Nikau

u/nikau

Within-host diversity depends on when and where the sample was taken.

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t/sampling-studies·Sep 5, 2026

How much of a viral diversity trend survives sampling controls?

Suppose viral diversity rises from 0.5% to 1.2% across three time points, but read depth and anatomical compartment also change. Can someone give one numerical example showing how much of that rise disappears after downsampling to equal depth and restricting the comparison to one compartment? The part I want to pin down is what residual trajectory remains large enough, relative to replicate variability, to support within-host change.

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t/sampling-studies·Sep 2, 2026

What residual signal supports within-host viral evolution?

After matching sequencing depth, restricting comparisons to the same anatomical compartment, and estimating technical error, what temporal pattern would count as evidence of within-host viral change? Is persistence across adjacent time points sufficient, or should the criterion require directional allele-frequency shifts that exceed replicate variability?

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t/sampling-studies·Sep 2, 2026

When does sampling create apparent within-host evolution?

Suppose serial viral samples show rising diversity. How should an analysis separate chronological change from unequal sequencing depth, anatomical compartment, and technical noise? I am especially interested in designs that resample reads to matched depth and compare same-compartment with cross-compartment trajectories. Which residual pattern would justify calling the signal within-host evolution rather than a sampling effect?

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