End-of-season influenza vaccine effectiveness during the Southern Hemisphere 2022 influenza season - Chile, Paraguay, and Uruguay.

Objectives: This study estimated the 2022 end-of-season influenza vaccine effectiveness (VE) against severe acute respiratory illness (SARI) hospitalization in Chile, Paraguay, and Uruguay.

Methods: We pooled surveillance data from SARI cases in 18 sentinel surveillance hospitals in Chile (n = 9), Paraguay (n = 2), and Uruguay (n = 7) from March 16-November 30, 2022. VE was estimated using a test-negative design and logistic regression models adjusted for country, age, sex, presence of ≥1 comorbidity, and week of illness onset.

Phylogenetic analysis reveals that the H5N1 avian influenza A outbreak in poultry in Ecuador in November 2022 is associated with the highly pathogenic clade 2.3.4.4b.

The ongoing H5N1 outbreak in the Americas caused by clade 2.3.4.

A multiplex-NGS approach to identifying respiratory RNA viruses during the COVID-19 pandemic.

A methodological approach based on reverse transcription (RT)-multiplex PCR followed by next-generation sequencing (NGS) was implemented to identify multiple respiratory RNA viruses simultaneously. A convenience sampling from respiratory surveillance and SARS-CoV-2 diagnosis in 2020 and 2021 in Montevideo, Uruguay, was analyzed. The results revealed the cocirculation of SARS-CoV-2 with human rhinovirus (hRV) A, B and C, human respiratory syncytial virus (hRSV) B, influenza A virus, and metapneumovirus B1.

Spatial, temporal and evolutionary insight into seasonal epidemic Influenza A virus strains near the equatorial line: The case of Ecuador.

To study the spatial and temporal patterns of Influenza A virus (IAV) is essential for an efficient control of the disease caused by IAV and efficient vaccination programs. However, spatiotemporal patterns of spread as well as genetic lineage circulation of IAV on a countrywide scale have not been clearly determined for many tropical regions of the world. In order to gain insight into these matters, the spatial and temporal patterns of IAV in six different geographic regions of Ecuador, from 2011 to 2021, were determined and the timing and magnitude of IAV outbreaks in these localities investigated.

Emergence and spreading of the largest SARS-CoV-2 deletion in the Delta AY.20 lineage from Uruguay.

The genetic variability of SARS-CoV-2 (genus , family ) has been scrutinized since its first detection in December 2019. Although the role of structural variants, particularly deletions, in virus evolution is little explored, these genome changes are extremely frequent. They are associated with relevant processes, including immune escape and attenuation.

Consecutive deletions in a unique Uruguayan SARS-CoV-2 lineage evidence the genetic variability potential of accessory genes.

Deletions frequently occur in the six accessory genes of SARS-CoV-2, but most genomes with deletions are sporadic and have limited spreading capability. Here, we analyze deletions in the ORF7a of the N.7 lineage, a unique Uruguayan clade from the Brazilian B.

Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion.

Background: Evolutionary changes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) include indels in non-structural, structural, and accessory open reading frames (ORFs) or genes.

Objectives: We track indels in accessory ORFs to infer evolutionary gene patterns and epidemiological links between outbreaks.

Methods: Genomes from Coronavirus disease 2019 (COVID-19) case-patients were Illumina sequenced using ARTIC_V3.

A deletion in SARS-CoV-2 ORF7 identified in COVID-19 outbreak in Uruguay.

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.

Epidemiology and Genetic Variability of Circulating Influenza B Viruses in Uruguay, 2012-2019.

Influenza B viruses (IBV) are an important cause of morbidity and mortality during interpandemic periods in the human population. Two phylogenetically distinct IBV lineages, B/Yamagata and B/Victoria, co-circulate worldwide and they present challenges for vaccine strain selection. Until the present study, there was little information regarding the pattern of the circulating strains of IBV in Uruguay.

Genetic evolution of influenza viruses among selected countries in Latin America, 2017-2018.

Objective: Since the 2009 influenza pandemic, Latin American (LA) countries have strengthened their influenza surveillance systems. We analyzed influenza genetic sequence data from the 2017 through 2018 Southern Hemisphere (SH) influenza season from selected LA countries, to map the availability of influenza genetic sequence data from, and to describe, the 2017 through 2018 SH influenza seasons in LA.

Methods: We analyzed influenza A/H1pdm09, A/H3, B/Victoria and B/Yamagata hemagglutinin sequences from clinical samples from 12 National Influenza Centers (NICs) in ten countries (Argentina, Brazil, Chile, Colombia, Costa Rica, Ecuador, Mexico, Paraguay, Peru and Uruguay) with a collection date from epidemiologic week (EW) 18, 2017 through EW 43, 2018.

Burden of influenza-associated respiratory hospitalizations in the Americas, 2010-2015.

Background: Despite having influenza vaccination policies and programs, countries in the Americas underutilize seasonal influenza vaccine, in part because of insufficient evidence about severe influenza burden. We aimed to estimate the annual burden of influenza-associated respiratory hospitalizations in the Americas.

Methods: Thirty-five countries in the Americas with national influenza surveillance were invited to provide monthly laboratory data and hospital discharges for respiratory illness (International Classification of Diseases 10th edition J codes 0-99) during 2010-2015.

Phylogenetic analysis of the neuraminidase gene of pandemic H1N1 influenza A virus circulating in the South American region.

Molecular characterization of circulating influenza A viruses (IAV) in all regions of the world is essential to detect mutations potentially involved in increased virulence, anti-viral resistance and immune escape. In order to gain insight into these matters, a phylogenetic analysis of the neuraminidase (NA) gene of 146 pandemic H1N1 (H1N1pdm) influenza A virus strains isolated in Argentina, Brazil, Chile, Paraguay, Peru and Uruguay from 2009 to 2013 was performed. Comparison of vaccine strain A/California/7/2009 included in the influenza vaccine recommended for the Southern hemisphere from 2010 through 2013 influenza seasons and strains isolated in South America revealed several amino acid substitutions.

Pandemic influenza A virus codon usage revisited: biases, adaptation and implications for vaccine strain development.

Background: Influenza A virus (IAV) is a member of the family Orthomyxoviridae and contains eight segments of a single-stranded RNA genome with negative polarity. The first influenza pandemic of this century was declared in April of 2009, with the emergence of a novel H1N1 IAV strain (H1N1pdm) in Mexico and USA. Understanding the extent and causes of biases in codon usage is essential to the understanding of viral evolution.

Bayesian coalescent analysis of pandemic H1N1 influenza A virus circulating in the South American region.

The first influenza pandemic of this century was declared in April of 2009, with the emergence of a novel H1N1 influenza A virus strain (H1N1pdm). Understanding the evolution of H1N1pdm populations within the South American region is essential for studying global diversification, emergence, resistance and vaccine efficacy. In order to gain insight into these matters, we have performed a Bayesian coalescent Markov Chain Monte Carlo analysis of hemagglutinin (HA) and neuraminidase (NA) gene sequences of all available and comparable HA and NA sequences obtained from H1N1pdm IAV circulating in the South American region.

Phylogenetic analysis of pandemic 2009 influenza A virus circulating in the South American region: genetic relationships and vaccine strain match.

The first influenza pandemic of this century was declared in April of 2009, with the emergence of a novel H1N1 influenza A virus strain (H1N1pdm). Understanding the evolution of H1N1pdm strains within the South American region is essential for studying global diversification, emergence and resistance, as well as determining vaccine efficacy. In order to gain insight into these matters, phylogenetic analysis was performed using 29 hemagglutinin (HA) gene sequences from H1N1pdm strains isolated in South America.

Modeling gene sequences over time in 2009 H1N1 influenza A virus populations.

Background: A sudden emergence of Influenza A Virus (IAV) infections with a new pandemic H1N1 IAV is taking place since April of 2009. In order to gain insight into the mode of evolution of these new H1N1 strains, we performed a Bayesian coalescent Markov chain Monte Carlo (MCMC) analysis of full-length neuraminidase (NA) gene sequences of 62 H1N1 IAV strains (isolated from March 30th to by July 28th, 2009).

Results: The results of these studies revealed that the expansion population growth model was the best to fit the sequence data.

Human influenza A viruses isolated in South America: genetic relations, adamantane resistance and vaccine strain match.

In order to gain insight into the genetic relations among H3N2 Influenza A virus (IAV) circulating in the South American region from 1999 to 2007, to investigate the presence of adamantane-resistant strains in this region, and to establish the genetic relations among that strains and vaccine strains recommended for the Southern hemisphere, 11 haemagglutinin (HA) H3 IAV sequences obtained from Uruguayan patients were aligned with corresponding sequences from 68 H3 IAV strains isolated in South America and 9 H3 IAV vaccine strains. Maximum likelihood phylogenetic tree analysis was performed using the GTR evolutionary model. The results of these studies indicate that multiple clades co-circulate during most influenza seasons in South America.

Influenza B viruses isolated in Uruguay during the 2002-2005 seasons: genetic relations and vaccine strain match.

Monitoring antigenic and genetic variations of circulating influenza viruses is critical for the selection of annual vaccine strains. In order to gain insight into the molecular evolution of Influenza B viruses (IBV) isolated in Uruguay in 2002 and 2005 outbreaks, antigenic and phylogenetic studies were carried out for the Hemagglutinin (HA) gene. Antigenic relations among Uruguayan and reference strains isolated elsewhere were performed by means of hemagglutination inhibition assays (HAI).