Influenza A virus (IAV) continuously threatens animal and public health globally, with swine serving as a crucial reservoir for viral reassortment and evolution. In Chile, H1N2 and H3N2 subtypes were introduced in the swine population before the H1N1 2009 pandemic, and the H1N1 was introduced from the H1N1pdm09 by successive reverse zoonotic events. Here, we report two novel introductions of IAV H3N2 human-origin in Chilean swine during 2023. Our study reveals a closer relationship between recent human seasonal H3N2 and novel swine strains. Interestingly, one strain maintains all the genes from the original human virus, but the other strain is already a reassortment of human H3N2 and an H1N2 previously observed on the farm. Observing global IAV sequences, a similar pattern was identified in the USA confirming the reverse zoonotic potential of current seasonal human H3N2 strains. These results highlight the importance of ongoing surveillance and reinforcing biosecurity in swine farms. These findings raise questions about their potential impact on viral dynamics in the swine population and public health, underscoring the need for further investigation into the origin and evolutionary dynamics of this emerging swine H3N2 reassortant virus.

Canine distemper virus (CDV) poses a significant threat to dogs and wildlife worldwide, and this study sought to provide an updated genetic characterization of CDV field strains in Chile during 2022-2023. We collected samples from 52 suspected CDV cases in domestic dogs and detected viral RNA through real-time RT-PCR in 28 dogs (54%). Factors like age and vaccination status were determinants of CDV positivity, with young adult and unvaccinated dogs facing a higher infection risk. We isolated CDV from positive samples in VeroDogSLAM cells. From these isolates and direct samples, we obtained sequences and estimated the phylogeny based on gene H. CDV isolates from nasal and conjunctival swabs exhibited cytopathic effects, and sequence analysis unveiled a substantial genetic diversity among the strains. Chilean CDV strains demonstrated a genetic distance to vaccine strains of approximately 10%, antigenic-change-related amino acid substitutions, and novel putative glycosylation sites. In the phylogeny, Chilean CDV field strains clustered into two lineages, Europe/South America-1 and North/South America-4, indicating the emergence of the North/South America-4 lineage in Chile and underscoring the genetic complexity of CDV in the country. Interestingly, certain Chilean viruses shared a close common ancestor with Brazilian and Peruvian viruses, suggesting viral spreading patterns. Further investigations are warranted to comprehend the potential antigenic implications of these genetically diverse CDV strains.

Rotavirus A (RVA) is a common cause of diarrhea in newborn pigs, leading to significant economic losses. RVA is considered a major public health concern due to genetic evolution, high prevalence, and pathogenicity in humans and animals. The objective of this study was to identify and characterize RVA in swine farms in Chile. A total of 154 samples (86 oral fluids and 68 fecal samples) were collected, from 22 swine farms. 58 (38%) samples belonging to 14 farms were found positive for RVA by real-time RT-PCR. The samples with low Ct values (21) and the two isolates were selected for whole genome sequencing. Nearly complete genomes were assembled from both isolates and partial genomes were assembled from five clinical samples. BLAST analysis confirmed that these sequences are related to human and swine-origin RVA. The genomic constellation was G5/G3-P[7]-I5-R1-C1-M1-A8-N1-T1-E1-H1. Phylogenetic analysis showed that VP4, VP1, VP2, NSP2, NSP3, NSP4, and NSP5 sequences were grouped in monophyletic clusters, suggesting a single introduction. The phylogenies for VP7, VP6, VP3, and NSP1 indicated two different origins of the Chilean sequences. The phylogenetic trees showed that most of the Chilean RVA sequences are closely related to human and swine-origin RVA detected across the world. The results highlight the potential zoonotic nature of RVA circulating in Chilean swine farms. Therefore, it is important to continue RVA whole genome sequencing globally to fully understand its complex epidemiology and early detection and characterization of zoonotic strains.

Seneca Valley virus (SVV) is a non-enveloped RNA virus and the only member of the Senecavirus A (SVA) species, in the Senecavirus genus, Picornaviridae family. SVV infection causes vesicular lesions in the oral cavity, snout and hooves of pigs. This infection is clinically indistinguishable from trade-restrictions-related diseases such as foot-and-mouth disease. Other clinical manifestations include diarrhoea, anorexia, lethargy, neurological signs and mortality in piglets during their first week of age. Before this study, Chile was considered free of vesicular diseases of swine, including SVV. In April 2022, a suspected case of vesicular disease in a swine farm was reported in Chile. The SVV was confirmed and other vesicular diseases were ruled out. An epidemiological investigation and phylogenetic analyses were performed to identify the origin and extent of the outbreak. Three hundred ninety-five samples from 44 swine farms were collected, including faeces (208), oral fluid (28), processing fluid (14), fresh semen (61), environmental samples (80) and tissue from lesions (4) for real-time RT-PCR detection. Until June 2022, the SVV has been detected in 16 out of 44 farms, all epidemiologically related to the index farm. The closest phylogenetic relationship of the Chilean SVV strain is with viruses collected from swine in California in 2017. The direct cause of the SVV introduction has not yet been identified; however, the phylogenetic analyses suggest the USA as the most likely source. Since the virus remains active in the environment, transmission by fomites such as contaminated feed cannot be discarded. Further studies are needed to determine the risk of the introduction of novel SVV and other transboundary swine pathogens to Chile.

Porcine Circovirus 2 (PCV2) can cause multiple clinical conditions known as porcine circovirus-associated diseases (PCVAD). Before the wide availability of PCV2 vaccines, PCVAD resulted in significant losses to the global swine industry. PCV2's rapid evolutionary dynamics are comparable to single-stranded RNA viruses. Thus, shifts in the dominance and distribution of different genotypes may frequently occur, resulting in the emergence and spread of varying PCV2 genotypes and recombinant strains in swine. This study aims at identifying the PCV2 genotypes currently circulating in Chile. Seven hundred thirty-eight samples were obtained from 21 swine farms between 2020 and 2021. The samples were tested using PCR for species detection and genotyping. Sequencing and phylogenetic analyses were conducted in selected samples. PCV2 was detected in 26.9% of the PCR reactions and 67% of the sampled farms. The genotypes were determined in nine farms, PCV2a in one farm, PCV2b in four, and PCV2d in five, with PCV2b and PCV2d co-circulating in one farm. The phylogenetic analysis of twelve ORF2 sequences obtained (PCV2a = 5; PCV2b = 4; PCV2d = 3) showed a PCV2a Chilean strains monophyletic cluster; closely related to Chilean viruses collected in 2012 and 2013. Of the three different PCV2b sequenced viruses, two viruses were close to the root of the PCV2b group, whereas the remaining one grouped with a South Korean virus. PCV2d sequences were closely related to Asian viruses. A previously reported PCV2a/PCV2d recombinant strain was not detected in this study. Our results suggest the emergence and potential shift to PCV2d genotype in Chilean farms.

Avian orthoavulavirus 1 (AOaV-1) causes Newcastle disease, one of the most important and contagious infections in poultry, where migratory birds can play a key role as a reservoir. Seven hundred and seven serum samples were collected from five penguin species (King, Magellanic, Gentoo, Chinstrap and Adelie penguins) in the Antarctic and Sub-Antarctic zones. Using a competitive ELISA to detect antibodies against AOaV-1, we identified positive individuals in all penguin species. The Magellanic penguin showed the highest seropositivity rate (30.3%), suggesting it could be a natural reservoir of this virus. At the Antarctic zones, Chinstrap penguin showed the highest occurrence (7.5%). Interesting, positive sera was only obtained in Sub-Antarctic and Northern zones at the Antarctic peninsula, no seroreactivity was observed in Southern locations. Further studies are needed to establish the role of these penguin species in the epidemiology of the AOaV-1 and determine the effects of this virus in these populations.

Avian orthoavulavirus 1 (AOaV-1) causes Newcastle disease, one of the most important and contagious infections in poultry, where migratory birds can play a key role as a reservoir. Seven hundred and seven serum samples were collected from five penguin species (King, Magellanic, Gentoo, Chinstrap, and Adelie penguins) in the Antarctic and Sub-Antarctic zones. Using a competitive ELISA to detect antibodies against AOaV-1 we identified positive individuals in all penguin species. The Magellanic penguin showed the highest seropositivity rate (30.3%), suggesting it could be a natural reservoir of this virus. At the Antarctic zones, Chinstrap penguin showed the highest occurrence (7.5%). Interesting, positive sera was only obtained in Sub-Antarctic and Northern zones at the Antarctic peninsula, no seroreactivity was observed in Southern locations. Further studies are needed to establish the role of these penguin species in the epidemiology of the AOaV-1 and determine the effects of this virus in these populations.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been detected in domestic and wild cats. However, little is known about natural viral infections of domestic cats, although their importance for modelling disease spread, informing strategies for managing positive human-animal relationships and disease prevention. Here, we describe the SARS-CoV-2 infection in a household of two human adults and sibling cats (one male and two females) using real-time RT–PCR, an ELISA test, viral sequencing, and virus isolation. On May 5th, 2020, the cat-owners tested positive for SARS-CoV-2. Two days later, the male cat showed mild respiratory symptoms and tested positive. Four days after the male cat, the two female cats became positive, asymptomatically. Also, one human and one cat showed antibodies against SARS-CoV-2. All cats excreted detectable SARS-CoV-2 RNA for a shorter duration than humans and viral sequences analysis confirmed human-to-cat transmission. We could not determine if cat-to-cat transmission also occurred.