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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 VSV-HA (Group III) macaques.The full-length envelope sequences obtained from al the control animals infected with SIVsmE660 were compared against the respective consensus sequence and were phylogenetically analyzed (A) FT80 (B) N288 (C) DD04 (D) FG05 (E) EN82 and (F) EP84. Multiple lineages of T/F viruses infecting the same animal were shown in different colors.
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pone-0109678-g007: Phylogenetic analysis of full-length env sequences from VSV-HA (Group III) macaques.The full-length envelope sequences obtained from al the control animals infected with SIVsmE660 were compared against the respective consensus sequence and were phylogenetically analyzed (A) FT80 (B) N288 (C) DD04 (D) FG05 (E) EN82 and (F) EP84. Multiple lineages of T/F viruses infecting the same animal were shown in different colors.

Mentions: This group of animals was primed and boosted twice with VSV expressing influenza HA. All the macaques in this group were infected after IR challenge with SIVsmE660. Three out of six macaques showed persistently high PVLs (EN82, FG05 and N288) (Fig. 1) whereas the remaining 3 exhibited relative control of SIVe660 with a decline in viral load after the peak viremia (FT80, DD04 and EP84). SGA was performed on the plasma samples of all control animals at peak viremia and phylogenetic trees were constructed. (Fig. 7). The variant lineages infecting the challenged macaques are depicted in different colors. In case of FT80 and N288 animals, we analyzed 22 and 26 full-length envelope sequences respectively. Only a single founder virus lineage was infecting these animals based on the highlighter plot analysis (Fig. 7A, B). In case of DD04, among 15 envelopes sequenced, several APOBEC mutations were present and after their elimination this animal was infected with only one founder virus (Fig. 7C). We sequenced 15 envelopes from FG05, noted 3 different founder virus lineages while EN82 was infected with at least 3 founder virus envelope sequences (Fig. 7D, E). We obtained 23 full-length envelope sequences from EP84 and detected more than 4 founder viruses from this animal (Fig. 7F). We also performed the Poisson-Fitter analysis on all the envelope sequences obtained from each animal (data not shown). The envelope sequences from N288, FT80 and DD04 all fit the Poisson distribution, since all of them were infected with a single founder virus that evolved randomly to exhibit star like phylogeny. Since the macaques FG05, EN82 and EP84 were infected with multiple viruses, their envelope sequences failed to follow Poisson-Fitter distribution.


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 VSV-HA (Group III) macaques.The full-length envelope sequences obtained from al the control animals infected with SIVsmE660 were compared against the respective consensus sequence and were phylogenetically analyzed (A) FT80 (B) N288 (C) DD04 (D) FG05 (E) EN82 and (F) EP84. Multiple lineages of T/F viruses infecting the same animal were shown in different colors.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0109678-g007: Phylogenetic analysis of full-length env sequences from VSV-HA (Group III) macaques.The full-length envelope sequences obtained from al the control animals infected with SIVsmE660 were compared against the respective consensus sequence and were phylogenetically analyzed (A) FT80 (B) N288 (C) DD04 (D) FG05 (E) EN82 and (F) EP84. Multiple lineages of T/F viruses infecting the same animal were shown in different colors.
Mentions: This group of animals was primed and boosted twice with VSV expressing influenza HA. All the macaques in this group were infected after IR challenge with SIVsmE660. Three out of six macaques showed persistently high PVLs (EN82, FG05 and N288) (Fig. 1) whereas the remaining 3 exhibited relative control of SIVe660 with a decline in viral load after the peak viremia (FT80, DD04 and EP84). SGA was performed on the plasma samples of all control animals at peak viremia and phylogenetic trees were constructed. (Fig. 7). The variant lineages infecting the challenged macaques are depicted in different colors. In case of FT80 and N288 animals, we analyzed 22 and 26 full-length envelope sequences respectively. Only a single founder virus lineage was infecting these animals based on the highlighter plot analysis (Fig. 7A, B). In case of DD04, among 15 envelopes sequenced, several APOBEC mutations were present and after their elimination this animal was infected with only one founder virus (Fig. 7C). We sequenced 15 envelopes from FG05, noted 3 different founder virus lineages while EN82 was infected with at least 3 founder virus envelope sequences (Fig. 7D, E). We obtained 23 full-length envelope sequences from EP84 and detected more than 4 founder viruses from this animal (Fig. 7F). We also performed the Poisson-Fitter analysis on all the envelope sequences obtained from each animal (data not shown). The envelope sequences from N288, FT80 and DD04 all fit the Poisson distribution, since all of them were infected with a single founder virus that evolved randomly to exhibit star like phylogeny. Since the macaques FG05, EN82 and EP84 were infected with multiple viruses, their envelope sequences failed to follow Poisson-Fitter distribution.

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