Purpose of review Improvements in sequencing approaches and robust mathematical modeling have dramatically increased information on viral genetics during acute infection with human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) NSC 105823 infection providing unprecedented insight into viral transmission and viral/immune Interactions. within a new host. Summary Acute HIV infection is a critical window of opportunity for vaccine and therapeutic intervention. New sequencing technologies and mathematical modeling of transmission and early evolution have provided a clearer understanding of the number of founder viruses that establish infection the rapid generation of diversity in these viruses and the subsequent evasion of host immunity. The information gained by identifying transmitted viruses monitoring the initial host responses to these viruses and then identifying mechanisms of viral escape could provide better strategies for vaccine development pre-exposure prophylaxis microbicides or other therapeutic interventions. induced point mutations and iii) no recombination. Firstly direct proportionality of sequences is attained using universal primers to reduce bias in which each viral genome is equally likely to be amplified and sequenced. Therefore if one generates 40 sequences and 10 have a shared polymorphism then one can predict that at the time of sampling ~25% of circulating viruses share this polymorphism. Secondly there is a lack of recombination cannot occur. These theoretical benefits of SGA were directly tested and confirmed experimentally by a number of investigators [5-7] thereby ensuring that the sequences being analyzed are identical to the sequences that exist modeling and cell culture experiments to identify non-lethal G-to-A mutations . With putatively functional genomes the authors predict that these low-level G-to-A mutations are likely to survive selection pressure and accumulate overtime within the population. These predictions were validated by the detection of G-to-A imprints on current HIV compared to the ancestral genome . Overall hypermutation may not affect disease progression directly but moderate mutations may be advantageous to the virus by rapidly accumulating genetic diversity. Recombination can occur very early after infection but has been found typically after peak viremia when potential targets become more limited . The effects of recombination are greatly increased in patients infected with more than one viral variant. This rapid increase in overall genetic diversity could lead to more efficient immune escape and increase progression to AIDS . Onafuwa-Nuga and Telesnitsky recently reviewed recombination in detail  but it is notable that recombination is seen very early in primary infection in humans  and in non-human primates infected NSC 105823 with SIV (Keele unpublished). Finally studies comparing HIV transmission to other sexually transmitted diseases and to airborne infections show that there is a cost to high diversity and that cost is a lower transmission rate . Understanding transmission of particular variants and early diversity is fundamental to eventually inhibiting these events. Early host responses to infection There are a number of host barriers to infection NSC NSC 105823 105823 that in total can explain the genetic bottleneck seen in HIV-1 transmission. Each mechanism of host defense represents a battle line at which the host and virus compete for life itself. In a typical NSC 105823 case if the host cannot eliminate the invader within days to perhaps weeks after exposure the battle is over and the fate of the host is sealed. For mucosal infections the mucus itself and an intact epithelial barrier most likely represent the greatest obstacle to infection. However even after this barrier is breached infecting virus must still find an appropriate target cell mediate entry via CD4 and coreceptor successfully reverse transcribe NSC 105823 and finally integrate its genome. Generating progeny from an integrated genome at a basic reproductive ratio large enough to overcome innate immune responses becomes the next challenge NY-REN-37 for viral survival. Recently Stacey et al.  measured cytokine and chemokine levels in plasma within the first days of HIV-1 infection. After synchronizing each individual based on first detectable vRNA (~10-21 days post infection) they found a rapid increase in many cytokines and chemokines including alpha interferon interleukin-15 (IL-15) inducible protein 10 tumor necrosis factor alpha and monocyte chemotactic protein 1 with more slowly initiated increases in IL-6 IL-8 IL-18 and gamma interferon. The magnitude of this “cytokine storm” was not observed in.