Case Report: First Report and Phylogenetic Analysis of Porcine Astroviruses in Chile

Flores, Carlos; Ariyama, Naomi; Bennett, Benjamín; Mena, Juan; Verdugo, Claudio; Mor, Sunil K.; Brito, Bárbara; Ramírez-Toloza, Galia; Neira, Víctor

doi:10.3389/fvets.2021.764837

Cited by 6 publications

(4 citation statements)

References 40 publications

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“…Importantly, while short-read sequencing approaches did not allow us to accurately determine mixed infections (i.e., different strains), this is possible when using long-read sequencing [ 39 ]. Targeted approaches were also applied for other RNA viruses (e.g., astrovirus [ 18 ]) and DNA viruses, including PCV2 and PCV3 [ 16 ]. Whenever a broader screening is needed, metagenomics could also be applied.…”

Section: Discussionmentioning

confidence: 99%

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Successful Whole Genome Nanopore Sequencing of Swine Influenza A Virus (swIAV) Directly from Oral Fluids Collected in Polish Pig Herds

Vereecke

Woźniak

Pauwels³

et al. 2023

Viruses

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Influenza A virus (IAV) is a single-stranded, negative-sense RNA virus and a common cause of seasonal flu in humans. Its genome comprises eight RNA segments that facilitate reassortment, resulting in a great variety of IAV strains. To study these processes, the genetic code of each segment should be unraveled. Fortunately, new third-generation sequencing approaches allow for cost-efficient sequencing of IAV segments. Sequencing success depends on various factors, including proper sample storage and processing. Hence, this work focused on the effect of storage of oral fluids and swIAV sequencing. Oral fluids (n = 13) from 2017 were stored at −22 °C and later transferred to −80 °C. Other samples (n = 21) were immediately stored at −80 °C. A reverse transcription quantitative PCR (RT-qPCR) pre- and post-storage was conducted to assess IAV viral loads. Next, samples were subjected to two IAV long-read nanopore sequencing methods to evaluate success in this complex matrix. A significant storage-associated loss of swIAV loads was observed. Still, a total of 17 complete and 6 near-complete Polish swIAV genomes were obtained. Genotype T, (H1avN2, seven herds), P (H1N1pdm09, two herds), U (H1avN1, three herds), and A (H1avN1, 1 herd) were circulated on Polish farms. In conclusion, oral fluids can be used for long-read swIAV sequencing when considering appropriate storage and segment amplification protocols, which allows us to monitor swIAV in an animal-friendly and cost-efficient manner.

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Section: Discussionmentioning

confidence: 99%

“…Targeted NGS has been performed for PRRSV, porcine astrovirus, and PCV3 with oral fluids [ 16 , 17 , 18 , 19 ]. With the availability of third-generation sequencing technologies (e.g., ONT), swIAV seems an ideal subject for targeted WGS from oral fluid samples.…”

Section: Introductionmentioning

confidence: 99%

Successful Whole Genome Nanopore Sequencing of Swine Influenza A Virus (swIAV) Directly from Oral Fluids Collected in Polish Pig Herds

Vereecke

Woźniak

Pauwels³

et al. 2023

Viruses

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“…In addition, several other swine enteric viruses such as Porcine astrovirus (PAstV) [15][16][17][18][19][20], Porcine kobuvirus (PKoV) [16, [21][22][23][24], Porcine torovirus (PToV) [25][26][27][28][29], Mammalian orthoreovirus (MRV) [30][31][32][33][34] or Porcine mastadenovirus (PAdV) [1,[35][36][37] have been detected in pigs with diarrhoea worldwide (Table 1), although their etiological role remains unclear. These viruses are frequently identi ed in co-infections with CoVs and RVs [4,[38][39][40][41][42][43][44][45], and are also commonly detected in healthy animals [39,[46][47][48][49][50].…”

Section: Introductionmentioning

confidence: 99%

Detection and genetic characterization of enteric viruses in diarrhoea outbreaks from swine farms in Spain

Puente

Argüello

Cortey

et al. 2023

Preprint

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Background: The aim of this work was to study the prevalence and distribution of Porcine astrovirus (PAstV), Porcine kobuvirus (PKoV), Porcine torovirus (PToV), Mammalian orthoreovirus (MRV) and Porcine mastadenovirus (PAdV) as well as their association with widely recognized virus that cause diarrhoea in swine such as coronavirus (CoVs) and rotavirus (RVs) in diarrhoea outbreaks from Spanish swine farms. Furthermore, a selection of the viral strains was genetically characterized. Results: PAstV, PKoV, PToV, MRV and PAdV were frequently detected. Particularly, PAstV and PKoV were detected in almost 50% and 30% of the investigated farms, respectively, with an age-dependent distribution; PAstV was mainly detected in postweaning and fattening pigs, while PKoV was more frequent in sucking piglets. Viral co-infections were detected in almost half of the outbreaks, combining CoVs, RVs and the viruses studied, with a maximum of 5 different viral species reported in three investigated farms. Using a next generation sequencing approach, we obtained a total of 24 ARN viral genomes (>90% genome sequence), characterizing for first time the full genome of circulating strains of PAstV2, PAstV4, PAstV5 and PToV on Spanish farms. Phylogenetic analyses showed that PAstV, PKoV and PToV from Spanish swine farms clustered together with isolates of the same viral species from neighboring pig producing countries. Conclusions: Although further studies to evaluate the role of these enteric viruses in diarrhoea outbreaks are required, their wide distribution and frequent association in co-infections cannot be disregard. Hence, their inclusion into routine diagnostic panels for diarrhoea in swine should be considered.

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“…In addition, PAstV has also been associated with respiratory infections and more recently with polyencep halomyelitis, indicating its greater clinical importance (Boros et al, 2017;Padmanabhan et al, 2016;Xiao et al, 2013). PAstVs is reported to be endemic in several European, North and South American countries and less common in Asian countries (Flores et al, 2021;Kumthip et al, 2018). However, very few researchers have examined the relationship between gastrointestinal disease and PAstV globally (Fang et al, 2019;Kumthip et al, 2018;Rawal and Linhares, 2022).…”

Section: Introductionmentioning

confidence: 99%

Porcine Astrovirus Detection and Characterization in Healthy and Diarrheic Pigs from Haryana, India

Kaur,

Kumar,

Jindal

et al. 2023

IJAR

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Background: Porcine astrovirus (PAstV) is an emerging pathogen detected from the feces of both healthy and diarrheic pigs with limited studies comparing the presence of PAstV and diarrhea in pigs. PAstV has been reported worldwide with a few reports from India. In addition, there are limited reports on variation in the amino acid sequence of the ORF2 region, which codes for viral capsid protein. The present study was aimed to study the presence of PAstV, association with diarrhea in pigs of various age groups and its molecular characterization from Haryana, a northern Indian state. Methods: A total of 176 rectal swabs of pigs were collected from different parts of Haryana. The samples were screened for PAstV by RT-PCR of the partial ORF1b/ORF2 genomic region. The positive samples were characterized by molecular typing and phylogenetic analysis. Result: In the present study, PAstV was detected in pigs in 16.47% of fecal samples, including 21/127 (16.53%) diarrheic and 8/49 (16.32%) non-diarrheic. The results indicated that weaning piglets were more susceptible to PAstV infection followed by suckling piglets. The phylogenetic analysis revealed the circulation of PAstV4 and PAstV2 lineages in Haryana. The study revealed endemic presence of virus in the region with high genetic diversity among the PAstV strains, suggesting a wide range of heterogeneity.

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Case Report: First Report and Phylogenetic Analysis of Porcine Astroviruses in Chile

Cited by 6 publications

References 40 publications

Successful Whole Genome Nanopore Sequencing of Swine Influenza A Virus (swIAV) Directly from Oral Fluids Collected in Polish Pig Herds

Successful Whole Genome Nanopore Sequencing of Swine Influenza A Virus (swIAV) Directly from Oral Fluids Collected in Polish Pig Herds

Detection and genetic characterization of enteric viruses in diarrhoea outbreaks from swine farms in Spain

Porcine Astrovirus Detection and Characterization in Healthy and Diarrheic Pigs from Haryana, India

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