Changes in codon-pair bias of human immunodeficiency virus type 1 have profound effects on virus replication in cell culture

Martrus, Glòria; Nevot, María; Andrés, Cristina; Clotet, Bonaventura; Martı́nez, Miguel Ángel

doi:10.1186/1742-4690-10-78

Cited by 79 publications

(98 citation statements)

References 38 publications

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“…It has previously been demonstrated that large-scale re-encoding generates attenuated viruses and the studies support the proposal that relative degree of attenuation or replicative fitness can be regulated by modulating the number of introduced synonymous mutations [18,19,20,21,22,23,24,25,26,27]. Indeed, a re-encoded strain of influenza A virus that displayed limited fitness in cellulo was highly attenuated when tested in a mouse model and showed potential for use as a vaccine candidate [25].…”

Section: Discussionmentioning

confidence: 52%

Attenuation of Tick-Borne Encephalitis Virus Using Large-Scale Random Codon Re-encoding

et al. 2015

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Large-scale codon re-encoding (i.e. introduction of a large number of synonymous mutations) is a novel method of generating attenuated viruses. Here, it was applied to the pathogenic flavivirus, tick-borne encephalitis virus (TBEV) which causes febrile illness and encephalitis in humans in forested regions of Europe and Asia. Using an infectious clone of the Oshima 5–10 strain ("wild-type virus"), a cassette of 1.4kb located in the NS5 coding region, was modified by randomly introducing 273 synonymous mutations ("re-encoded virus"). Whilst the in cellulo replicative fitness of the re-encoded virus was only slightly reduced, the re-encoded virus displayed an attenuated phenotype in a laboratory mouse model of non-lethal encephalitis. Following intra-peritoneal inoculation of either 2.105 or 2.106 TCID50 of virus, the frequency of viraemia, neurovirulence (measured using weight loss and appearance of symptoms) and neuroinvasiveness (detection of virus in the brain) were significantly decreased when compared with the wild-type virus. Mice infected by wild-type or re-encoded viruses produced comparable amounts of neutralising antibodies and results of challenge experiments demonstrated that mice previously infected with the re-encoded virus were protected against subsequent infection by the wild-type virus. This constitutes evidence that a mammalian species can be protected against infection by a virulent wild-type positive-stranded RNA virus following immunisation with a derived randomly re-encoded strain. Our results demonstrate that random codon re-encoding is potentially a simple and effective method of generating live-attenuated vaccine candidates against pathogenic flaviviruses.

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Section: Discussionmentioning

confidence: 52%

Attenuation of Tick-Borne Encephalitis Virus Using Large-Scale Random Codon Re-encoding

et al. 2015

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“…Four synthetic live RSV mutants were designed and readily recovered. It is noteworthy that Min FLC was readily recovered even though 9 of the 11 RSV ORFs (representing almost 94% of the protein-coding sequence) in this virus had been subjected to CPD; for comparison, to date, CPD has been reported for substantially smaller regions of the genomes of poliovirus or HIV-1 (∼23% and 4% of the proteincoding sequence, respectively) or influenza virus (three segments out of eight) (5,10,11,13).…”

Section: Discussionmentioning

confidence: 93%

“…Because amino acid coding is unaffected, CPD strains provide the same repertoire of epitopes for inducing cellular and humoral immunity as the WT pathogen. Recently, the CPD approach has been used successfully to attenuate poliovirus, influenza A virus, Streptococcus pneumonia, and HIV type 1 (5,(10)(11)(12)(13).…”

mentioning

confidence: 99%

Attenuation of human respiratory syncytial virus by genome-scale codon-pair deoptimization

Nouën

Brock

Luongo

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

117

130

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Human respiratory syncytial virus (RSV) is the most important viral agent of serious pediatric respiratory-tract disease worldwide. A vaccine or generally effective antiviral drug is not yet available. We designed new live attenuated RSV vaccine candidates by codon-pair deoptimization (CPD). Specifically, viral ORFs were recoded by rearranging existing synonymous codons to increase the content of underrepresented codon pairs. Amino acid coding was completely unchanged. Four CPD RSV genomes were designed in which the indicated ORFs were recoded: Min A (NS1, NS2, N, P, M, and SH), Min B (G and F), Min L (L), and Min FLC (all ORFs except M2-1 and M2-2). Surprisingly, the recombinant CPD viruses were temperature-sensitive for replication in vitro (level of sensitivity: Min FLC > Min L > Min B > Min A). All of the CPD mutants grew less efficiently in vitro than recombinant wild-type (WT) RSV, even at the typically permissive temperature of 32°C (growth efficiency: WT > Min L > Min A > Min FLC > Min B). CPD of the ORFs for the G and F surface glycoproteins provided the greatest restrictive effect. The CPD viruses exhibited a range of restriction in mice and African green monkeys comparable with that of two attenuated RSV strains presently in clinical trials. This study provided a new type of attenuated RSV and showed that CPD can rapidly generate vaccine candidates against nonsegmented negativestrand RNA viruses, a large and expanding group that includes numerous pathogens of humans and animals.negative strand RNA virus | pneumovirus | live attenuated vaccine H uman respiratory syncytial virus (RSV) is a negative-strand RNA virus of genus Pneumovirus, family Paramyxoviridae. RSV is the most important viral agent of serious respiratory tract illness in infants and children worldwide (1-3). Worldwide, nearly all children are infected by RSV at least once by the age of 2 y. RSV disease ranges from rhinitis to bronchiolitis or pneumonia. The RSV genome consists of a single-stranded negative-sense 15.2-kb RNA and has 10 genes in the order 3′ NS1-NS2-N-P-M-SH-F-G-M2-L 5′ (for a review, see ref. 4). The M2 gene encodes two separate proteins, M2-1 and M2-2, from overlapping ORFs.RSV vaccines and new antiviral drugs are in preclinical and clinical development; however, no RSV vaccines or antiviral drugs suitable for routine use are commercially available. The goal of the present study was to design and generate new vaccine candidates for RSV using the recently described strategy of codon-pair deoptimization (CPD) (5). By this strategy, one or more ORFs in a virus or other pathogen are recoded by rearranging existing synonymous codons so as to increase the presence of underrepresented codon pairs within the ORF. CPD can be done without changing codon use although, in the present study, codon use was occasionally changed slightly when we manually edited the sequence to remove features such as long homooligomers. Amino acid coding was completely unaffected, and nontranslated genome regions were unchanged. A major effect of CPD is...

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“…However, alternative mechanisms involving the induction of innate immunity as a result of changing dinucleotide frequency have been proposed by other authors (23). Furthermore, codon pair bias deoptimization of other viruses, including respiratory syncytial virus (RSV) (24), human immunodeficiency virus type 1 (25), dengue virus (26), and vesicular stomatitis virus (27), have also led to attenuated strains. All these reports indicate that codon and codon pair bias deoptimization can also be a useful tool to develop attenuated vaccine candidates against RNA viruses.…”

Section: Foot-and-mouth Disease (Fmd) Ismentioning

confidence: 99%

Synonymous Deoptimization of Foot-and-Mouth Disease Virus Causes Attenuation In Vivo while Inducing a Strong Neutralizing Antibody Response

Segundo

Medina

Ramírez-Medina

et al. 2016

J Virol

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Codon bias deoptimization has been previously used to successfully attenuate human pathogens, including poliovirus, respiratory syncytial virus, and influenza virus. We have applied a similar technology to deoptimize the capsid-coding region (P1) of foot-andmouth disease virus (FMDV). Despite the introduction of 489 nucleotide changes (19%), synonymous deoptimization of the P1 region rendered a viable FMDV progeny. The resulting strain was stable and reached cell culture titers similar to those obtained for wild-type (WT) virus, but at reduced specific infectivity. Studies in mice showed that 100% of animals inoculated with the FMDV A12 P1 deoptimized mutant (A12-P1 deopt) survived, even when the animals were infected at doses 100 times higher than the dose required to cause death by WT virus. All mice inoculated with the A12-P1 deopt mutant developed a strong antibody response and were protected against subsequent lethal challenge with WT virus at 21 days postinoculation. Remarkably, the vaccine safety margin was at least 1,000-fold higher for A12-P1 deopt than for WT virus. Similar patterns of attenuation were observed in swine, in which animals inoculated with A12-P1 deopt virus did not develop clinical disease until doses reached 1,000 to 10,000 times the dose required to cause severe disease in 2 days with WT A12. Consistently, high levels of antibody titers were induced, even at the lowest dose tested. These results highlight the potential use of synonymous codon pair deoptimization as a strategy to safely attenuate FMDV and further develop live attenuated vaccine candidates to control such a feared livestock disease. Our work demonstrates that newly developed codon pair bias deoptimization technologies can be applied to FMD virus to obtain attenuated strains with potential for further development as novel live attenuated vaccine candidates that may rapidly control disease without reverting to virulence.

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Changes in codon-pair bias of human immunodeficiency virus type 1 have profound effects on virus replication in cell culture

Cited by 79 publications

References 38 publications

Attenuation of Tick-Borne Encephalitis Virus Using Large-Scale Random Codon Re-encoding

Attenuation of Tick-Borne Encephalitis Virus Using Large-Scale Random Codon Re-encoding

Attenuation of human respiratory syncytial virus by genome-scale codon-pair deoptimization

Synonymous Deoptimization of Foot-and-Mouth Disease Virus Causes Attenuation In Vivo while Inducing a Strong Neutralizing Antibody Response

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