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Transmitted/founder simian immunodeficiency virus envelope sequences in vesicular stomatitis and Semliki forest virus vector immunized rhesus macaques.

Gambhira R, Keele BF, Schell JB, Hunter MJ, Dufour JP, Montefiori DC, Tang H, Rose JK, Rose N, Marx PA - PLoS ONE (2014)

Bottom Line: We used single genome amplification and phylogenetic analyses to characterize transmitted/founder SIVs both in the inoculum and in immunized-infected rhesus monkeys.We obtained 246 full-length envelope sequences from SIVsmE660 infected macaques at the peak of infection and determined the number of transmitted/founder variants per animal.Because there were only 2 infected animals in the gag-env vaccinated rhesus compared to 10 infected rhesus in the other 2 groups, the significance of finding single env variants in the gag-env vaccinated group could not be established.

View Article: PubMed Central - PubMed

Affiliation: Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, Louisiana, United States of America.

ABSTRACT
Identification of transmitted/founder simian immunodeficiency virus (SIV) envelope sequences responsible for infection may prove critical for understanding HIV/SIV mucosal transmission. We used single genome amplification and phylogenetic analyses to characterize transmitted/founder SIVs both in the inoculum and in immunized-infected rhesus monkeys. Single genome amplification of the SIVsmE660 inoculum revealed a maximum diversity of 1.4%. We also noted that the consensus sequence of the challenge stock differed from the vaccine construct in 10 amino acids including 3 changes in the V4 loop. Viral env was prepared from rhesus plasma in 3 groups of 6 immunized with vesicular stomatitis virus (VSV) vectors and boosted with Semliki forest virus (SFV) replicons expressing (a) SIVsmE660 gag-env (b) SIVsmE660 gag-env plus rhesus GM-CSF and (c) control influenza hemagglutinin protein. Macaques were immunized twice with VSV-vectors and once with SFV vector and challenged intrarectally with 4000 TCID50. Single genome amplification characterized the infections of 2 unprotected animals in the gag-env immunized group, both of which had reduced acute plasma viral loads that ended as transient infections indicating partial immune control. Four of 6 rhesus were infected in the gag-env + GM-CSF group which demonstrated that GM-CSF abrogated protection. All 6 animals from the control group were infected having high plasma viral loads. We obtained 246 full-length envelope sequences from SIVsmE660 infected macaques at the peak of infection and determined the number of transmitted/founder variants per animal. Our analysis found that 2 of 2 gag-env vaccinated but infected macaques exhibited single but distinct virus envelope lineages whereas rhesus vaccinated with gag-env-GM-CSF or HA control exhibited both single and multiple env lineages. Because there were only 2 infected animals in the gag-env vaccinated rhesus compared to 10 infected rhesus in the other 2 groups, the significance of finding single env variants in the gag-env vaccinated group could not be established.

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Phylogenetic analysis of full-length env sequences from Gag-Env-GM-CSF group (Group II)) macaques.All the macaques in this group were vaccinated and challenged with SIVsmE660. The full-length envelope sequences were compared to a derived consensus sequence from each animal (A) EA28 (B) EF23 (C) EF28 and (D) EJ74. Multiple lineages of T/F viruses infecting the same macaque were shown in different colors.
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pone-0109678-g006: Phylogenetic analysis of full-length env sequences from Gag-Env-GM-CSF group (Group II)) macaques.All the macaques in this group were vaccinated and challenged with SIVsmE660. The full-length envelope sequences were compared to a derived consensus sequence from each animal (A) EA28 (B) EF23 (C) EF28 and (D) EJ74. Multiple lineages of T/F viruses infecting the same macaque were shown in different colors.

Mentions: Following challenge with SIVsmE660, 5 of the 6 RhMs were infected in gag-env-GM-CSF group with relatively high PVLs that were comparable to the control group [Fig. 1C]. The results demonstrated that VSV-vectored GM-CSF abrogated the protective effect of the vaccine, since 4 of 6 animals were protected in gag-env group, whereas addition of GM-CSF reduced protection to 1 of 6 animals in gag-env-GM-CSF group as previously reported [26]. We performed SGA analysis on 4 of 5 infected animals at the peak of their viremia. After repeated attempts only partial sequences were obtained from the 5th animal FD21, so this animal could not be analized. All the full-length envelope sequences were compared phylogenetically including the derived consensus sequence. The major lineages of different founder viruses are highlighted in various colors on the phylogenetic tree (Fig. 6). We obtained 21 full-length envelope sequences from EA28 and found only 1 transmitted virus (Fig. 6A). We analyzed 18 full-length envelope sequences from EF23 and noted only 1 founder virus (Fig. 6B). However, we found 3 different founder viruses, after analyzing 22 full-length Envelope sequences from EF28 (Fig. 6C) and 6 variants in 26 full-length envelope sequences from EJ74. There were a few other envelope sequences that were either recombinants or independent founder viruses but couldn't be categorized appropriately due to their limited number. None of the animals in this group showed APOBEC mutations (except 5 sequences from EF28). We also performed Poisson-Fitter analysis on the full-length envelope sequences obtained from various infected macaques (data not shown). The results demonstrate that EA28 and EF23 fit the Poisson-Fitter analysis, since both the samples were infected with only 1 founder virus and it did follow the star like phylogeny of evolution. However, both EF28 and EJ74 failed to fit this analysis, since they were infected with more than one transmitted viruses. Therefore, in this group two macaques (EF28, EJ74) were infected with multiple founder viruses and the other two (EA28, EF23) were infected with only one founder virus.


Transmitted/founder simian immunodeficiency virus envelope sequences in vesicular stomatitis and Semliki forest virus vector immunized rhesus macaques.

Gambhira R, Keele BF, Schell JB, Hunter MJ, Dufour JP, Montefiori DC, Tang H, Rose JK, Rose N, Marx PA - PLoS ONE (2014)

Phylogenetic analysis of full-length env sequences from Gag-Env-GM-CSF group (Group II)) macaques.All the macaques in this group were vaccinated and challenged with SIVsmE660. The full-length envelope sequences were compared to a derived consensus sequence from each animal (A) EA28 (B) EF23 (C) EF28 and (D) EJ74. Multiple lineages of T/F viruses infecting the same macaque were shown in different colors.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4215841&req=5

pone-0109678-g006: Phylogenetic analysis of full-length env sequences from Gag-Env-GM-CSF group (Group II)) macaques.All the macaques in this group were vaccinated and challenged with SIVsmE660. The full-length envelope sequences were compared to a derived consensus sequence from each animal (A) EA28 (B) EF23 (C) EF28 and (D) EJ74. Multiple lineages of T/F viruses infecting the same macaque were shown in different colors.
Mentions: Following challenge with SIVsmE660, 5 of the 6 RhMs were infected in gag-env-GM-CSF group with relatively high PVLs that were comparable to the control group [Fig. 1C]. The results demonstrated that VSV-vectored GM-CSF abrogated the protective effect of the vaccine, since 4 of 6 animals were protected in gag-env group, whereas addition of GM-CSF reduced protection to 1 of 6 animals in gag-env-GM-CSF group as previously reported [26]. We performed SGA analysis on 4 of 5 infected animals at the peak of their viremia. After repeated attempts only partial sequences were obtained from the 5th animal FD21, so this animal could not be analized. All the full-length envelope sequences were compared phylogenetically including the derived consensus sequence. The major lineages of different founder viruses are highlighted in various colors on the phylogenetic tree (Fig. 6). We obtained 21 full-length envelope sequences from EA28 and found only 1 transmitted virus (Fig. 6A). We analyzed 18 full-length envelope sequences from EF23 and noted only 1 founder virus (Fig. 6B). However, we found 3 different founder viruses, after analyzing 22 full-length Envelope sequences from EF28 (Fig. 6C) and 6 variants in 26 full-length envelope sequences from EJ74. There were a few other envelope sequences that were either recombinants or independent founder viruses but couldn't be categorized appropriately due to their limited number. None of the animals in this group showed APOBEC mutations (except 5 sequences from EF28). We also performed Poisson-Fitter analysis on the full-length envelope sequences obtained from various infected macaques (data not shown). The results demonstrate that EA28 and EF23 fit the Poisson-Fitter analysis, since both the samples were infected with only 1 founder virus and it did follow the star like phylogeny of evolution. However, both EF28 and EJ74 failed to fit this analysis, since they were infected with more than one transmitted viruses. Therefore, in this group two macaques (EF28, EJ74) were infected with multiple founder viruses and the other two (EA28, EF23) were infected with only one founder virus.

Bottom Line: We used single genome amplification and phylogenetic analyses to characterize transmitted/founder SIVs both in the inoculum and in immunized-infected rhesus monkeys.We obtained 246 full-length envelope sequences from SIVsmE660 infected macaques at the peak of infection and determined the number of transmitted/founder variants per animal.Because there were only 2 infected animals in the gag-env vaccinated rhesus compared to 10 infected rhesus in the other 2 groups, the significance of finding single env variants in the gag-env vaccinated group could not be established.

View Article: PubMed Central - PubMed

Affiliation: Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, Louisiana, United States of America.

ABSTRACT
Identification of transmitted/founder simian immunodeficiency virus (SIV) envelope sequences responsible for infection may prove critical for understanding HIV/SIV mucosal transmission. We used single genome amplification and phylogenetic analyses to characterize transmitted/founder SIVs both in the inoculum and in immunized-infected rhesus monkeys. Single genome amplification of the SIVsmE660 inoculum revealed a maximum diversity of 1.4%. We also noted that the consensus sequence of the challenge stock differed from the vaccine construct in 10 amino acids including 3 changes in the V4 loop. Viral env was prepared from rhesus plasma in 3 groups of 6 immunized with vesicular stomatitis virus (VSV) vectors and boosted with Semliki forest virus (SFV) replicons expressing (a) SIVsmE660 gag-env (b) SIVsmE660 gag-env plus rhesus GM-CSF and (c) control influenza hemagglutinin protein. Macaques were immunized twice with VSV-vectors and once with SFV vector and challenged intrarectally with 4000 TCID50. Single genome amplification characterized the infections of 2 unprotected animals in the gag-env immunized group, both of which had reduced acute plasma viral loads that ended as transient infections indicating partial immune control. Four of 6 rhesus were infected in the gag-env + GM-CSF group which demonstrated that GM-CSF abrogated protection. All 6 animals from the control group were infected having high plasma viral loads. We obtained 246 full-length envelope sequences from SIVsmE660 infected macaques at the peak of infection and determined the number of transmitted/founder variants per animal. Our analysis found that 2 of 2 gag-env vaccinated but infected macaques exhibited single but distinct virus envelope lineages whereas rhesus vaccinated with gag-env-GM-CSF or HA control exhibited both single and multiple env lineages. Because there were only 2 infected animals in the gag-env vaccinated rhesus compared to 10 infected rhesus in the other 2 groups, the significance of finding single env variants in the gag-env vaccinated group could not be established.

Show MeSH
Related in: MedlinePlus