Natalia Ramos

Editorial: Porcine respiratory disease complex: dynamics of polymicrobial infections, synergistic effects and management strategies

Data regarding PRRSV-2 in South America are scant and a coordinated criterion for molecular characterization is needed. A phylogenetic analysis was performed using a dataset of 76 ORF5 sequences from South America, and results showed the identification of lineage 5 in the early 2000s and the predominance of lineage 1 at least since 2013. Lineage 1 sequences were further classified into sub-lineages according to a recent molecular characterization study of PRRSV-2 in United States. Our results revealed the recent identification in Uruguay of PRRSV-2 ORF5 sequences of lineage 1 sub-lineage C. Two additional sub-lineages were identified in South America, 1G in Chile and 1A in Peru. Continuous updating the molecular epidemiology of circulating viruses with coordinated investigations among countries is required to control and prevent the emergence of genetic variants of PRRSV-2.

The analysis of genetic diversity in SARS‐CoV‐2 is the focus of several studies, providing insights into how the virus emerged and evolves. Most common changes in SARS CoV‐2 are single or point nucleotide substitutions, meanwhile insertions and deletions (indels) have been identified as a less frequent source of viral genetic variability. Here, we report the emergence of a 12‐nucleotide deletion in ORF7a, resulting in a 4‐amino‐acid in‐frame deletion. The Δ12 variant was identified in viruses from patients of a single outbreak and represents the first report of this deletion in South American isolates. Phylogenetic analysis revealed that Δ12 strains belong to the lineage B.1.1 and clustered separated from the remaining Uruguayan strains. The ∆12 variant was detected in 14 patients of this outbreak by NGS sequencing and/or two rapid and economic methodologies: Sanger amplicon sequencing and capillary electrophoresis. The presence of strong molecular markers as the deletion described here are useful for tracking outbreaks and reveal a significant aspect of the SARS‐CoV‐2 evolution on the robustness of the virus to keep its functionality regardless loss of genetic material.

Within the last two decades, several high-impact viruses have emerged in the global swine population, including porcine reproductive and respiratory syndrome virus (PRRSV). In Uruguay, the more recent serological survey for PRRSV and other notifiable diseases such as Aujeszky's disease virus (ADV) and classical swine fever virus (CSFV) dated from year 2000. The main purpose of this study was to update our information on the infection status of PRRSV, ADV and CSFV in Uruguayan pig herds, in order to keep informed about the epidemiological situation of these notifiable infections in the country. For serological testing, a total of 524 swine serum samples collected during the period 2014–2016 were assayed by commercial ELISAs. Our results revealed the (unexpected) presence of PRRSV antibodies in Uruguayan domestic swine herds and confirmed the absence of ADV and CSFV antibodies in all of the assessed samples. Following such initial finding, PRRSV antibodies were further investigated in 23 retrospective samples collected during 2010-2014. Thirteen of these 23 samples resulted seropositive. Subsequently, a molecular detection approach in frozen serum samples was implemented to confirm PRRSV infection, and viral RNA was identified by reverse transcription–nested polymerase chain reaction (RT-nPCR). Fourteen of 86 evaluated 2014–2016 samples resulted positive for viral RNA, while molecular analysis of four retrospective samples also revealed the presence of PRRSV type 2. Viral isolation of selected samples was carried out in porcine alveolar macrophages (PAM) and MARC 145 simian kidney cells, and the virus identity was confirmed by cytopathic effect (CPE) and immunofluorescence assay (IFA) using specific monoclonal antibodies for PRRSV nucleocapsid. Data reported here evidence for the first time the circulation of PRRSV type 2 in Uruguay, and retrospective serology results suggest that the virus has been infecting pigs in this country at least since 2011.

Porcine circovirus type 2 (PCV2) is a very small, non-enveloped and icosahedral virus, with circular single stranded DNA genome. This virus is the most ubiquitous and persistent pathogen currently affecting the swine industry worldwide. PCV2 has been implicated as the major causative agent of postweaning multisystemic wasting syndrome (PMWS), a disease which is characterized by severe immunosuppressive effects in the porcine host. Worldwide PCV2 isolates have been classified into four different genotypes, PCV2a, PCV2b, PCV2c and PCVd. The goal of this work was to conduct the first phylogenetic analysis of PCV2 in Chile. PCV2 partial ORF2 sequences (462 nt) obtained from 29 clinical cases of PMWS in 22 Chilean intensive swine farms, covering over the 90% of the local pork-production, were analyzed. 14% and 52% of sequences belonged to the genotypes PCV2a and PCV2b, respectively. Surprisingly, 34% of sequences were PCV2a/PCV2d recombinant viruses. Our findings suggested that a novel cluster of Chilean sequences emerged resulting from intergenotypic recombination between PCV2a and PCV2d.