July 23, 2015  |  General

SMRT Sequencing Provides Novel View of Long-Term Viral Evolution in a Single Patient

A group of scientists from the University of Pittsburgh School of Medicine and New York University used long-read sequencing from PacBio for a remarkable new study characterizing influenza virus evolution with unprecedented precision.
Intrahost Dynamics of Antiviral Resistance in Influenza A Virus Reflect Complex Patterns of Segment Linkage, Reassortment, and Natural Selection,” published in mBio by lead author Matthew Rogers and senior author Elodie Ghedin, reports a two-year study tracking the flu virus in one person. Although normally limited to acute infection, in this case the patient, a three-year-old with severe combined immunodeficiency disease, received multiple antiviral therapies but kept shedding virus over the course of 21 months. The team was able to study 10 samples collected during that time period, using sequencing to track viral evolution in great detail. “This unique natural experiment provides a rare view into the patterns, dynamics, and mechanisms of drug resistance of influenza virus,” the team wrote.
The influenza virus is known to develop rapid resistance to antiviral medications, but the extremely short infection cycle — less than two weeks in an average healthy host — has historically made it difficult to pinpoint evolutionary mutations as they arise. The team used SMRT® Sequencing, performed by the Icahn Institute at Mount Sinai, to analyze the H3N2 viral genome and reconstruct haplotypes, providing a clear phylogenetic view of the virus evolving over time within the host.
Among the findings, the scientists report that “individual resistance mutations appeared weeks before they became dominant, evolved independently on co-circulating lineages, led to a genome-wide reduction in genetic diversity through a selective sweep, and were placed into new combinations by reassortment.”
Based on the long-read data, the scientists were able to reconstruct haplotypes for several large segments of the viral genome to learn more about gene reassortment in persistent influenza infection. This allowed the team to track viral lineage dynamics, observing minor lineages becoming dominant over time, particularly as drug-resistant variants emerged. The authors note that even though reassortment was an important driver in H3N2 evolution, “it may not always be frequent enough to break all patterns of segment linkage.” This conclusion was based on phylogenetic evidence demonstrating these linkage patterns, particularly between hemagglutinin- and matrix-encoding genome segments. These association matches have also been observed across the general population, according to the scientists.
Rogers et al. hope this work will contribute to the ability to predict the emergence of drug-resistant influenza strains and to the development of antiviral therapies that prevent or reduce the occurrence of resistance. They note, however, that the evolutionary processes they documented must be studied in more detail. “In particular, a better understanding of segment linkage and reassortment, and whether they differ between mammalian and avian influenza viruses, may enable more accurate predictions of the rapidity with which particular genomic combinations can be obtained, including those mediating drug resistance, antigenic escape, and host adaptation,” they conclude.
Want to know more about viral sequencing using PacBio® technology? Check out these additional resources:
Human immunodeficiency virus (HIV) sequencing
Characterization of adeno-associated virus (AAV) genomic integration sites
De novo assembly of Pseudorabies virus
Human papilloma virus (HPV) sequencing

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