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Prevalence of errors at each nucleotide position within the entire viral protein-coding sequence (vCDS) from simplex and duplex reads. The nucleotide sequences were determined by nanopore sequencing using a mixture of three independent amplicons for HIV-1 NL4-3 or HIV-1 JRCSF propagated in cell cultures. The prevalence (%) of all mutations (ALL), substitutions (SUB), insertions (INS) and deletions (DEL) at each position in mixture from three is plotted. The horizontal dotted lines highlight the 15% prevalence threshold.

Journal: Scientific Reports

Article Title: Population-based nanopore sequencing of the HIV-1 pangenome to identify drug resistance mutations

doi: 10.1038/s41598-024-63054-3

Figure Lengend Snippet: Prevalence of errors at each nucleotide position within the entire viral protein-coding sequence (vCDS) from simplex and duplex reads. The nucleotide sequences were determined by nanopore sequencing using a mixture of three independent amplicons for HIV-1 NL4-3 or HIV-1 JRCSF propagated in cell cultures. The prevalence (%) of all mutations (ALL), substitutions (SUB), insertions (INS) and deletions (DEL) at each position in mixture from three is plotted. The horizontal dotted lines highlight the 15% prevalence threshold.

Article Snippet: In contrast, deep sequencing approaches based on Illumina or Ion Torrent technologies that have recently been developed for DR testing are able to detect less abundant mutations (~ 1%), although the clinical impact of detecting such low-abundance mutations remains controversial , .

Techniques: Sequencing, Nanopore Sequencing

Comparisons of nanopore sequencing DR data with archive DR test data obtained by Sanger sequencing. ( A ) Concordance rates (%) of the DR tests between Sanger and nanopore sequencing. The prevalence of detected DR to each drug is displayed with bar graphs. The “Concordant” and “Discordant” columns represent fully matched and inconsistent results between the two sequencing methods. LPV/r: lopinavir boosted with ritonavir, ATV: atazanavir, DRV: darunavir, RTV: ritonavir, ZDV: zidovudine, 3TC: lamivudine, FTC: emtricitabine, ABC: abacavir, TDF: tenofovir, TAF: tenofovir alafenamide, ISL: islatravir, EFV: efavirenz, NVP: nevirapine, ETR: etravirine, RPV: rilpivirine, DOR: doravirine, RAL: raltegravir, EVG: elvitegravir, DTG: dolutegravir, CAB: cabotegravir, BIC: bictegravir, LEN: lenacapavir. ( B ) Concordance rates of coreceptor tropism results based on V3 sequences between the two sequencing methods. The concordance rates of CXR4 (X4) tropism are displayed with a bar graph. Putative tropisms were determined by geno2pheno-C_NGS-Sanger ( https://coreceptor.geno2pheno.org/ ). ( C ) The concordance rates of nucleotide sequences in the pol PR-RT , pol IN, gag capsid, matrix and env c2c5 regions are plotted for each sample with medians and interquartile ranges.

Journal: Scientific Reports

Article Title: Population-based nanopore sequencing of the HIV-1 pangenome to identify drug resistance mutations

doi: 10.1038/s41598-024-63054-3

Figure Lengend Snippet: Comparisons of nanopore sequencing DR data with archive DR test data obtained by Sanger sequencing. ( A ) Concordance rates (%) of the DR tests between Sanger and nanopore sequencing. The prevalence of detected DR to each drug is displayed with bar graphs. The “Concordant” and “Discordant” columns represent fully matched and inconsistent results between the two sequencing methods. LPV/r: lopinavir boosted with ritonavir, ATV: atazanavir, DRV: darunavir, RTV: ritonavir, ZDV: zidovudine, 3TC: lamivudine, FTC: emtricitabine, ABC: abacavir, TDF: tenofovir, TAF: tenofovir alafenamide, ISL: islatravir, EFV: efavirenz, NVP: nevirapine, ETR: etravirine, RPV: rilpivirine, DOR: doravirine, RAL: raltegravir, EVG: elvitegravir, DTG: dolutegravir, CAB: cabotegravir, BIC: bictegravir, LEN: lenacapavir. ( B ) Concordance rates of coreceptor tropism results based on V3 sequences between the two sequencing methods. The concordance rates of CXR4 (X4) tropism are displayed with a bar graph. Putative tropisms were determined by geno2pheno-C_NGS-Sanger ( https://coreceptor.geno2pheno.org/ ). ( C ) The concordance rates of nucleotide sequences in the pol PR-RT , pol IN, gag capsid, matrix and env c2c5 regions are plotted for each sample with medians and interquartile ranges.

Article Snippet: In contrast, deep sequencing approaches based on Illumina or Ion Torrent technologies that have recently been developed for DR testing are able to detect less abundant mutations (~ 1%), although the clinical impact of detecting such low-abundance mutations remains controversial , .

Techniques: Nanopore Sequencing, Sequencing