Pandemic (H1N1) 2009 virus was detected in breeding turkeys on 2 farms in Valparaiso, Chile. Infection was associated with measurable declines in egg production and shell quality. Although the source of infection is not yet known, the outbreak was controlled, and the virus was eliminated from the birds.

Porcine reproductive and respiratory syndrome (PRRS) is endemic in most pork producing countries. In Chile, eradication of PRRS virus (PRRSV) was successfully achieved in 2009 as a result of the combined efforts of producers and the animal health authorities. In October 2013, after several years without detecting PRRSV under surveillance activities, suspected cases were confirmed on a commercial swine farm. Here, we describe the PRRS epidemic in Chile between October 2013 and April 2015, and we studied the origins and spread of PRRSV throughout the country using official surveillance data and Bayesian phylogenetic analysis. Our results indicate that the outbreaks were caused by a PRRSV closely related to viruses present in swine farms in North America, and different from the strain that circulated in the country before 2009. Using divergence time estimation analysis, we found that the 2013–2015 PRRSV may have been circulating in Chile for at least one month before the first detection. A single strain of PRRSV spread into a limited number of commercial and backyard swine farms. New infections in commercial systems have not been reported since October 2014, and eradication is underway by clearing the disease from the few commercial and backyard farms that remain positive. This is one of the few documented experiences of PRRSV introduction into a disease-free country.

No abstract

H5N1 highly pathogenic avian influenza viruses (HPAIV) emerged in wild birds in Chile in December 2022 and spilled over into poultry, marine mammals, and one human. Between December 9, 2022 to March 14, 2023, a coordinated government/academic response detected HPAIV by real-time RT-PCR in 8.5% (412/4735) of samples from 23 avian and 3 mammal orders. Whole-genome sequences obtained from 77 birds and 8 marine mammals revealed that all Chilean H5N1 viruses belong to lineage 2.3.4.4b and cluster monophyletically with viruses from Peru, indicating a single introduction from North America into Peru/Chile. Mammalian adaptations were identified in the PB2 segment: D701N in two sea lions, one human, and one shorebird, and Q591K in the human and one sea lion. Minor variant analysis revealed that D701N was present in 52.9 to 70.9% of sequence reads, indicating the presence of both genotypes within hosts. Further surveillance of spillover events is warranted to assess the emergence and potential onward transmission of mammalian adapted H5N1 HPAIV in South America.

In December 2022, HPAI H5N1 clade 2.3.4.4b emerged in Chile. We detected the virus in 93 wild bird samples and sequenced the whole genome of nine Chilean strains from pelicans and gulls. Phylogenetic analysis suggests at least two different HPAI viral clusters in South America.