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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 and highlighter plots of the SIVsmE660 challenge stock.A total of 58 full-length envelope sequences were analyzed from the SIVsmE660 stock viral swarm and were compared to the derived consensus E660 sequence for silent and non-silent mutations. (A) Neighbor-joining phylogenetic tree with all the 58 env sequences compared to consensus sequence derived from SIVsmE660 inoculum. (B) Highlighter plot showing the silent (green)/non-silent (red) mutations among different full-length envelope sequences as compared to the consensus SIVsmE660 sequence.
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pone-0109678-g002: Phylogenetic analysis and highlighter plots of the SIVsmE660 challenge stock.A total of 58 full-length envelope sequences were analyzed from the SIVsmE660 stock viral swarm and were compared to the derived consensus E660 sequence for silent and non-silent mutations. (A) Neighbor-joining phylogenetic tree with all the 58 env sequences compared to consensus sequence derived from SIVsmE660 inoculum. (B) Highlighter plot showing the silent (green)/non-silent (red) mutations among different full-length envelope sequences as compared to the consensus SIVsmE660 sequence.

Mentions: To determine the genetic diversity and the phylogenetic relationships among different envelope sequences, SGA was done on the stock in 2 laboratories. Twenty-nine full-length envelope sequences were obtained at the Tulane primate center (Fig. 2A, Tulane sequences in green) and 29 full-length envelope sequences from the same stock virus provided by Dr. David Montefiori's group from Duke University (Duke sequences in red). Sequence were aligned, analyzed and are shown in Fig. 2. Nucleotide sequences from both the institutions were interspersed in the phylogenetic tree indicating their close relationship of being from the same stock. The maximum overall env diversity for the stock was 1.4%. A consensus sequence was generated from inoculum envelope sequences and was compared to each sequence (Fig. 2A). Three out of fifty-eight envelope sequences had an insertion of proline, threonine and alanine (P, T, A) from 136–138 amino acid position of V1 loop. No major changes were seen in the rest of the variable loops of gp120. Several notable amino acid differences were seen in the gp41 cytoplasmic tail (I882V L885F and T888A) as compared to the SIVsmE660 consensus sequence (data not shown). Additional silent (synonymous) and amino acid altering mutations (non-synonymous) were identified in the stock envelope sequences as depicted in the highlighter plot (Fig. 2B). Taken together the viral inoculum contained diversified envelope sequences and these sequences will be deposited in the Genbank.


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 and highlighter plots of the SIVsmE660 challenge stock.A total of 58 full-length envelope sequences were analyzed from the SIVsmE660 stock viral swarm and were compared to the derived consensus E660 sequence for silent and non-silent mutations. (A) Neighbor-joining phylogenetic tree with all the 58 env sequences compared to consensus sequence derived from SIVsmE660 inoculum. (B) Highlighter plot showing the silent (green)/non-silent (red) mutations among different full-length envelope sequences as compared to the consensus SIVsmE660 sequence.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0109678-g002: Phylogenetic analysis and highlighter plots of the SIVsmE660 challenge stock.A total of 58 full-length envelope sequences were analyzed from the SIVsmE660 stock viral swarm and were compared to the derived consensus E660 sequence for silent and non-silent mutations. (A) Neighbor-joining phylogenetic tree with all the 58 env sequences compared to consensus sequence derived from SIVsmE660 inoculum. (B) Highlighter plot showing the silent (green)/non-silent (red) mutations among different full-length envelope sequences as compared to the consensus SIVsmE660 sequence.
Mentions: To determine the genetic diversity and the phylogenetic relationships among different envelope sequences, SGA was done on the stock in 2 laboratories. Twenty-nine full-length envelope sequences were obtained at the Tulane primate center (Fig. 2A, Tulane sequences in green) and 29 full-length envelope sequences from the same stock virus provided by Dr. David Montefiori's group from Duke University (Duke sequences in red). Sequence were aligned, analyzed and are shown in Fig. 2. Nucleotide sequences from both the institutions were interspersed in the phylogenetic tree indicating their close relationship of being from the same stock. The maximum overall env diversity for the stock was 1.4%. A consensus sequence was generated from inoculum envelope sequences and was compared to each sequence (Fig. 2A). Three out of fifty-eight envelope sequences had an insertion of proline, threonine and alanine (P, T, A) from 136–138 amino acid position of V1 loop. No major changes were seen in the rest of the variable loops of gp120. Several notable amino acid differences were seen in the gp41 cytoplasmic tail (I882V L885F and T888A) as compared to the SIVsmE660 consensus sequence (data not shown). Additional silent (synonymous) and amino acid altering mutations (non-synonymous) were identified in the stock envelope sequences as depicted in the highlighter plot (Fig. 2B). Taken together the viral inoculum contained diversified envelope sequences and these sequences will be deposited in the Genbank.

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