                <partialScore mutation="G73T" score="5"/>
                <partialScore mutation="A71V" score="3"/>
                <partialScore mutation="V77I" score="2"/>
                <partialScore mutation="L10I" score="2"/>
                <partialScore mutation="L90M" score="50"/>
            </drug>
            <drug code="NVP" type="NNRTI" score="0" levelStanford="1" levelSIR="S" >
            </drug>
            <drug code="SQV" type="PI" score="51" levelStanford="4" levelSIR="I" >
                <partialScore mutation="L63P" score="1"/>
                <partialScore mutation="I93L" score="0"/>
                <partialScore mutation="G73T" score="10"/>
                <partialScore mutation="A71V" score="3"/>
                <partialScore mutation="V77I" score="0"/>
                <partialScore mutation="L10I" score="2"/>
                <partialScore mutation="L90M" score="35"/>
            </drug>
            <drug code="TDF" type="NRTI" score="40" levelStanford="4" levelSIR="I" >
                <partialScore mutation="L74IL" score="0"/>
                <partialScore mutation="D67N" score="5"/>
                <partialScore mutation="M41L" score="12"/>
                <partialScore mutation="T69N" score="5"/>
                <partialScore mutation="K219Q" score="0"/>
                <partialScore mutation="T215F" score="10"/>
                <partialScore mutation="K70R" score="8"/>
            </drug>
            <drug code="TMC114" type="PI" score="16" levelStanford="3" levelSIR="I" >
                <partialScore mutation="L63P" score="1"/>
                <partialScore mutation="I93L" score="0"/>
                <partialScore mutation="G73T" score="5"/>
                <partialScore mutation="A71V" score="2"/>
                <partialScore mutation="V77I" score="0"/>
                <partialScore mutation="L10I" score="2"/>
                <partialScore mutation="L90M" score="6"/>
            </drug>
            <drug code="TPV" type="PI" score="13" levelStanford="2" levelSIR="S" >
                <partialScore mutation="L63P" score="1"/>
                <partialScore mutation="I93L" score="0"/>
                <partialScore mutation="G73T" score="2"/>
                <partialScore mutation="A71V" score="3"/>
                <partialScore mutation="V77I" score="0"/>
                <partialScore mutation="L10I" score="2"/>
                <partialScore mutation="L90M" score="5"/>
            </drug>
            <drug code="fAPV" type="PI" score="23" levelStanford="3" levelSIR="I" >
                <partialScore mutation="L63P" score="1"/>
                <partialScore mutation="I93L" score="0"/>
                <partialScore mutation="G73T" score="2"/>
                <partialScore mutation="A71V" score="3"/>
                <partialScore mutation="V77I" score="0"/>
                <partialScore mutation="L10I" score="2"/>
                <partialScore mutation="L90M" score="15"/>
            </drug>
        </drugScores>

        <comments>
            <comment id="PR_POS10">L10I/V/F/R are associated with resistance to each of the PIs when present with other mutations. L10F may be more significant because it rarely occurs in the absence of PI therapy. </comment>
            <comment id="PR_POS63">L63P is a common polymorphism that becomes even more common in persons receiving PIs. </comment>
            <comment id="PR_POS71">A71T/V are polymorphisms that occur in 1-2% of untreated persons but which become much more frequent in persons receiving PIs. A71I is an uncommon mutation that appears to occur only with PI therapy; its significance is not known. </comment>
            <comment id="PR_POS73">G73S/T/C/A are associated with decreased susceptibility to most, if not all, PIs </comment>
            <comment id="PR_POS77">V77I is a common polymorphism that is associated with NFV therapy. </comment>
            <comment id="PR_POS90">L90M causes resistance to SQV and NFV. When present with other mutations it also compromises the activity of IDV, RTV, APV, LPV, ATV, and TPV. Its effect on TMC114 is not known. </comment>
            <comment id="PR_POS93">I93L is a common polymorphism that becomes even more common in persons receiving PIs. I93M is a rare PI-associated mutation; its effect on susceptibility is not known. </comment>
            <comment id="RT_POS41">M41L usually occurs with T215Y. Together these mutations confer intermediate-to-high level resistance to AZT and d4T and a lower level of resistance to ddI, ABC, and TDF. </comment>
            <comment id="RT_POS67NEG">D67N contributes some degree of resistance to each of the NRTIs except 3TC and FTC. It usually occurs with mutations at positions 70 or 215. D67E/G occur in heavily treated patients and probably have a similar effect as D67N. </comment>
            <comment id="RT_POS69DNASIG">T69D contributes resistance to ddI, d4T, and ABC when present with multiple TAMs. T69N/S/A/I are additional NRTI-related mutations but their effect on NRTI susceptibility is not known. T69G occurs in isolates with a deletion at position 67. </comment>
            <comment id="RT_POS70">K70R causes low-level AZT and probably d4T resistance but appears to have little effect on the other NRTIs. K70E reduces TDF susceptibility. K70G/N are rare variants of unknown significance </comment>
            <comment id="RT_POS74">L74V causes intermediate resistance to ddI and low-level resistance to ABC. L74V increases AZT and TDF susceptibility, but in 2 studies was associated with reduced response to TDF. L74I occurs in heavily treated persons but fewer phenotypic and clinical data are available for this mutation. </comment>
            <comment id="RT_POS215">T215Y/F cause AZT and D4T resistance and limits the effectiveness of ABC, ddI, and TDF particularly when it occurs in combination with M41L and L210W. 215S/C/D/E/I/V represent transitions between wild type and the mutations Y and F. Most of these have do not decrease drug susceptibility. But their presence suggests that a resistant virus that harbors T215Y or F may have been transmitted. </comment>
            <comment id="RT_POS219">K219Q/E increase AZT and probably d4T resistance when present with K70R or T215Y/F but may not have any effect on the remaining NRTIs. K219N/R occur commonly in heavily NRTI-treated patients. </comment>
            <comment id="RT3">Y181C partially reverse(s) AZT resistance caused by other mutations. </comment>
        </comments>
    </success>

    <success>
        <sequence>CCTCAGATCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAATTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATTTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCTATCAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAGGACTTCTGGGAAGTTCAATTAGGGATACCACATCCCGCAGGGTTAAAAAAGAACAAATCAGTAACAGTACTAGATGTGGGTGATGCATATTTCTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTCACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTGCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGATAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACGTGGATGATTTGTATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAACAAAAATAGAGGAACTGAGACAGCATCTGTTGAGGTGGGGATTCACCACACCTGACAAAAAACATCAGAAAGAGCCTCCATTCCTGTGGMTGGGTTATGAACTCCATCCWGATAAATGGACAGTGCAGCCTATAGAGCTGCCAGAAAAAGACAGTTGGACTGTCAAYGACATACAGAAGTTAGTGGGAAAATTGAATTGGGCAAGTCAGATTTACGCAGGGATTAAAGTAAGGCAMTTATGTAAACTCCTT</sequence>
        <summary>
            <PR>
                <present>true</present>
                <consensus>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF</consensus>
                <alignedNASequence>CCTCAGATCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAATTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATTTGTTGACTCAGATTGGTTGCACTTTAAATTTT</alignedNASequence>
                <alignedAASequence>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF</alignedAASequence>
                <firstAA>1</firstAA>
                <lastAA>99</lastAA>
                <subtype type="B" percentSimilarity="99.0"/>
            </PR>
            <RT>
                <present>true</present>
                <consensus>PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDKDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGFTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYAGIKVKQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKIATESIVIWGKTPKFKLPIQKETWEAWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTDRGRQKVVSLTDTTNQKTELQAIHLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVSQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKVL</consensus>
                <alignedNASequence>CCTATCAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAGGACTTCTGGGAAGTTCAATTAGGGATACCACATCCCGCAGGGTTAAAAAAGAACAAATCAGTAACAGTACTAGATGTGGGTGATGCATATTTCTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTCACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTGCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGATAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACGTGGATGATTTGTATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAACAAAAATAGAGGAACTGAGACAGCATCTGTTGAGGTGGGGATTCACCACACCTGACAAAAAACATCAGAAAGAGCCTCCATTCCTGTGGMTGGGTTATGAACTCCATCCWGATAAATGGACAGTGCAGCCTATAGAGCTGCCAGAAAAAGACAGTTGGACTGTCAAYGACATACAGAAGTTAGTGGGAAAATTGAATTGGGCAAGTCAGATTTACGCAGGGATTAAAGTAAGGCAMTTATGTAAACTCCTT</alignedNASequence>
                <alignedAASequence>PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMIKILEPFRKQNPDIVIYQYVDDLYVGSDLEIGQHRTKIEELRQHLLRWGFTTPDKKHQKEPPFLWLGYELHPDKWTVQPIELPEKDSWTVNDIQKLVGKLNWASQIYAGIKVRHLCKLL</alignedAASequence>
                <firstAA>1</firstAA>
                <lastAA>283</lastAA>
                <subtype type="B" percentSimilarity="96.2"/>
            </RT>
        </summary>

        <PR_mutations>
        </PR_mutations>

        <RT_mutations>
            <mutation classification="NNRTI">K103N</mutation>
            <mutation classification="OTHER">K122E</mutation>
            <mutation classification="OTHER">T165I</mutation>
            <mutation classification="NRTI">M184V</mutation>
            <mutation classification="NNRTI">M230LM</mutation>
            <mutation classification="OTHER">V245E</mutation>
            <mutation classification="OTHER">K277R</mutation>
            <mutation classification="OTHER">Q278HQ</mutation>
        </RT_mutations>

        <SequenceQA>
            <RT>
                <atypical>245</atypical>
            </RT>
        </SequenceQA>

        <drugScores>
            <drug code="3TC" type="NRTI" score="60" levelStanford="5" levelSIR="R" >
                <partialScore mutation="M184V" score="60"/>
            </drug>
            <drug code="ABC" type="NRTI" score="12" levelStanford="2" levelSIR="S" >
                <partialScore mutation="M184V" score="12"/>
            </drug>
            <drug code="ATV" type="PI" score="0" levelStanford="1" levelSIR="S" >
            </drug>
            <drug code="AZT" type="NRTI" score="-8" levelStanford="1" levelSIR="S" >
                <partialScore mutation="M184V" score="-8"/>
            </drug>
            <drug code="D4T" type="NRTI" score="-5" levelStanford="1" levelSIR="S" >
                <partialScore mutation="M184V" score="-5"/>
            </drug>
            <drug code="DDI" type="NRTI" score="5" levelStanford="1" levelSIR="S" >
                <partialScore mutation="M184V" score="5"/>
            </drug>
            <drug code="DLV" type="NNRTI" score="120" levelStanford="5" levelSIR="R" >
                <partialScore mutation="M230LM" score="60"/>
                <partialScore mutation="K103N" score="60"/>
            </drug>
            <drug code="EFV" type="NNRTI" score="100" levelStanford="5" levelSIR="R" >
                <partialScore mutation="M230LM" score="40"/>
                <partialScore mutation="K103N" score="60"/>
            </drug>
            <drug code="FTC" type="NRTI" score="60" levelStanford="5" levelSIR="R" >
                <partialScore mutation="M184V" score="60"/>
            </drug>
            <drug code="IDV" type="PI" score="0" levelStanford="1" levelSIR="S" >
            </drug>
            <drug code="LPV" type="PI" score="0" levelStanford="1" levelSIR="S" >
            </drug>
            <drug code="NFV" type="PI" score="0" levelStanford="1" levelSIR="S" >
            </drug>
            <drug code="NVP" type="NNRTI" score="130" levelStanford="5" levelSIR="R" >
                <partialScore mutation="M230LM" score="60"/>
                <partialScore mutation="K103N" score="70"/>
            </drug>
            <drug code="SQV" type="PI" score="0" levelStanford="1" levelSIR="S" >
            </drug>
            <drug code="TDF" type="NRTI" score="-8" levelStanford="1" levelSIR="S" >
                <partialScore mutation="M184V" score="-8"/>
            </drug>
            <drug code="TMC114" type="PI" score="0" levelStanford="1" levelSIR="S" >
            </drug>
            <drug code="TPV" type="PI" score="0" levelStanford="1" levelSIR="S" >
            </drug>
            <drug code="fAPV" type="PI" score="0" levelStanford="1" levelSIR="S" >
            </drug>
        </drugScores>

        <comments>
            <comment id="RT_POS103">K103N causes high-level resistance to NVP (50-fold), DLV (50-fold), and EFV (25-fold). K103S causes intermediate resistance to DLV and EFV and high-level resistance to NVP. K103R occurs in about 1%-2% of untreated persons and by itself has no effect on NNRTI susceptibility. The combination of K103R + V179D, however, reduces susceptibility to each of the NNRTIs about 15-fold. K103Q/T are rare mutations at this position. Preliminary data suggest that K103Q causes minimal resistance whereas K103T causes intermediate resistance to each NNRTI. </comment>
            <comment id="RT_POS184">M184V/I cause high-level resistance to 3TC and FTC. It causes low-level in vitro resistance to ddI and ABC. However, it has not been shown to limit the effectiveness of ddI and it has been shown to limit the effectiveness of ABC only when it occurs in combination with multiple TAMs. M184V partially reverses T215Y-mediated resistance to AZT, TDF, and d4T. </comment>
            <comment id="RT_POS230">M230L causes intermediate-to-high-level resistance to each of the available NNRTI. </comment>
        </comments>
    </success>
</Stanford_Algorithm_Interpretation>