Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Strains Circulating in East African Smallholder Pig Farms

Amimo, Joshua O.; Machuka, Eunice; Abworo, Edward Okoth; Vlasova, Anastasia N.; Pellé, Roger

doi:10.3390/v12111262

Cited by 8 publications

(7 citation statements)

References 53 publications

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“…MHC I processing (this tool combines predictors of proteasomal processing, TAP transport and MHC binding to produce an overall score for each peptides potential of being a T cell epitope). Based on this overall score, six best epitopes were selected for further evaluation (Zhang et al 2015 ; Amimo et al 2020 ). The degree of similarity between the epitope and the target (i.e.…”

Section: Resultsmentioning

confidence: 99%

“…This was confirmed by Clustal omega, an algorithm of multiple amino acid sequence alignment available at ( http://www.ebi.ac.uk/Tools/msa/Clustalo ). BLAST search was used to assemble the sequences of antigen reported for different serotypes (Zhang et al 2015 ; Amimo et al 2020 ). The resulting consensus sequence would characterize all of the virus’s major serotypes.…”

Section: Methodsmentioning

confidence: 99%

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Computational Design and Analysis of a Multi-epitope Against Influenza A virus

Rostaminia

Aghaei

Farahmand

et al. 2021

Int J Pept Res Ther

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Influenza A viruses are among the most studied viruses, however no effective prevention against influenza infection has been developed. So, designing an effective vaccine against Influenza A virus is a critical issue in the field of medical biotechnology. For this reason, to combat this disease, we have designed a novel multi-epitope vaccine candidate based on the several conserved and potential linear B-cell and T-cell binding epitopes by using the in silico approach. This vaccine consists of an ER signal conserved sequence, the PADRE conserved epitope and two conserved epitopes of Influenza matrix protein 2. T-cell binding epitopes from Matrix protein 2 were predicted by in silico tools of epitope prediction. The selected epitopes were joined by flexible linkers and physicochemical properties, toxicity, and allergenecity were investigated. The designed vaccine was antigenic, immunogenic, and non-allergenic with suitable physicochemical properties and has higher solubility. The final multi-epitope construct was modeled, confirmed by different programs and the molecular interactions with immune receptors were considered. The molecular docking assay indicated the interactions with immune-stimulatory toll-like receptor 3 (TLR3) and major histocompatibility complex class I (MHCI). The HADDOCK and H DOCK servers were used to make docking analysis, respectively. The docking analysis indicated a strong and stable binding interaction between the vaccine construct with major histocompatibility complex (MHC) class I and toll-like receptor 3. Overall, the findings suggest that the current vaccine may be a promising vaccine to prevent Influenza infection.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Computational Design and Analysis of a Multi-epitope Against Influenza A virus

Rostaminia

Aghaei

Farahmand

et al. 2021

Int J Pept Res Ther

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“…In members of the genus Mamastrovirus , experimental evidence has previously inferred the presence of a VPg linked to infectious viral RNA, and in human astrovirus, this has been shown to be essential for in vitro infectivity [ 36 , 45 , 46 ]. In this study we identified a conserved polyprotein within the ORF1ab of USA PoAstV3 strains spanning between previously described cleavage sites encompassing the putative human astrovirus VPg.…”

Section: Discussionmentioning

confidence: 99%

“…In addition to the PoAstV3 sequences obtained in this study, 14 more PoAstV3 strains from the USA (GenBank accession number: JX556691, KY940545, MT394895, MT394896), Europe (GenBank accession number: MK962341, MK962342, KY073229, KY073231, KY073232), and Japan (GenBank accession number: LC201595, LC201596, LC201597, LC201598, LC20159) were retrieved to compare intrinsic PoAstV3 features. Mamastrovirus 3 GER/L00919-K17/2014 (LT898424), which was previously identified in other studies to cluster closely to PoAstV3 strains was also included in the analysis [ 45 , 46 ]. All sequences were retrieved from GenBank.…”

Section: Methodsmentioning

confidence: 99%

Comparative Analysis of Novel Strains of Porcine Astrovirus Type 3 in the USA

Ferreyra

Harmon

Bradner

et al. 2021

Viruses

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Porcine astrovirus type 3 (PoAstV3) has been previously identified as a cause of polioencephalomyelitis in swine and continues to cause disease in the US swine industry. Herein, we describe the characterization of both untranslated regions, frameshifting signal, putative genome-linked virus protein (VPg) and conserved antigenic epitopes of several novel PoAstV3 genomes. Twenty complete coding sequences (CDS) were obtained from 32 diagnostic cases originating from 11 individual farms/systems sharing a nucleotide (amino acid) percent identity of 89.74–100% (94.79–100%), 91.9–100% (96.3–100%) and 90.71–100% (93.51–100%) for ORF1a, ORF1ab and ORF2, respectively. Our results indicate that the 5′UTR of PoAstV3 is highly conserved highlighting the importance of this region in translation initiation while their 3′UTR is moderately conserved among strains, presenting alternative configurations including multiple putative protein binding sites and pseudoknots. Moreover, two predicted conserved antigenic epitopes were identified matching the 3′ termini of VP27 of PoAstV3 USA strains. These epitopes may aid in the design and development of vaccine components and diagnostic assays useful to control outbreaks of PoAstV3-associated CNS disease. In conclusion, this is the first analysis predicting the structure of important regulatory motifs of neurotropic mamastroviruses, which differ from those previously described in human astroviruses.

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“…PAstV2 and PAstV4 were detected from the blood and fecal samples, causing viremia and circulate in pig herds (19). It is worth noting that genetic recombination events among PAstVs or other astrovirus species were frequently reported, which may contribute to the genetic diversity and evolution of PAstVs (19)(20)(21)(22)(23)(24). Multiple genotypes of PAstV coinfections will further accelerate the genetic variation of this virus and bring challenges to the monitoring of PAstVs.…”

Section: Introductionmentioning

confidence: 99%

Establishment of a Multiplex RT-PCR Method for the Detection of Five Known Genotypes of Porcine Astroviruses

et al. 2021

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Porcine astroviruses (PAstVs) are prevalent in pigs worldwide, and five genotypes have been reported to circulate in China. However, little is known about the coinfection status of PAstVs. For differential and simultaneous diagnoses of these five genotypes of PAstVs, a multiplex RT-PCR method was established on the basis of the ORF2 gene of type 1 PAstV, and the ORF1ab genes of type two to five PAstVs. This quintuple PCR system was developed through optimization of multiplex PCR and detection sensitivity and specificity. The results showed that this multiplex RT-PCR method could specifically detect all the five PAstV genotypes without cross-reaction to any other major viruses circulating in Chinese pig farms. The detection limit of this method was as low as 10 pg of standard plasmids of each PAstV genotype. In addition, a total of 275 fecal samples collected from different districts of Guangxi, China, between April 2019 and November 2020, were tested by this newly established multiplex RT-PCR. Moreover, the sensitivity and specificity of monoplex and multiplex RT-PCR methods were compared by detecting the same set of clinical positive samples. The results revealed that PAstV1 (31/275), PAstV2 (49/275), PAstV3 (36/275), PAstV4 (41/275), and PAstV5 (22/275) were all detected, and dual (PAstV1+PAstV2, PAstV1+PAstV3, PAstV2+PAstV3, PAstV2+PAstV4, PAstV3+PAstV4, and PAstV4+PAstV5) or triple genotypes (PAstV1+PAstV2+PAstV3 and PAstV2+PAstV3+PAstV4) of coinfections were also unveiled in this study. The detection result of multiplex PCR was consistent with that of monoplex PCR. Compared with monoplex PCR, this multiplex PCR method showed obvious advantages such as time and cost efficiency and high sensitivity and specificity. This multiplex RT-PCR method offered a valuable tool for the rapid and accurate detection of PAstV genotypes circulating in pig herds and will facilitate the surveillance of PAstV coinfection status.

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Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Strains Circulating in East African Smallholder Pig Farms

Cited by 8 publications

References 53 publications

Computational Design and Analysis of a Multi-epitope Against Influenza A virus

Computational Design and Analysis of a Multi-epitope Against Influenza A virus

Comparative Analysis of Novel Strains of Porcine Astrovirus Type 3 in the USA

Establishment of a Multiplex RT-PCR Method for the Detection of Five Known Genotypes of Porcine Astroviruses

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