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The productivity of potato in Colombia is far from its full potential mainly due to the high prevalence of viruses in seed-tubers. To gain a deeper insight into the health status of S. tuberosum and S. phureja seed-tubers used by farmers in the province of Antioquia (Colombia), we have investigated the prevalence of PVY, PVV, PVS, PVX, PRLV, PYVV, PMTV and PVB in certified and uncertified seed lots. The presence of viruses was determined by RT-qPCR, RT-PCR, Sanger and High-Throughput Sequencing (HTS). The eight viruses were detected in at least one lot sample of S. tuberosum or S. phureja and for most of the viruses, no significant differences in prevalence were observed between certified and uncertified seed-tuber lots; however, the number of co-infecting viruses and viral loads seem to be lower in the certified seeds. These results confirm the urgent need to improve current seed-tuber production standards in Colombia. [ABSTRACT FROM AUTHOR]

Livestock plays a crucial role in ensuring food security and driving the global economy. However, viral infections can have far-reaching consequences beyond economic productivity, affecting the health of cattle, as well as posing risks to human health and other animals. Identifying viruses present in fecal samples, a primary route of pathogen transmission, is essential for developing effective prevention, control, and surveillance strategies. Viral metagenomic approaches offer a broader perspective and hold great potential for detecting previously unknown viruses or uncovering previously undescribed agents. Ubaté Province is Colombia's dairy capital and a key center for livestock production in the country. Therefore, the purpose of this study was to characterize viral communities in fecal samples from cattle in this region. A total of 42 samples were collected from three municipalities in Ubaté Province, located in central Colombia, using a convenient non-probabilistic sampling method. We utilized metagenomic sequencing with Oxford Nanopore Technologies (ONT), combined with diversity and phylogenetic analysis. The findings revealed a consistent and stable viral composition across the municipalities, primarily comprising members of the Picornaviridae family. At the species level, the most frequent viruses were Enterovirus E (EVE) and Bovine Astrovirus (BoAstV). Significantly, this study reported, for the first time in Colombia, the presence of viruses with veterinary importance occurring at notable frequencies: EVE (59%), Bovine Kobuvirus (BKV) (52%), and BoAstV (19%). Additionally, the study confirmed the existence of Circular replicase-encoding single-stranded (CRESS) Virus in animal feces. These sequences were phylogenetically grouped with samples obtained from Asia and Latin America, underscoring the importance of having adequate representation across the continent. The virome of bovine feces in Ubaté Province is characterized by the predominance of potentially pathogenic viruses such as BoAstV and EVE that have been reported with substantial frequency and quantities. Several of these viruses were identified in Colombia for the first time. This study showcases the utility of using metagenomic sequencing techniques in epidemiological surveillance. It also paves the way for further research on the influence of these agents on bovine health and their frecuency across the country. [Display omitted] • First report of Bovine Astrovirus, Bovine Kobuvirus (BKV), and Enterovirus E in Colombian cattle. • A consistent and stable viral composition across sites. • BKV sequence phylogenetically clustered with Brazilian sequences. [ABSTRACT FROM AUTHOR]

Colombia is the largest worldwide producer of Cape gooseberry (Physalis peruviana L.), which is an exotic tropical fruit with increasing high demand in international markets. Unfortunately, the rapid expansion of this crop has occurred without implementing adequate surveillance measures that enforce the use of healthy planting material for the establishment of new crops. This study investigated the prevalence of viruses in P. peruviana using seeds, plantlets, and adult plants with or without symptoms typical of viral infection in the province of Antioquia. Detection of viruses by RT-qPCR revealed widespread infection with potato virus Y (PVY), potato virus X (PVX), potato virus S (PVS), Cape gooseberry ilarvirus 1 (CGIV-1), and Physalis vein necrosis virus (PhyVNV), a proposed new nepovirus species. Co-infections were also common in all samples tested. Further high-throughput sequencing analysis confirmed the presence of most of these viruses and revealed the presence of a new torradovirus (Physalis torrado virus, PhyTV), a new potexvirus (Physalis virus X, PhyVX), and a divergent tobacco mosaic virus isolate. These results reveal that the P. peruviana virome is largely unexplored, and urgent measures should be implemented to certify the health status of planting material, and crops. • Colombia is the largest worldwide producer of Cape gooseberry. •Virus diseases are one the main limitations of Cape gooseberry. •Detection of viruses by RT-qPCR showed infection by PVY, PVX, PVS, CGIV-1 and PhyVNV. •HTS analysis revealed the presence of three putative new virus species in Cape gooseberry. [ABSTRACT FROM AUTHOR]

Ticks are a group of obligate blood-sucking ectoparasites that play a critical role in transmitting several important zoonotic pathogens that can infect animals and humans. Viruses are part of the tick microbiome and are involved in the transmission of important diseases. Furthermore, the little information on these as etiological agents of zoonoses suggests the need to study these microorganisms. For this reason, in this study, we sought to characterize the virome in Rhipicephalus microplus, Dermacentor nitens, and Rhipicephalus sanguineus s.l., which were collected from different domestic animals in Antioquia, Colombia. RNA sequencing was used for virome characterization in these three tick species, using RNA-dependent polymerase as a marker gene. Forty-eight sequences corresponding to 14 different viruses were identified, some of which were previously identified in the tick's virome. Overall, these data indicate that ticks from domestic animals in cattle farms harbor a wide viral diversity at the local scale. Thus, the metatranscriptomic approach provides important baseline information for monitoring the tick virome and to develop future studies on their biology, host-virus interactions, host range, worldwide distribution, and finally, their potential role as emerging vector-borne agents., (Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.)

High-throughput sequencing methods are becoming an essential tool in disease management programs. Unfortunately, the implementation of these techniques in developing countries can be hindered by a limited availability of well-trained bioinformaticians and/or high-performance computing centers that can process and analyze the data with reliability and speed. In this work we present a stand-alone plant virus detection pipeline (PVDP) optimized for the surveillance of potato viruses but also useful in other plant hosts. This open source pipeline runs under Python and includes a curated database of plant viruses in addition to an R script for presenting results as a user-friendly html report. The pipeline scripts are freely-available in GitHub, can be executed locally under LINUX, macOS or Windows, and does not require data submission to third-parties or access to high performance computing centers. The pipeline was calibrated using twelve previously obtained potato datasets and validated with new samples collected in Solanum tuberosum and S. phureja fields from eastern Antioquia (Colombia). The plant virus detection pipeline revealed high infection levels of PVY (1678.4 RPM) and lower levels of PMTV (1.2–2 RPM) infecting S. tuberosum. In S. phureja, the pipeline detected high infection levels of PVX, PVS and PVV (RPM > 2044) and lower levels of PMTV, PVY, and PYVV (RPM <82.1). Results also suggest the probable infection of S. phureja by pepino mosaic virus (PepMV) and by a putative unidentified potyvirus. Hopefully, this plant virus detection pipeline will facilitate the implementation of HTS methods in developing countries, such as Colombia, where there is an urgent need to improve the current plant and seed health standards. • We present a stand-alone plant virus detection pipeline (PVDP). • The pipeline scripts are freely-available at GitHub. • PVDP validation revealed high infection levels of PVY in S. tuberosum. • PVDP validation detected high infection levels of PVX, PVS and PVV in S. phureja. [ABSTRACT FROM AUTHOR]

Solanum quitoense Lam. is a solanaceous fruit shrub native to South America that produces a tomato-sized fruit popular in the preparation of fresh juice, fermented beverages, nectars, ice cream and fruit concentrates. Unfortunately, this crop is highly susceptible to insects, nematodes, fungi, oomycetes, bacteria, and a wide range of viral diseases. With the arrival of High-Throughput Sequencing (HTS) methods, our understanding of the viruses affecting this crop has increased at a steady pace. In this work, we investigate the virome of S. quitoense in Antioquia (Colombia) using the Illumina HTS platform and analyze the effect of using ribosomal RNA depleted total RNA and dsRNA templates. Our results suggest that total RNA outputs a larger amount of viral sequences but fails to detect viruses present at lower loads. Both templates allowed detection and assembly of Potato leafroll virus (PLRV), Potato yellow vein virus (PYVV), and Potato mop-top virus (PMTV); however, the dsRNA input was more sensitive for detection of Potato virus Y (PVY), Potato virus X (PVX), Potato virus S (PVS), and Bell pepper alphaendornavirus (BPEV). These results suggest that the combination of different RNA inputs in HTS studies of plant viromes can give a more complete picture of the real virus diversity. • Different RNA inputs in HTS studies of plant viromes improve virus detection. • Total RNA gives higher coverage for viruses present at high levels. • dsRNA allows detection of viruses present a low titers and persistent viruses. • Using HTS, seven RNA viruses were found in S. quitoense in Colombia. [ABSTRACT FROM AUTHOR]

Ticks (Ixodida) are hematophagous ectoparasites that harbor and transmit diverse species of viruses, some of which cause serious diseases with worldwide veterinary and human health consequences. Rhipicephalus microplus is an important cattle tick in Colombia, where it causes significant economic losses. Despite the importance of this tick, its viral profile is unknown. RNA sequencing was used in this study as a surveillance method for virus detection in R. microplus. Most of the viral origin contigs were assigned to two putative viruses: one chuvirus (Wuhan tick virus 2) and one phlebovirus-like (Lihan tick virus). In addition, viral contigs corresponding to two jingmenviruses previously reported in R. microplus from China and Brazil were detected, as well as a novel putative tymovirus, named here as Antioquia tymovirus-like 1 (ATV-like 1). The presence of some of these viruses across numerous regions in the world could have several explanations, including i) a long-term association between those viruses and R. microplus and ii) a consequence of livestock historical trade. Our results shed new light on the virus diversity of this tick species and provide a basis for further studies on the evolutionary history and pathogenic potential of these interesting viruses., (Copyright © 2020 Elsevier GmbH. All rights reserved.)