Exploring the Genomic Dynamics of the Monkeypox Epidemic in Paraguay.

In recent months, Paraguay has been grappled with a notable monkeypox outbreak, straining its healthcare infrastructure. The sudden spike in cases underlines the imperative need for a comprehensive understanding of the virus's dynamics, enabling the formulation of robust containment measures. To address this challenge, our team joined forces with the Central Public Health Laboratory of Asunción and the Pan-American Health Organization. Through this collaboration, we employed portable whole-genome sequencing combined with phylodynamic analysis to examine the MPXV strains circulating in Paraguay. Our genomic monitoring approach has produced the first 30 whole-genome sequences from Paraguay, all of which were identified under lineage IIb. Interestingly, our data suggest that the origin of the monkeypox virus in Paraguay at the beginning of 2022 can be traced back to Brazil. This introduction subsequently catalyzed further community spread that was further exacerbated by several independent introduction events as time progressed. These findings not only shed light on the transmission patterns of the virus but also highlight the pivotal role such insights play in sculpting effective response strategies and driving impactful public health measures. Furthermore, our findings strongly advocate intensified surveillance at international borders, ensuring swift detection and proactive countermeasures against potential outbreaks in the future.

Rapid Epidemic Expansion of Chikungunya Virus East/Central/South African Lineage, Paraguay.

The spread of Chikungunya virus is a major public health concern in the Americas. There were >120,000 cases and 51 deaths in 2023, of which 46 occurred in Paraguay. Using a suite of genomic, phylodynamic, and epidemiologic techniques, we characterized the ongoing large chikungunya epidemic in Paraguay.

Retrospective Spatio-Temporal Dynamics of Dengue Virus 1, 2 and 4 in Paraguay.

Dengue virus (DENV) has been a major public health concern in Paraguay, with frequent outbreaks occurring since early 1988. Although control measures have been implemented, dengue remains a significant health threat in the country, and continued efforts are required for prevention and control. In response to that, in collaboration with the Central Public Health Laboratory in Asunción, we conducted a portable whole-genome sequencing and phylodynamic analysis to investigate DENV viral strains circulating in Paraguay over the past epidemics. Our genomic surveillance activities revealed the co-circulation of multiple DENV serotypes: DENV-1 genotype V, the emerging DENV-2 genotype III, BR4-L2 clade, and DENV-4 genotype II. Results additionally highlight the possible role of Brazil as a source for the international dispersion of different viral strains to other countries in the Americas emphasizing the need for increased surveillance across the borders, for the early detection and response to outbreaks. This, in turn, emphasizes the critical role of genomic surveillance in monitoring and understanding arbovirus transmission and persistence locally and over long distances.

Rapid epidemic expansion of chikungunya virus-ECSA lineage in Paraguay.

The spread of vector-borne viruses, such as CHIKV, is a significant public health concern in the Americas, with over 120,000 cases and 51 deaths in 2023, of which 46 occurred in Paraguay. Using a suite of genomic, phylodynamic, and epidemiological techniques, we characterized the ongoing large CHIKV epidemic in Paraguay. Article Summary Line: Genomic and epidemiological characterization of the ongoing Chikungunya virus epidemic in Paraguay.

Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil

The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre of the pandemic. SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, but important gaps remain in our understanding of virus transmission dynamics at a national scale. We use 17,135 near-complete genomes sampled from 27 Brazilian states and bordering country Paraguay. From March to November 2020, we detected co-circulation of multiple viral lineages that were linked to multiple importations (predominantly from Europe). After November 2020, we detected large, local transmission clusters within the country. In the absence of effective restriction measures, the epidemic progressed, and in January 2021 there was emergence and onward spread, both within and abroad, of variants of concern and variants under monitoring, including Gamma (P.1) and Zeta (P.2). We also characterized a genomic overview of the epidemic in Paraguay and detected evidence of importation of SARS-CoV-2 ancestor lineages and variants of concern from Brazil. Our findings show that genomic surveillance in Brazil enabled assessment of the real-time spread of emerging SARS-CoV-2 variants.

Epidemiologic History and Genetic Diversity Origins of Chikungunya and Dengue Viruses, Paraguay.

Paraguay has been severely affected by emergent Zika and chikungunya viruses, and dengue virus is endemic. To learn more about the origins of genetic diversity and epidemiologic history of these viruses in Paraguay, we deployed portable sequencing technologies to strengthen genomic surveillance and determine the evolutionary and epidemic history of arthropod-borne viruses (arboviruses). Samples stored at the Paraguay National Central Laboratory were sequenced and subjected to phylogenetic analysis. Among 33 virus genomes generated, we identified 2 genotypes of chikungunya and 2 serotypes of dengue virus that circulated in Paraguay during 2014-2018; the main source of these virus lineages was estimated to be Brazil. The evolutionary history inferred by our analyses precisely matched the available travel history of the patients. The genomic surveillance approach used was valuable for describing the epidemiologic history of arboviruses and can be used to determine the origins and evolution of future arbovirus outbreaks.

Evolución Genética del Virus Influenza A(H1N1) pdm09 en Paraguay 2009-2016

RESUMEN Una cepa triple reasortante del virus Influenza A emergió en al año 2009 dando origen a una pandemia que alcanzó a Paraguay en junio del mismo año. Con el fin de investigar la evolución genética del virus influenza A (H1N1) pdm09 en Paraguay fueron analizadas las secuencias nucleotídicas del Gen de la Hemaglutinina de 20 cepas de Influenza A(H1N1)pdm09, aisladas en el Centro Nacional de Influenza de Paraguay entre los años 2009 y 2016, y secuenciadas en el Centro Colaborador de OPS/OMS en Atlanta USA. El análisis filogenético muestra la circulación de al menos 5 grupos genéticos bien diferenciados de Influenza A(H1N1)pdm09 en Paraguay desde el 2009. Solamente los virus aislados en el 2016 pertenecen al sub Grupo genético 6B.1 en el cual se encuentra la actual cepa vacunal A/Michigan/45/2015 recomendada para el hemisferio Sur desde el año 2017. Los virus circulantes en años anteriores pertenecen a grupos antigénicamente indistinguibles de la cepa vacunal previa A/California/7/2009. No se encontraron diferencias resaltantes en las secuencias de los virus, relacionadas a severidad clínica ni a distribución geográfica. Los resultados de este estudio reafirman la necesidad de una vigilancia virológica sistemática para orientar el establecimiento de estrategias adecuadas de prevención y control de la influenza.

ABSTRACT A triple reassortant strain of Influenza A virus emerged in 2009, leading to a pandemic that reached Paraguay by June the same year. In order to investigate the genetic evolution of influenza A (H1N1)pdm09 virus in Paraguay, we analized the nucleotide sequences of the Hemagglutinin gene of 20 Influenza A (H1N1)pdm09 strains, isolated at the Paraguayan National Influenza Centre between 2009 and 2016, and sequenced at the PAHO/WHO Collaborating Center in Atlanta, USA. Phylogenetic analysis shows the circulation of at least 5 well-differentiated genetic groups of Influenza A (H1N1) pdm09 in Paraguay since 2009. Only the viruses isolated in 2016 belong to genetic subgroup 6B.1, the same as the current vaccine strain A/Michigan/45/2015, recommended for the Southern hemisphere since 2017. The viruses circulated previous years belong to groups antigenically indistinguishable from the previous vaccine strain A/California/7/2009. No significant differences were found in sequences of the viruses, related to clinical severity or geographic distribution. The results of this study reaffirm the need for systematic virological surveillance to guide the establishment of adequate strategies for the prevention and control of influenza.

Detección de Metapneumovirus Humano en niños menores de 5 años hospitalizados en Paraguay / Detection of Human Metapneumovirus in Children under Age 5 Hospitalized in Paraguay

El Metapneumovirus humano (hMPV) constituye una importante causa de Infecciones Respiratorias Agudas (IRAs) en niños hospitalizados. En Paraguay, las IRAs están entre las primeras causas de hospitalización durante la infancia, siendo los virus los principales agentes causales. Sin embargo, aún persiste una alta proporción de casos sin etiología identificada. La pandemia de Influenza en el año 2009, condujo a una intensificación de la vigilancia de las infecciones respiratorias, lo cual permitió al mismo tiempo la búsqueda de otros virus como el hMPV. Nuestro objetivo fue detectar hMPV en niños hospitalizados por IRAs en Paraguay durante el año 2009. Fueron estudiadas 240 muestras respiratorias de niños < 5 años internados por IRAs en Paraguay durante el año 2009, que habían resultado negativas para otros virus respiratorios. Fue utilizado el reactivo LightMix Kit human MPV de TIBMOLBIOL, para la detección del gen N de hMPV por PCR en Tiempo Real, siguiendo el procedimiento indicado por el fabricante. De las 240 muestras estudiadas, 29 (12%) resultaron positivas para hMPV, con la mayor detección en julio y agosto; predominando en mayores de 1 año. Los principales signos y síntomas fueron tos, fiebre y dificultad respiratoria; y las complicaciones más frecuentes neumonía y bronquiolitis. Estos resultados proveen las primeras evidencias en Salud Pública, de la importancia del hMPV asociado a niños hospitalizados por IRAs en Paraguay.

Human metapneumovirus (hMPV) is a significant cause of acute respiratory infection (ARI) in hospitalized children. In Paraguay, ARI is one of the leading causes of childhood hospitalization, with viruses being the primary causal agents. However, a large number of cases of unknown etiology remain. The influenza pandemic of 2009 led to intensified vigilance concerning respiratory infections and more thorough efforts to confirm the presence of viruses such as hMPV. Our objective was to detect hMPV in children hospitalized for ARI in Paraguay during 2009. We studied respiratory samples from 240 children age < 5 years hospitalized for IRAs in Paraguay during 2009 who had tested negative for other respiratory viruses. We used the hMPV-reactive LightMix® kit from TIB MOLBIOL for the detection of the nucleoprotein (N) gene by real-time PCR according to manufacturer-specified procedures. Of the 240 samples studied, 29 (12%) were positive for hMPV, with the highest rates detected in July and August (winter) predominating in children over 1 year of age. The most common signs and symptoms were cough, fever, and respiratory distress; while the most common complications were pneumonia and bronchiolitis. These results provide the first evidence concerning the prevalence of hMPV in children hospitalized for ARI in Paraguay.

Detección de metapneumovirus humano en niños menores de 5 años hospitalizados en Paraguay / Detection of human metapneumovirus in children under age 5 Hospitalized in Paraguay

El Metapneumovirus humano (hMPV) constituye una importante causa de Infecciones Respiratorias Agudas (IRAs) en niños hospitalizados. En Paraguay, las IRAs están entre las primeras causas de hospitalización durante la infancia, siendo los virus los principales agentes causales. Sin embargo, aún persiste una alta proporción de casos sin etiología identificada. La pandemia de Influenza en el año 2009, condujo a una intensificación de la vigilancia de las infecciones respiratorias, lo cual permitió al mismo tiempo la búsqueda de otros virus como el hMPV. Nuestro objetivo fue detectar hMPV en niños hospitalizados por IRAs en Paraguay durante el año 2009. Fueron estudiadas 240 muestras respiratorias de niños <5 años internados por IRAs en Paraguay durante el año 2009, que habían resultado negativas para otros virus respiratorios. Fue utilizado el reactivo LightMix Kit human MPV de TIBMOLBIOL, para la detección del gen N de hMPV por PCR en Tiempo Real, siguiendo el procedimiento indicado por el fabricante. De las 240 muestras estudiadas, 29 (12%) resultaron positivas para hMPV, con la mayor detección en julio y agosto; predominando en mayores de 1 año. Los principales signos y síntomas fueron tos, fiebre y dificultad respiratoria; y las complicaciones más frecuentes neumonía y bronquiolitis. Estos resultados proveen las primeras evidencias en Salud Pública, de la importancia del hMPV asociado a niños hospitalizados por IRAs en Paraguay.