第9回千葉県胆膵研究会 11.

Additional file 13: Table S5. Statistical analysis of all experiments separated for transmission pairs with high and low diversity transmitters and for transmission pairs where recipient is closer to ancestral genotype, respectively

Additional file 1: of Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples

Table S1. Characteristics of viruses used in the virus-spike experiments. Table S2. Analysis of variance Figure S1 (extraction experiments). Table S3. Analysis of Variance Fig. 1 (filtration experiments). Table S4. Analysis of variance Fig. 2 (nuclease digestion experiments). Table S5. Analysis of variance Fig. 2 (nuclease digestion experiments). Table S6. Analysis of variance Fig. 3 (separate workflow experiments). Table S7. Analysis of variance Figure S3 (input experiments). Table S8. Analysis of variance Fig. 6 (other sample types). Table S9. Raw sequencing data files (available at Zenodo 10.5281/zenodo.814807 ). Figure S1. Extraction with the NucliSENS EasyMAG resulted in the highest virus concentrations. Figure S2. Reads assigned to spiked virus were uniformly distributed along the reference genomes. Figure S3. Increasing the PCR input volume had no effect on viral enrichment. Figure S4. After extraction, viral amplicons were quantified in the eluate and the ratio of spiked viruses was perfectly maintained. (PDF 540 kb

MOESM6 of Tracing HIV-1 transmission: envelope traits of HIV-1 transmitter and recipient pairs

Additional file 6: Table S2. Distances of transmitter and recipient env sequences to the most recent common ancestor (MRCA)

MOESM7 of Tracing HIV-1 transmission: envelope traits of HIV-1 transmitter and recipient pairs

Additional file 7: Figure S5. Maximal neutralization capacities of transmitter plasma samples. Maximal percent neutralization (MPN) of transmitter (red) and recipient (blue) Env-pseudoviruses by transmitter plasma from the closest time point to the EDT at the highest plasma concentration tested of 1:40. Line indicates 50 % neutralization and difference between median transmitter and recipient value was determined with a Wilcoxon matched-pairs signed rank test. No plasma sample to estimate neutralization capacity was available from transmitters T1 and T2; therefore they were excluded from this part of the analysis

MOESM8 of Tracing HIV-1 transmission: envelope traits of HIV-1 transmitter and recipient pairs

Additional file 8: Table S3. 50 % neutralization titers of plasma samples from transmitters and recipients against transmitter and recipient Env-pseudoviruses

MOESM10 of Tracing HIV-1 transmission: envelope traits of HIV-1 transmitter and recipient pairs

Additional file 10: Figure S6. Transmitter and recipient viruses do not exhibit different replication fitness. Replicative capacity on PBMCs was measured over a 14 day period and different measures of replication fitness were compared between transmitter and recipient virus isolates. (a) Median area under the curve (AUC) until day 7. (b) Median absolute p24 concentration at day 7. (c) Median absolute p24 concentration at day 10. (d) Median p24 value maximally reached over the 14 day period. Values are medians of the two PBMC pools tested. Wilcoxon matched-pairs signed rank test was used to determine statistical significance