@article {Pang444877, author = {Juanita Pang and Cristina Venturini and Asif U. Tamuri and Sunando Roy and Judith Breuer and Richard A. Goldstein}, title = {Haplotype assignment of longitudinal viral deep-sequencing data using co-variation of variant frequencies}, elocation-id = {444877}, year = {2020}, doi = {10.1101/444877}, publisher = {Cold Spring Harbor Laboratory}, abstract = {Longitudinal deep sequencing of viruses can provide detailed information about intra-host evolutionary dynamics including how viruses interact with and transmit between hosts. Many analyses require haplotype reconstruction, identifying which variants are co-located on the same genomic element. Most current methods to perform this reconstruction are based on a high density of variants and cannot perform this reconstruction for slowly evolving viruses. We present a new approach, HaROLD (HAplotype Reconstruction Of Longitudinal Deep sequencing data), which performs this reconstruction based on identifying co-varying variant frequencies using a probabilistic framework. We test this method with synthetic data sets of mixed cytomegalovirus and norovirus genomes, demonstrating high accuracy when longitudinal samples are available.Competing Interest StatementThe authors have declared no competing interest.}, URL = {https://www.biorxiv.org/content/early/2020/08/27/444877}, eprint = {https://www.biorxiv.org/content/early/2020/08/27/444877.full.pdf}, journal = {bioRxiv} }