Thirty-Five Years of IBV Evolution in Chile Reveals a Novel Lineage and Evidence of Vaccine-Driven Recombination.

Infectious bronchitis virus (IBV) remains a major threat to poultry health worldwide due to frequent genetic changes mainly driven by recombination and limited cross-protection between genotypes. In this study, we analyzed IBV strains collected from clinical outbreaks in Chile between 1986 and 2021 to assess the long-term impacts of live-attenuated vaccines (Massachusetts and 4/91) on viral evolution. Phylogenetic analysis of the S1 and N genes revealed four major lineages circulating in Chile-GI-1, GI-13, GI-16, and a novel monophyletic clade we propose as GI-31.

Genetic Characterization of (Canine Distemper Virus) Field Strains in Dogs, Chile, 2022-2023.

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.

An assessment of the Chilean COVID-19 surveillance program through the comparison between reported and true SARS-CoV-2 infection prevalence: A case study of three urban centers in southern Chile.

Objectives: Estimate the detection limits of the COVID-19 surveillance system (SS) in Chile, by estimating the SARS-CoV-2 true prevalence (TP) and the reported official positivity prevalence (OPP) gap.

Study Design: Randomized cross-sectional.

Methods: Two sampling campaigns (SC) were conducted (October-November 2020 and December 2020-January 2021) in the cities of Temuco, Valdivia, and Osorno.

The Chilean COVID-19 Genomics Network Biorepository: A Resource for Multi-Omics Studies of COVID-19 and Long COVID in a Latin American Population.

Although a lack of diversity in genetic studies is an acknowledged obstacle for personalized medicine and precision public health, Latin American populations remain particularly understudied despite their heterogeneity and mixed ancestry. This gap extends to COVID-19 despite its variability in susceptibility and clinical course, where ethnic background appears to influence disease severity, with non-Europeans facing higher hospitalization rates. In addition, access to high-quality samples and data is a critical issue for personalized and precision medicine, and it has become clear that the solution lies in biobanks.

Host genetic diversity and body condition influence parasite resistance and clearance in a wild marine mammal population.

Host genetic variability can modulate infection resistance, although its role in infection clearance remains unclear. Hookworm disease ( sp.) is the leading cause of pup mortality in several otariid species, although the parasite can be cleared through immune-mediated processes.

Antibiotic resistance in wildlife from Antarctic Peninsula.

Although considered one of the most pristine ecosystems, Antarctica has been largely influenced by human activities during the last 50 years, affecting its unique biodiversity. One of the major global threats to health is the emergence of antibiotic-resistant bacteria that may be actively transferred to wildlife. We cultured and tested for antibiotic resistance in 137 cloacal and fresh fecal samples of several avian and marine mammal species from the Antarctic Peninsula, the most impacted area in Antarctica.

Abundance and associated factors of Amblyomma tigrinum (Acari: Ixodidae) infesting wild foxes in north-central Chile.

The tick Amblyomma tigrinum inhabits areas with diverse climatic conditions, with adult stages parasitizing wild canids, such as chilla (Lycalopex griseus) and culpeo (Lycalopex culpaeus) foxes. We described the infestation loads in wild foxes captured at three sites (periurban, rural and wild) through an anthropization gradient in north-central Chile. We tested whether local-scale environmental and/or individual host factors can predict tick abundance by using negative binomial models.

Performance estimation of two in-house ELISA assays for COVID-19 surveillance through the combined detection of anti-SARS-CoV-2 IgA, IgM, and IgG immunoglobulin isotypes.

The main objective of this study was to estimate the performance, under local epidemiological conditions, of two in-house ELISA assays for the combined detection of anti-SARS-CoV-2 IgA, IgM, and IgG immunoglobulins. A total of 94 serum samples were used for the assessment, where 44 corresponded to sera collected before the pandemic (free of SARS-CoV-2 antibodies), and 50 sera were collected from confirmed COVID-19 patients admitted to the main public hospital in the city of Valdivia, southern Chile. The Nucleocapsid (Np) and the receptor-binding domain (RBD) proteins were separately used as antigens (Np and RBD ELISA, respectively) to assess their diagnostic performance.

Gastrointestinal parasites in wild rodents in Chiloé Island-Chile.

Gastrointestinal parasites are well-documented in small mammals from north-central Chile, but little is known about endoparasites of rodents in southern Chile. A survey was conducted between January and February 2018 to evaluate gastrointestinal parasites and risk factors of wild rodents that live in rural areas in Northern Chiloé Island, Chile. A total of 174 fecal samples from rodents of six native and one introduced species were collected and examined using the Mini-FLOTAC method.

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

Porcine Astrovirus (PoAstV) causes mild diarrhea in young pigs and is considered an emerging virus in the swine industry worldwide. PoAstV has high genetic diversity and has been classified into five genetic lineages, PoAstV1-5. In Chile, only human astroviruses have been reported.

Circulation patterns of human seasonal Influenza A viruses in Chile before H1N1pdm09 pandemic.

Understanding the diversity and circulation dynamics of seasonal influenza viruses is key to public health decision-making. The limited genetic information of pre-pandemic seasonal IAVs in Chile has made it difficult to accurately reconstruct the phylogenetic relationships of these viruses within the country. The objective of this study was to determine the genetic diversity of pre-pandemic human seasonal IAVs in Chile.

Improving the sensitivity of gastrointestinal helminth detection using the Mini-FLOTAC technique in wild birds.

High-performance-validated tests are essential for successful epidemiological monitoring, surveillance of parasitic infections, and comparative studies in wildlife populations. The Mini-FLOTAC is a novel flotation-based technique for the sensitive detection and quantification of gastrointestinal parasites that is recently being explored for use in wildlife. A limitation of any flotation-based copromicroscopic method is the selection of the flotation solution (FS), which might influence the performance of the test.

Molecular identification and morphological variations of Dermacentor albipictus collected from two deer species in northern Mexico.

In total, 57 ticks were collected from six white-tailed deer (Odocoileus virginianus) and three mule deer (O. hemionus) in northern Mexico during the 2017, 2018 and 2019 hunting seasons. Morphological features of adult male and female ticks were observed and photographed using a stereo-microscope and scanning electron micrography.

Upraising a silent pollution: Antibiotic resistance at coastal environments and transference to long-distance migratory shorebirds.

Large amounts of antibiotics from different sources have been released into coastal environments, especially in high human-populated areas, but comprehensive studies of antibiotic footprint in wildlife are scarce. Here we assess occurrence of antibiotic resistant bacteria (ARB) and antibiotic resistance gene (ARG) both in sediments and gut microbiota of a long-distance migratory shorebird species in two coastal wetlands at a sparsely-populated area in Pacific Patagonian coasts with contrasting potential antibiotic sources, especially from aquaculture. We found 62% of sediment samples showing ARB, and ARGs similarly occurring in sediments at both bays.

The mitochondrial genome of two long-distance migratory shorebirds: the Hudsonian godwit () and the Red knot ().

We report the mitochondrial genome sequences of two migratory shorebirds, the Hudsonian godwit () and the Red knot () obtained through shotgun sequencing. The mitogenome is of 16.445 bp for the godwit and 15.

Role of wastewater treatment plants on environmental abundance of Antimicrobial Resistance Genes in Chilean rivers.

Background: Point sources such as wastewater treatment plants (WWTPs) commonly discharge their effluent into rivers. Their waste may include antibiotic residues, disinfectants, antibiotic resistant bacteria (ARB), and Antimicrobial Resistance Genes (ARG). There is evidence that ARG can be found in the natural environment, but attribution to specific point sources is lacking.

Assessing the effects of human activities on the foraging opportunities of migratory shorebirds in Austral high-latitude bays.

Human presence at intertidal areas could impact coastal biodiversity, including migratory waterbird species and the ecosystem services they provide. Assessing this impact is therefore essential to develop management measures compatible with migratory processes and associated biodiversity. Here, we assess the effects of human presence on the foraging opportunities of Hudsonian godwits (Limosa haemastica, a trans-hemispheric migratory shorebird) during their non-breeding season on Chiloé Island, southern Chile.

in the Endangered Patagonian Huemul ().

Cystic echinococcosis (CE) is a zoonotic parasitic disease associated with . The parasite is maintained by domestic and wild canids as definitive hosts with several ungulate species as intermediate hosts in domestic and peridomestic transmission cycles. In Chile, CE is endemic, and the role of livestock and dogs () in the cycle and the accidental infection of humans are widely documented at rural sites.

Low occurrence of hemosporidian parasites in the Neotropic cormorant (Phalacrocorax brasilianus) in Chile.

Hemosporidian parasites rarely infect aquatic birds. Few studies have been conducted in South America identifying some lineages of the genera Plasmodium, Leucocytozoon, and Haemoproteus, but none has been done in the Neotropic cormorant (Phalacrocorax brasilianus). This species is widely distributed through the American continent, from Southern USA to Tierra del Fuego, using a wide range of aquatic habitats.

MOLECULAR IDENTIFICATION OF AVIAN VIRUSES IN NEOTROPIC CORMORANTS ( PHALACROCORAX BRASILIANUS) IN CHILE.

We identified two RNA (paramyxovirus and coronavirus) and two DNA (adenovirus and herpesvirus) viruses in a common aquatic bird, the Neotropic Cormorant ( Phalacrocorax brasilianus), and determined their phylogenetic relationships to other global circulating variants. We analyzed 104 cloacal swabs from individuals collected at locations in Central Chile. Sequences were obtained from amplicons using consensus primers targeting conserved genes of the virus families Paramyxoviridae, Coronaviridae, Adenoviridae, and Herpesviridae.

Taxonomy of the order Mononegavirales: update 2018.

In 2018, the order Mononegavirales was expanded by inclusion of 1 new genus and 12 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.

Respiratory Mites ( Orthohalarachne diminuata) and β-hemolytic Streptococci-Associated Bronchopneumonia Outbreak in South American Fur Seal Pups ( Arctocephalus australis).

Although mites of the Orthohalarachne genus are common parasites of otariids, their role as agents of disease and in causing population-level mortality is unknown. In the austral summer of 2016, there was an increase in mortality among South American fur seal ( Arctocephalus australis) pups at Guafo Island, Northern Chilean Patagonia. Pups found dead or terminally ill had moderate to marked, multifocal, mucopurulent bronchopneumonia associated with large numbers of respiratory mites ( Orthohalarachne diminuata) and rare Gram-positive cocci.

Complete mitochondrial genome of the South American fur seal ().

The complete mitochondrial DNA sequence of the South America fur seal () was obtained by a shotgun sequencing approach. The mitogenome is 16,372 bp in length and includes the genes coding for the two rRNA species (12S and 16S), 13 protein-coding genes, 22 transfer RNA genes, and a control region. The base composition is 33.

Novel Avulaviruses in Penguins, Antarctica.

We identified 3 novel and distinct avulaviruses from Gentoo penguins sampled in Antarctica. We isolated these viruses and sequenced their complete genomes; serologic assays demonstrated that the viruses do not have cross-reactivity between them. Our findings suggest that these 3 new viruses represent members of 3 novel avulavirus species.

A genetic signature of the evolution of loss of flight in the Galapagos cormorant.

We have a limited understanding of the genetic and molecular basis of evolutionary changes in the size and proportion of limbs. We studied wing and pectoral skeleton reduction leading to flightlessness in the Galapagos cormorant (). We sequenced and de novo assembled the genomes of four cormorant species and applied a predictive and comparative genomics approach to find candidate variants that may have contributed to the evolution of flightlessness.