Geometric mean titer and tier 1A and 1B classification (n = 200).

(A) Viruses are rank ordered according to neutralization sensitivity to 30 clade C chronic infection serum samples, from the least sensitive to the most sensitive along the x-axis by average log₁₀ GMTs. Two viruses were classified as highly sensitive tier 1A and an additional 17 as above-average sensitive tier 1B. A previously determined cut off ID₅₀ = 200, was used to distinguish between tier 1A and tier 1B is indicated on the graph, with tier 1B classified viruses above this cut off colored in red and those below in orange [16]. Twelve pseudoviruses classified by both Seaman et al., (2010) and this study were found to be discrepant (S1 Table): Du156.12 consistently falls near the boundary of the tier 2 and tier 1B, was classified as tier 1B here however was previously classified as tier 2; and ZM197M and SM109F were classified as tier 2 here, however were previously classified as 1B. (B) Maximum likelihood phylogenetic analysis of southern African clade C acute/early envelope nucleotide sequences (n = 200) with branches colored according to tier. Bootstrap values > 80% of 100 resampled replicates are illustrated as filled circles on nodes.