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Synonymous Co-Variation across the E1/E2 Gene Junction of Hepatitis C Virus Defines Virion Fitness

View Article: PubMed Central - PubMed

ABSTRACT

Hepatitis C virus is a positive-sense single-stranded RNA virus. The gene junction partitioning the viral glycoproteins E1 and E2 displays concurrent sequence evolution with the 3′-end of E1 highly conserved and the 5′-end of E2 highly heterogeneous. This gene junction is also believed to contain structured RNA elements, with a growing body of evidence suggesting that such structures can act as an additional level of viral replication and transcriptional control. We have previously used ultradeep pyrosequencing to analyze an amplicon library spanning the E1/E2 gene junction from a treatment naïve patient where samples were collected over 10 years of chronic HCV infection. During this timeframe maintenance of an in-frame insertion, recombination and humoral immune targeting of discrete virus sub-populations was reported. In the current study, we present evidence of epistatic evolution across the E1/E2 gene junction and observe the development of co-varying networks of codons set against a background of a complex virome with periodic shifts in population dominance. Overtime, the number of codons actively mutating decreases for all virus groupings. We identify strong synonymous co-variation between codon sites in a group of sequences harbouring a 3 bp in-frame insertion and propose that synonymous mutation acts to stabilize the RNA structural backbone.

No MeSH data available.


Pronounced epistasis was evident for both L1a and L1b sequence sets covering 10 years of continuous adaptive evolution of the E1/E2 gene junction.Nodes (representing codon positions) within the graph are connected by an edge if the probability of a change detected simultaneously at both sites was statistically significant (p-value < 0.01). (A) L1a epistasis was highly ordered with the majority of significantly linked sites participating in a single large connected component. (B) Epistasis within the L1b sequence set was observed among a greater number of codon sites overall. The majority of sites identified for L1b exclusively underwent synonymous mutation. (C) Two sites were observed in L2 sequences that were below the significance threshold. White nodes define codons within the E1 coding sequence, while grey nodes identify E2 codons. Sites containing nonsynonymous mutations are identified by black numbers while sites exclusively undergoing synonymous mutation are given by red numbers. Nodes are numbered in accordance with the amino acid positions of the H77 reference genome (Genbank accession: AF009606).
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pone.0167089.g003: Pronounced epistasis was evident for both L1a and L1b sequence sets covering 10 years of continuous adaptive evolution of the E1/E2 gene junction.Nodes (representing codon positions) within the graph are connected by an edge if the probability of a change detected simultaneously at both sites was statistically significant (p-value < 0.01). (A) L1a epistasis was highly ordered with the majority of significantly linked sites participating in a single large connected component. (B) Epistasis within the L1b sequence set was observed among a greater number of codon sites overall. The majority of sites identified for L1b exclusively underwent synonymous mutation. (C) Two sites were observed in L2 sequences that were below the significance threshold. White nodes define codons within the E1 coding sequence, while grey nodes identify E2 codons. Sites containing nonsynonymous mutations are identified by black numbers while sites exclusively undergoing synonymous mutation are given by red numbers. Nodes are numbered in accordance with the amino acid positions of the H77 reference genome (Genbank accession: AF009606).

Mentions: Co-variation between codon sites identified epistatic evolution within E1, within E2 and across the E1/E2 gene junction (Fig 3). It was observed that co-variation was deterministic with the same codon-codon switching events being replicated between unique sequences in the majority of instances (S2 and S3 Tables).


Synonymous Co-Variation across the E1/E2 Gene Junction of Hepatitis C Virus Defines Virion Fitness
Pronounced epistasis was evident for both L1a and L1b sequence sets covering 10 years of continuous adaptive evolution of the E1/E2 gene junction.Nodes (representing codon positions) within the graph are connected by an edge if the probability of a change detected simultaneously at both sites was statistically significant (p-value < 0.01). (A) L1a epistasis was highly ordered with the majority of significantly linked sites participating in a single large connected component. (B) Epistasis within the L1b sequence set was observed among a greater number of codon sites overall. The majority of sites identified for L1b exclusively underwent synonymous mutation. (C) Two sites were observed in L2 sequences that were below the significance threshold. White nodes define codons within the E1 coding sequence, while grey nodes identify E2 codons. Sites containing nonsynonymous mutations are identified by black numbers while sites exclusively undergoing synonymous mutation are given by red numbers. Nodes are numbered in accordance with the amino acid positions of the H77 reference genome (Genbank accession: AF009606).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5120871&req=5

pone.0167089.g003: Pronounced epistasis was evident for both L1a and L1b sequence sets covering 10 years of continuous adaptive evolution of the E1/E2 gene junction.Nodes (representing codon positions) within the graph are connected by an edge if the probability of a change detected simultaneously at both sites was statistically significant (p-value < 0.01). (A) L1a epistasis was highly ordered with the majority of significantly linked sites participating in a single large connected component. (B) Epistasis within the L1b sequence set was observed among a greater number of codon sites overall. The majority of sites identified for L1b exclusively underwent synonymous mutation. (C) Two sites were observed in L2 sequences that were below the significance threshold. White nodes define codons within the E1 coding sequence, while grey nodes identify E2 codons. Sites containing nonsynonymous mutations are identified by black numbers while sites exclusively undergoing synonymous mutation are given by red numbers. Nodes are numbered in accordance with the amino acid positions of the H77 reference genome (Genbank accession: AF009606).
Mentions: Co-variation between codon sites identified epistatic evolution within E1, within E2 and across the E1/E2 gene junction (Fig 3). It was observed that co-variation was deterministic with the same codon-codon switching events being replicated between unique sequences in the majority of instances (S2 and S3 Tables).

View Article: PubMed Central - PubMed

ABSTRACT

Hepatitis C virus is a positive-sense single-stranded RNA virus. The gene junction partitioning the viral glycoproteins E1 and E2 displays concurrent sequence evolution with the 3&prime;-end of E1 highly conserved and the 5&prime;-end of E2 highly heterogeneous. This gene junction is also believed to contain structured RNA elements, with a growing body of evidence suggesting that such structures can act as an additional level of viral replication and transcriptional control. We have previously used ultradeep pyrosequencing to analyze an amplicon library spanning the E1/E2 gene junction from a treatment na&iuml;ve patient where samples were collected over 10 years of chronic HCV infection. During this timeframe maintenance of an in-frame insertion, recombination and humoral immune targeting of discrete virus sub-populations was reported. In the current study, we present evidence of epistatic evolution across the E1/E2 gene junction and observe the development of co-varying networks of codons set against a background of a complex virome with periodic shifts in population dominance. Overtime, the number of codons actively mutating decreases for all virus groupings. We identify strong synonymous co-variation between codon sites in a group of sequences harbouring a 3 bp in-frame insertion and propose that synonymous mutation acts to stabilize the RNA structural backbone.

No MeSH data available.