David Tapia

Infectious pancreatic necrosis (IPN) is one of the most economically important viral diseases affecting salmonid aquaculture worldwide. Resistance to infectious pancreatic necrosis virus (IPNV) has been widely studied in rainbow trout (Oncorhynchus mykiss) by using SNP-based approaches. For instance, genome-wide association studies have led to the identification of moderate- to major-effect quantitative trait loci (QTL) controlling the trait. However, causative mutations underlying IPNV resistance in rainbow trout remains poorly understood. The potential contribution of structural variants (SVs) to the genetic architecture of resistance has received little attention despite their recognized role in shaping phenotypic variation and complex traits. In this study, we used whole-genome sequencing combined with a multi-tool SV detection approach to identify structural variants associated with IPNV-resistant and susceptible rainbow trout. A total of 2,564 SVs (2,358 deletions, 206 insertions) were identified as highly associated between resistant and susceptible individuals. Functional annotation showed that twelve of these variants overlapped genes with known immune-related functions, suggesting that they may contribute to variation in host antiviral responses. These findings provide further evidence that structural variation may contribute to resistance-related phenotypes in rainbow trout. Further incorporation of SVs into genomic analyses may improve the resolution of association studies and support the development of more comprehensive genomic selection strategies for disease resistance in aquaculture breeding programs.

Introduction: Influenza A virus (IAV) is a zoonotic pathogen with pandemic potential that infects a wide range of species, including companion animals. Although surveillance efforts have primarily focused on North America, Europe and Asia, data from South America remain scarce. This study evaluated the molecular and serological evidence of IAV circulation in dogs and cats from shelters and multi‐pet households in central Chile. Methods: Between June and November 2020, oropharyngeal swabs and serum samples were collected from dogs and cats in shelters and multi‐pet households in central Chile. Samples were analysed by RT‐qPCR, NP‐ELISA and hemagglutination inhibition assay. Results: IAV was detected by RT‐qPCR in 3.2% (11/342) of dogs (95% CI: 1.3%–5.1%) and 5.8% (4/69) of cats (95% CI: 0.3%–11.3%). Serological analysis revealed IAV seropositivity in 55.5% (96/173) of dogs (95% CI: 48.1%–62.9%) and 50.0% (10/20) of cats (95% CI: 28.1%–71.9%). Additionally, pdmH1N1 antibodies were detected in 26 animals (25.7%; 95% CI: 17.2%–34.2%) out of 101 NP‐ELISA‐positive serum samples, with higher median titres for cats (median = 160) compared to dogs (median = 20). Low‐level antibody titres against Canine/H3N2 (range = 10–20) were identified in three dogs (3.0%; 95% CI: 0.0%–6.3%), whereas no antibodies were detected against Canine/H3N8 or Avian/H3N6. No significant associations were observed between seropositivity and animal age, sex, origin or area. Conclusions: This study presents the first report of IAV detection in cats in South America and highlights a high level of IAV exposure among companion animals in central Chile. These findings underscore the importance of including pets in IAV surveillance efforts under a One Health approach and highlight the need for expanded monitoring and genetic characterization of circulating strains to assess zoonotic risk.

This study presents a comprehensive molecular and epidemiological characterisation of infectious pancreatic necrosis virus (IPNV) in Chilean salmon aquaculture. Between 2015 and 2016, 26 sampling events were conducted in freshwater and seawater farms spanning a broad latitudinal gradient (30.3° S to 52.6° S). Three diagnostic methods were used: Quantitative real‐time Polymerase Chain Reaction (PCR) (qRT‐PCR) (targeting VP1 and VP2 protein coding genes), nested PCR and virus isolation in CHSE‐214 cells. In addition, a 523‐bp VP2 gene fragment was sequenced directly from samples. These approaches were employed to assess detection sensitivity and to explore IPNV genogroup distribution and persistence. Nested PCR and viral isolation detected IPNV in 50 of 53 samples, outperforming qRT‐PCR, which detected only 39. Phylogenetic analysis of the 523‐bp VP2 gene fragment classified the isolates into two genogroups—5 ( Salmo salar ) and 1 ( Oncorhynchus spp.), confirming host‐specific associations. Identical or near‐identical sequences were identified in geographically distant farms and temporally spaced samples, suggesting persistent isolates and potential long‐distance spread, likely via egg transfers or fish movement. The most severe mortality event (> 125,000 fish) occurred during a genogroup 1 outbreak (Isla del Rey, GMTS, O. kisutch ), followed by genogroup 5 outbreaks documented in Molco Alto (PMLC, S. salar ) and Chayahue ( S. salar ). Although less frequently detected, genogroup 1 was associated with higher virulence, particularly in coho salmon. These findings highlight the need of integrated diagnostic strategies, genogroup‐specific monitoring and strengthened biosecurity to mitigate the impact of IPNV in Chilean salmon farming.

Backyard production systems (BPSs) are common in Chile and play an important role in food access and local trade. However, these systems often lack basic biosecurity and disease prevention practices, which increases the risk of disease spreading. In this study, we evaluated the presence of two major avian respiratory viruses, infectious bronchitis virus (IBV) and infectious laryngotracheitis virus (ILTV), in BPSs located near wetlands in central Chile. These areas are known as the country’s main poultry production zones. We collected 449 poultry serum samples from 88 BPSs and performed serological tests using ELISA. Additionally, we analyzed 250 poultry tracheal swabs from 31 BPSs using qPCR. The results showed high seroprevalence levels: 95.5% of BPSs tested positive for IBV and 85.2% for ILTV. At the animal level, 82.2% were positive for IBV and 57.2% for ILTV. Most birds had antibodies to both viruses. However, active infections were less frequent, with 4.3% of tracheal swabs testing positive for IBV and 14.1% for ILTV during 2021 and 0.6% and 3.8% for IBV and ILTV, respectively, during 2024. This is the first serological and molecular evidence of IBV and ILTV circulation in backyard poultry in central Chile. Since this region includes most of the country’s poultry industry, these findings raise concern about the risk of virus transmission to commercial farms. The high circulation rates suggest that backyard poultry could act as reservoirs and may contribute to decreased productivity. Our results highlight the need for improved disease surveillance and enhancement of biosecurity in BPSs in Chile.

Backyard production systems (BPS) are common in Chile and play an important role in food access and local trade. However, these systems often lack basic biosecurity and disease prevention practices, which increases the risk of disease spreading. In this study, we evaluated the presence of two major avian respiratory viruses, infectious bronchitis virus (IBV) and infectious laryngotracheitis virus (ILTV), in BPS located near wetlands in central Chile. These areas are known as the country’s main poultry production zones. We collected 449 poultry serum samples from 88 BPS and performed serological tests using ELISA. Additionally, we analyzed 250 poultry tracheal swabs from 31 BPS using qPCR. The results showed high seroprevalence levels: 95.5% of BPS tested positive for IBV and 85.2% for ILTV. At the animal level, 82.2% were positive for IBV and 57.2% for ILTV. Most birds had antibodies to both viruses. However, active infections were less frequent, with 4.3% of tracheal swabs testing positive for IBV and 14.1% for ILTV during 2021, and 0.6% and 3.8% for IBV and ILTV, respectively, during 2024. This is the first serological and molecular evidence of IBV and ILTV circulation in backyard poultry in central Chile. Since this region includes most of the country’s poultry industry, these findings raise concern about the risk of virus transmission to commercial farms. The high circulation rates suggest that backyard poultry could act as reservoirs and may contribute to decreased productivity. Our results highlight the need for improved disease surveillance and enhancement of biosecurity in BPS in Chile.

Salmonids play vital ecological and economic roles and have been introduced to many regions worldwide. When not held captive in farms, they can be classified as free‐living salmonids, a group that includes native, feral, and naturalized populations, as well as fish that have escaped from aquaculture facilities. Compared to farmed salmonids, knowledge of viral infections affecting free‐living populations remains limited, creating a significant gap in understanding the ecological impacts of interactions between aquaculture and natural ecosystems. To address this knowledge gap, we reviewed global reports and summarized the information on viruses infecting free‐living salmonids. Most viral detections reported in the reviewed studies were found in native wild salmonids, with escaped salmon ranking second in detection frequency. Atlantic salmon (Salmo salar), sockeye salmon (Oncorhynchus nerka), and brown trout (Salmo trutta) were the most commonly reported host species. The most frequently reported viruses included infectious hematopoietic necrosis virus (IHNV), piscine orthoreovirus (PRV), infectious pancreatic necrosis virus (IPNV), and infectious salmon anemia virus (ISAV). Evidence from some studies suggests a bidirectional transmission of viruses between farmed and free‐living salmonids, highlighting the complex interplay between these groups. Beyond their potential role as reservoirs for aquaculture pathogens, free‐living salmonids may also be negatively impacted by viruses from farmed fish, contributing to the decline of native populations. By enhancing our understanding of the prevalence and impacts of viral infections in free‐living salmonids, we can inform future research and management strategies to protect the health of both farmed and wild fish populations.

The IPN virus (IPNV) causes a highly contagious disease that affects farmed salmonids. IPNV isolates have been phylogenetically classified into seven genogroups, of which two are present in Chile, genogroups 1 and 5. This study aimed to compare the transcriptomic response of rainbow trout fry challenged with two Chilean isolates of IPNV, RTTX (genogroup 1), and ALKA (genogroup 5). Tissue samples from challenged individuals and controls were taken at 1, 7, and 20 days post-challenge and analyzed by RNA-Seq. The results revealed that infection with RTTX elicited a greater modulation of the trout transcriptome compared to ALKA infection, generating a greater number of highly differentially expressed genes in relation to the control fish. Gene Ontology enrichment indicated that functions related to the inflammatory and immune responses were modulated in fish challenged with both isolates throughout the trial, but with different regulation patterns. On day 1 post challenge, these functions were activated in those challenged with ALKA, but suppressed in RTTX-challenged fish. These results suggest that rainbow trout exhibit a differential transcriptomic response to infection with the two genetically distinct IPNV isolates, especially at early times post-infection.

Infectious pancreatic necrosis virus (IPNV) is one of the most pervasive pathogens in aquaculture worldwide. It causes a highly contagious disease in salmonids that has a significant economic impact in almost every country where salmonid fish are farmed. For decades IPNV studies have focussed on the molecular characterisation of isolates collected from around the world and the discovery of molecular markers associated with virulence and pathogenicity. The great success of selective breeding for resistance to IPNV has caused special emphasis to be put on the immune response of salmon genetically resistant/susceptible to IPNV. In this work, we review the classification of IPNV, summarise virulence markers and add recent findings about the molecular epidemiology and worldwide distribution of the virus. We also review genetic improvements for IPNV resistance, the kinetics of the immune response to IPNV and the transcriptomic response of salmonids, made possible through the use high‐throughput technologies.