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.

An expanded toolkit of drug resistance cassettes for Candida glabrata, Candida auris, and Candida albicans leads to new insights into the ergosterol pathway.

IMPORTANCE: The increasing problem of drug resistance and emerging pathogens is an urgent global health problem that necessitates the development and expansion of tools for studying fungal drug resistance and pathogenesis. Prior studies in Candida glabrata, Candida auris, and Candida albicans have been mainly limited to the use of NatMX/SAT1 and HphMX/CaHyg for genetic manipulation in prototrophic strains and clinical isolates. In this study, we demonstrated that NatMX/SAT1, HphMX, KanMX, and/or BleMX drug resistance cassettes when coupled with a CRISPR-ribonucleoprotein (RNP)-based system can be efficiently utilized for deleting or modifying genes in the ergosterol pathway of C. glabrata, C. auris, and C. albicans. Moreover, the utility of these tools has provided new insights into ERG genes and their relationship to azole resistance in Candida. Overall, we have expanded the toolkit for Candida pathogens to increase the versatility of genetically modifying complex pathways involved in drug resistance and pathogenesis.

COVID-19 vaccine effectiveness against hospitalizations in Paraguay, May 2021-April 2022: A test-negative design.

BACKGROUND: Vaccine effectiveness (VE) estimates vary by population characteristics and circulating variants. North America and Europe have generated many COVID-19 VE estimates but relied heavily on mRNA vaccines. Fewer estimates are available for non-mRNA vaccines and from Latin America. We aimed to estimate the effectiveness of several COVID-19 vaccines in preventing SARS-CoV-2-associated severe acute respiratory infection (SARI) in Paraguay from May 2021 to April 2022. METHODS: Using sentinel surveillance data from four hospitals in Paraguay, we conducted a test-negative case-control study to estimate COVID-19 vaccine effectiveness against SARI by vaccine type/brand and period of SARS-CoV-2 variant predominance (Gamma, Delta, Omicron). We used multivariable logistic regression adjusting for month of symptom onset, age group, and presence of ≥1 comorbidity to estimate the odds of COVID-19 vaccination in SARS-CoV-2 test-positive SARI case-patients compared to SARS-CoV-2 test-negative SARI control-patients. RESULTS: Of 4,229 SARI patients, 2,381 (56%) were SARS-CoV-2-positive case-patients and 1,848 (44%) were SARS-CoV-2-negative control-patients. A greater proportion of case-patients (73%; 95% CI: 71-75) than of control-patients (40%; 95% CI: 38-42) were unvaccinated. During the Gamma variant-predominant period, VE estimates for partial vaccination with mRNA vaccines and Oxford/AstraZeneca Vaxzevria were 90.4% (95% CI: 66.4-97.6) and 52.2% (95% CI: 25.0-69.0), respectively. During the Delta variant-predominant period, VE estimates for complete vaccination with mRNA vaccines, Oxford/AstraZeneca Vaxzevria, or Gamaleya Sputnik V were 90.4% (95% CI: 74.3-97.3), 83.2% (95% CI: 67.8-91.9), and 82.9% (95% CI: 53.0-95.2), respectively. The effectiveness of all vaccines declined substantially during the Omicron variant-predominant period. CONCLUSIONS: This study contributes to our understanding of COVID-19 VE in Latin America and to global understanding of vaccines that have not been widely used in North America and Europe. VE estimates from Paraguay can parameterize models to estimate the impact of the national COVID-19 vaccination campaign in Paraguay and similar settings.

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.

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. VE estimates were stratified by influenza virus type and subtype (when available) and influenza vaccine target population, categorized as children, individuals with comorbidities, and older adults, defined per countries' national immunization policies. RESULTS: Among the 3147 SARI cases, there were 382 (12.1%) influenza test-positive case patients; 328 (85.9%) influenza case patients were in Chile, 33 (8.6%) were in Paraguay, and 21 (5.5%) were in Uruguay. In all countries, the predominant subtype was influenza A(H3N2) (92.6% of influenza cases). Adjusted VE against any influenza-associated SARI hospitalization was 33.8% (95% confidence interval: 15.3%, 48.2%); VE against influenza A(H3N2)-associated SARI hospitalization was 30.4% (95% confidence interval: 10.1%, 46.0%). VE estimates were similar across target populations. CONCLUSION: During the 2022 influenza season, influenza vaccination reduced the odds of hospitalization among those vaccinated by one-third. Health officials should encourage influenza vaccination in accordance with national recommendations.

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.

Actualización de áreas de riesgo y perfil epidemiológico de hantavirus en Paraguay (2013-2020)

El síndrome pulmonar por hantavirus (SPH) en el Paraguay es una infección relacionada a extensas áreas geográficas del Chaco o Región Occidental. Sin embargo, en los últimos años se han reportado casos fuera del área endémica conocida. Con el objetivo de describir el perfil epidemiológico de la enfermedad en nuestro país, y actualizar las áreas de transmisión, se realizó una revisión retrospectiva de los casos registrados desde el 2013 al 2020. Fueron confirmados 90 casos de SPH, siendo la Región Occidental la de mayor proporción de casos, con 92% en dicho periodo. La Región Oriental registró el 5,5% de los casos, mientras que en el 2,5% de los casos no fue posible determinar el territorio de ocurrencia del contagio. El perfil de la enfermedad en el país se presenta como una afección principalmente de hombres en la edad adulta - joven, ligados a actividades de campo. Los principales desafíos para el abordaje de esta enfermedad son sensibilizar a la población de las nuevas áreas de riesgo identificadas, fortalecer la vigilancia en dichos lugares a fin de captar en forma oportuna a los casos, y actualizar los conocimientos sobre los virus circulantes y los reservorios zoonóticos de la enfermedad.

Hantavirus Pulmonary Syndrome in Paraguay is an infection related to the Chaco area or Western Region. However, in recent years cases it has been reported outside the known endemic area. In order to describe the epidemiological profile of the disease in our country, and update the transmission areas, a retrospective review of the cases registered from 2013 to 2020. Ninety HPS cases were confirmed, being the Western Region the one that contributed the highest proportion of cases, with 92% in the study period. The Eastern Region registered 5.5% of the cases, while in 2.5% of the cases it was not possible to determine the place. The profile of the disease in the country is presented as a condition mainly of men in adulthood - young, linked to field activities. The main challenges were to sensitize the population of the newly identified risk areas, strengthen the surveillance in these places in order to capture cases in a timely manner and update knowledge about the circulating viruses and zoonotic reservoirs of the disease.

[COVID 19 infection: age-stratified population-based cohort seroepidemiological study in Asunción and Central]. / Infección por COVID 19: estudio seroepidemiológico de cohorte de base poblacional, estratificado por edad, en Asunción y Central.

BACKGROUND: COVID-19, caused by the severe acute respiratory syndrome virus type-2 (SARS-CoV-2), was declared a pandemic in March 2020. Seroprevalence studies are useful to estimate the proportion of the population previously infected, quantify the magnitude of transmission, estimate the fatality rate, evaluate the effect of interventions, and estimate the degree of immunity of the population. AIM: To determine the extension of the infection and the cumulative incidence of age-specific infection, determined by seropositivity in the population of the sanitary regions of Asunción and the Central Department of Paraguay. METHODS: Population-based cohort study. In Asunción 126 households and in the Central Department 609 were surveyed between December 2020 to March 2021. Three visits were made to the selected households. RESULTS: The testing rate was 66.6%, 1,699 people (324 in Asunción and 1,375 in Central) of the 2,553 people registered. In the first, second and third rounds, seroprevalences were 15.5%, 15.4% and 14.3% in Asunción, respectively; in Central 23.1%, 27.8% and 26.9%, respectively. There was a seroconversion between the first and second rounds of 5.9%, and in the third round 6.5%; the accumulated global seroprevalence was 26.9% (95% CI: 24.8-19.1); in Asunción 23.1% (95% CI: 18.9-28.0) and in Central 27.8% (95% CI: 25.5-30.2). 8.5% of the participants reported symptoms; of them, 54.2% had positive serology. CONCLUSION: The sero-prevalence was high with a low proportion of people with symptoms.

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.

Infección por COVID 19: estudio seroepidemiológico de cohorte de base poblacional, estratificado por edad, en Asunción y Central / COVID 19 infection: age-stratified population-based cohort seroepidemiological study in Asunción and Central

INTRODUCCIÓN: La COVID-19, causada por el virus del síndrome respiratorio agudo severo tipo-2 (SARS-CoV-2), fue declarada pandémica en marzo de 2020. Los estudios de seroprevalencia son útiles para efectuar diversas estimaciones: la proporción de la población previamente infectada, cuantificar la magnitud de la transmisión, la tasa de letalidad, evaluar el efecto de intervenciones, y el grado de inmunidad de una población. OBJETIVOS: Determinar la extensión de la infección y la incidencia acumulada de infección mediante el estudio de seropositividad en pobladores de las regiones sanitarias de Asunción y Departamento Central de Paraguay. METODOLOGÍA: Estudio de cohorte poblacional. Se encuestaron 126 hogares en Asunción y 609 en el Departamento Central entre diciembre 2020 y marzo 2021. Se realizaron tres visitas a los hogares seleccionados. RESULTADOS: La tasa de testeo fue 66,6%, 1.699 personas (324 en Asunción y 1.375 en Central) de las 2.553 personas censadas. En la primera, segunda y tercera rondas, las seroprevalencias fueron en Asunción 15,5%, 15,4% y 14,3%, respectivamente; en Central 23,1%, 27,8% y 26,9%, respectivamente. Hubo una seroconversión entre la primera y segunda ronda de 5,9% y en la tercera ronda 6,5%. La seroprevalencia global acumulada fue de 26,9% (IC95%: 24,8-19,1); en Asunción 23,1% (IC95%: 18,9-28,0) y en Central 27,8% (IC95%: 25,5-30,2). El 8,5% de los participantes reportó síntomas; de estos, el 54,2% presentó serología positiva. CONCLUSIÓN: La sero-prevalencia fue alta con una baja proporción de encuestados sintomáticos.

BACKGROUND: COVID-19, caused by the severe acute respiratory syndrome virus type-2 (SARS-CoV-2), was declared a pandemic in March 2020. Seroprevalence studies are useful to estimate the proportion of the population previously infected, quantify the magnitude of transmission, estimate the fatality rate, evaluate the effect of interventions, and estimate the degree of immunity of the population. AIM: To determine the extension of the infection and the cumulative incidence of age-specific infection, determined by seropositivity in the population of the sanitary regions of Asunción and the Central Department of Paraguay. METHODS: Population-based cohort study. In Asunción 126 households and in the Central Department 609 were surveyed between December 2020 to March 2021. Three visits were made to the selected households. RESULTS: The testing rate was 66.6%, 1,699 people (324 in Asunción and 1,375 in Central) of the 2,553 people registered. In the first, second and third rounds, seroprevalences were 15.5%, 15.4% and 14.3% in Asunción, respectively; in Central 23.1%, 27.8% and 26.9%, respectively. There was a seroconversion between the first and second rounds of 5.9%, and in the third round 6.5%; the accumulated global seroprevalence was 26.9% (95% CI: 24.8-19.1); in Asunción 23.1% (95% CI: 18.9-28.0) and in Central 27.8% (95% CI: 25.5-30.2). 8.5% of the participants reported symptoms; of them, 54.2% had positive serology. CONCLUSION: The sero-prevalence was high with a low proportion of people with symptoms.

Public health and budget impacts of switching from a trivalent to a quadrivalent inactivated influenza vaccine in Paraguay.

This study aimed to investigate the public health and economic benefit of using a quadrivalent influenza vaccine (QIV) instead of a trivalent influenza vaccine (TIV) in past seasons in Paraguay. The budget impact of switching from TIV to QIV in the Immunization Program was also evaluated. The adapted model includes two modules. The first compared retrospectively Health and Economic outcomes resulting from the use of QIV instead of TIV. The second forecast the spending and savings that would be associated with the switch from TIV to QIV. Our findings estimate that the switch from TIV to QIV during the seasons 2012 to 2017 could have prevented around 2,600 influenza cases, 67 hospitalizations and 10 deaths. An alternative scenario using standardized estimates of the burden of influenza showed that 234 influenza-related hospitalizations and 29 deaths could have been prevented. The estimated annual budget impact of a full switch from TIV to QIV was around USD1,6 million both from the payer and societal perspectives. Those results are mainly driven by vaccine prices and coverage rate. In sum, this manuscript describes how the use of QIV instead of TIV could have prevented influenza cases and subsequent complications that led to hospitalizations and deaths. This could have generated savings for the health system and society, offsetting part of the additional investment needed to switch from TIV to QIV.

Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil.

Brazil has experienced some of the highest numbers of COVID-19 cases and deaths globally and from May 2021 made Latin America a pandemic epicenter. Although SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, important gaps remain in our understanding of virus transmission dynamics at the national scale. Here, we describe the genomic epidemiology of SARS-CoV-2 using near-full genomes sampled from 27 Brazilian states and a bordering country - Paraguay. We show that the early stage of the pandemic in Brazil was characterised by the co-circulation of multiple viral lineages, linked to multiple importations predominantly from Europe, and subsequently characterized by large local transmission clusters. As the epidemic progressed under an absence of effective restriction measures, there was a local emergence and onward international spread of Variants of Concern (VOC) and Variants Under Monitoring (VUM), including Gamma (P.1) and Zeta (P.2). In addition, we provide a preliminary genomic overview of the epidemic in Paraguay, showing evidence of importation from Brazil. These data reinforce the usefulness and need for the implementation of widespread genomic surveillance in South America as a toolkit for pandemic monitoring that provides a means to follow the real-time spread of emerging SARS-CoV-2 variants with possible implications for public health and immunization strategies.

Caregivers' divergent perspectives on patients' well-being and attitudes towards hastened death in Germany, Poland and Sweden.

Background: During the course of amyotrophic lateral sclerosis (ALS), patients and their families are faced with existential decisions concerning life-prolonging and -shortening measures. Correct anticipation of patient's well-being and preferences is a prerequisite for patient-centered surrogate decision making. Methods: In Germany (N = 84), Poland (N = 77) and Sweden (N = 73) patient-caregiver dyads were interviewed. Standardized questionnaires on well-being (ADI-12 for depressiveness; ACSA for global quality of life) and wish for hastened death (SAHD) were used in ALS patients. Additionally, caregivers were asked to fill out the same questionnaires by anticipating patients' perspective (surrogate perspective). Results: Caregivers significantly underestimated patients' well-being in Germany and Poland. For Swedish caregivers, there were just as many who underestimated and overestimated well-being. The same was true for wish for hastened death in all three countries. For Swedish and Polish patients, caregivers' estimation of well-being was not even associated with patients' responses and the same was true for estimation of wish for hastened death in all three countries. Older caregivers and those with the most frequent encounter with the patient were the closest in their rating of well-being and wish for hastened death to the patients' actual state, while caregivers with chronic disease him/herself were more likely to underestimate patient's well-being. Discussion: Despite distinct cultural differences, there was a clear discrepancy between patients' and caregivers' perspective on patients' well-being and preferences towards life in all three countries. This possible bias in caregivers' judgment needs to be taken into account in surrogate decision making.

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.

Regulatory T Cells as an Escape Mechanism to the Immune Response in Taenia crassiceps Infection.

Murine cysticercosis by Taenia crassiceps is a model for human neurocysticercosis. Genetic and/or immune differences may underlie the higher susceptibility to infection in BALB/cAnN with respect to C57BL/6 mice. T regulatory cells (Tregs) could mediate the escape of T. crassiceps from the host immunity. This study is aimed to investigate the role of Tregs in T. crassiceps establishment in susceptible and non-susceptible mouse strains. Treg and effector cells were quantified in lymphoid organs before infection and 5, 30, 90, and 130 days post-infection. The proliferative response post-infection was characterized in vitro. The expression of regulatory and inflammatory molecules was assessed on days 5 and 30 post-infection. Depletion assays were performed to assess Treg functionality. Significantly higher Treg percentages were observed in BALB/cAnN mice, while increased percentages of activated CD127+ cells were found in C57BL/6 mice. The proliferative response was suppressed in susceptible mice, and Treg proliferation occurred only in susceptible mice. Treg-mediated suppression mechanisms may include IL-10 and TGFß secretion, granzyme- and perforin-mediated cytolysis, metabolic disruption, and cell-to-cell contact. Tregs are functional in BALB/cAnN mice. Therefore Tregs could be allowing parasite establishment and survival in susceptible mice but could play a homeostatic role in non-susceptible strains.