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Deep Sequencing Uncovers HIV Adaptations to Escape Early Immune Response

NEW YORK (GenomeWeb News) – By watching the ways in which HIV changes to elude host defenses during the earliest stages of infection, researchers are getting genetic pointers that they hope will improve HIV vaccine design.

In PLoS Pathogens last night, an international group of researchers led by investigators at the Ragon Institute and the Broad Institute demonstrated that they could find even relatively low frequency mutations in HIV-1 genomes when they sequenced dozens of clinical samples by Roche 454 deep sequencing and analyzed the data with specialized assembly and variant detection algorithms.

For one patient, the team took their analyses even further, using viral genetic patterns, viral load data, and immune cell counts over several years to chart the genetic events and viral sub-populations contributing to HIV-1's escape from the immune system.

Within the infected individual, the overall viral load initially decreased after infection as the immune system mounted a response to HIV-1. But genetically distinct forms of HIV-1 with the ability to dodge this early immune response managed to survive, with most of the viral changes during the first few months of infection falling within HIV-1 codons targeted by CD8+ "killer" T-cells.

"These data reveal the ability of HIV to rapidly avoid front-line immune responses attempting to contain the infection," Ragon Institute researcher Todd Allen, the study's senior author, said in a statement.

"[L]imiting the ability of HIV to become resistant to the earliest immune responses may be a critical component of a successful vaccine," he said, adding that "the key to controlling a highly variable pathogen such as HIV may lie in a vaccine's ability to redirect immune responses towards more critical, highly conserved regions of the virus that are unable to successfully mutate."

Past research has illustrated the importance of CD8+ T cells in HIV response, Allen and his colleagues explained, with at least half of the mutations identified in HIV during infection turning up in sequences that affect the virus' interactions with these immune cells.

From their perspective, though, there was still much to be learned about genome-wide changes in HIV during the initial stages of infection, since past conclusions have been based largely on Sanger sequencing, which can miss low frequency mutations in the viral population tested, or on single genome sequence data representing a subset of the overall viral population.

"[A] sensitive and comprehensive understanding of the genetic pathways and kinetics of viral adaptation to acute phase immune selection pressures across the entire HIV-1 genome, likely a critical determinant of the success or failure of both natural and vaccine-elicited immune responses, is lacking," authors of the new study argued.

For their research, the investigators relied on Roche 454 sequencing to get deep coverage across the entire viral population, using their own assembly and variant detection methods to find mutations across the HIV-1 genome, including those occurring at low frequency.

After demonstrating the feasibility of this approach by sequencing 89 clad B HIV-1 clinical samples and comparing the results to those obtained by Sanger sequencing or single genome amplification, the team applied it to a study of early, acute infection in a single individual.

The individual, believed to have been infected 15 to 20 days before the first sample was obtained, was tested regularly for viral load and immune cell count over several years.

For the current analysis, researchers did whole-genome deep sequencing on six viral samples collected during the first four years of infection.

At the earliest stages of infection, they found very little viral genetic diversity, suggesting the individual was infected with a single HIV lineage. Around two months into the infection, the virus began shifting genetically, with mutations showing up across more and more codons as time went on.

Mutations were especially common at known CD8+ targets between around two months and five-and-a-half months after infection, researchers reported, consistent with a role for the CD8+ immune cells in shaping HIV's genetic patterns.

From these and other findings, the team concluded that "the majority of early, low-frequency mutations arising during the acute phase of infection reflect adaptation to host CD8+ T cell responses."

"Moreover," they added, "the temporal link observed between interruption of the decline in peak viremia and escape from the most immunodominant CD8+ T cell responses through low-frequency mutations suggests that the rate of escape from a few key acute phase CD8+ T cell responses may strongly influence primary control of HIV-1, and potentially viral set point."

Along with adding to what's known about viral load patterns and HIV adaptation in the host, the study authors noted that an improved understanding of interactions between the immune interactions and viral escape during acute and chronic infection will likely prove useful for informing future vaccine design efforts.

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