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BACKGROUND: In June 2019, the Bolivian Ministry of Health reported a cluster of cases of hemorrhagic fever that started in the municipality of Caranavi and expanded to La Paz. The cause of these cases was unknown. METHODS: We obtained samples for next-generation sequencing and virus isolation. Human and rodent specimens were tested by means of virus-specific real-time quantitative reverse-transcriptase–polymerase-chain-reaction assays, next-generation sequencing, and virus isolation. RESULTS: Nine cases of hemorrhagic fever were identified; four of the patients with this illness died. The etiologic agent was identified as Mammarenavirus Chapare mammarenavirus, or Chapare virus (CHAPV), which causes Chapare hemorrhagic fever (CHHF). Probable nosocomial transmission among health care workers was identified. Some patients with CHHF had neurologic manifestations, and those who survived had a prolonged recovery period. CHAPV RNA was detected in a variety of human body fluids (including blood; urine; nasopharyngeal, oropharyngeal, and bronchoalveolar-lavage fluid; conjunctiva; and semen) and in specimens obtained from captured small-eared pygmy rice rats (Oligoryzomys microtis). In survivors of CHHF, viral RNA was detected up to 170 days after symptom onset; CHAPV was isolated from a semen sample obtained 86 days after symptom onset. CONCLUSIONS: M. Chapare mammarenavirus was identified as the etiologic agent of CHHF. Both spillover from a zoonotic reservoir and possible person-to-person transmission were identified. This virus was detected in a rodent species, O. microtis. (Funded by the Bolivian Ministry of Health and others.)

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 LineGenomic and epidemiological characterization of the ongoing Chikungunya virus epidemic in Paraguay

The emergence and reemergence of mosquito-borne diseases in Brazil such as Yellow Fever, Zika, Chikungunya, and Dengue have had serious impacts on public health. Concerns have been raised due to the rapid dissemination of the chikungunya virus (CHIKV) across the country since its first detection in 2014 in Northeast Brazil. Faced with this scenario, on-site training activities in genomic surveillance carried out in partnership with the National Network of Public Health Laboratories have led to the generation of 422 CHIKV genomes from 12 Brazilian states over the past two years (2021-2022), a period that has seen more than 312 thousand chikungunya fever cases reported in the country. These new genomes increased the amount of available data and allowed a more comprehensive characterization of the dispersion dynamics of the CHIKV East-Central-South-African (ECSA) lineage in Brazil. Tree branching patterns revealed the emergence and expansion of two distinct subclades. Phylogeographic analysis indicated that the northeast region has been the leading hub of virus spread towards other regions. Increased frequency of C>T transitions among the new genomes suggested that host restriction factors from the immune system such as ADAR and AID/APOBEC deaminases might be driving CHIKV ECSA lineage genetic diversity in Brazil.

Objetivos: Estandarizar una prueba RT-LAMP in house para la detección de SARS-CoV-2 y validarla con muestras de laboratorio y de campo en pacientes con sospecha clínica de COVID-19. Materiales y métodos: Se estandarizó una prueba molecular RT-LAMP in house para la detección de SARS-CoV-2 estableciéndose el límite de detección con células Vero de cepas peruanas aisladas de SARS-CoV-2. Se validó la prueba en laboratorio con 384 muestras de hisopado nasal y faríngeo (HNF) obtenidas entre marzo y julio de 2020. Para la validación de campo se obtuvieron muestras de HNF de 383 casos sintomáticos sospechosos de COVID-19. Todas las muestras fueron evaluadas por RT-LAMP y RT-qPCR. Para la validación de laboratorio y de campo se consideró como estándar de referencia al RT-qPCR, se calcularon medidas de concordancia y rendimiento diagnóstico. Resultados: El límite de detección fue consistente en los casos con umbral de ciclo (Ct) Ct 30 en ambas pruebas, mostrando eficiencia para detectar hasta 1000 copias/μL del gen diana. Se evidenció robustez con la mitad de las concentraciones de cebadores y 20 μL de volumen final. Se identificó ausencia de amplificación para otros coronavirus humanos. La concordancia en laboratorio obtuvo un Kappa de 0,88 (IC 95%: 0,83–0,93) y en campo fue de 0,89 (IC 95%: 0,84−0,94); la sensibilidad en laboratorio fue de 87,4% (IC 95%: 80,8−92,4) y en campo fue de 88,1% (IC 95%: 81,6−92,9), la especificidad en ambos escenarios fue de 98,8% (IC 95%: 96,4−99,7). Conclusiones: La prueba RT-LAMP in house fue validada por presentar una adecuada robustez, sin reacciones cruzadas, buena concordancia y rendimiento diagnóstico comparado con el RT-qPCR.

OBJECTIVES: To standardize and validate an in-house RT-LAMP test for the detection of SARS-CoV-2, based on laboratory and field assays using samples from COVID-19 suspected patients. MATERIALS AND METHODS: An in-house SARS-CoV-2 RT-LAMP molecular test was standardized, establishing the detection limit with Vero cells of isolated Peruvian strains of SARS-CoV-2, and the robustness to various concentrations of primers. The laboratory validation was performed with 384 nasal and pharyngeal swab samples (UFH) obtained between March and July 2020. The field validation was performed with 383 UFH obtained from COVID-19 suspected symptomatic cases. All samples were tested by RT-LAMP and RT-qPCR. The RT-qPCR was considered as the reference standard test. The concordance measures and diagnostic performance were calculated. RESULTS: The detection limit was consistent in cases with Ct

Objectives To measure protocol adherence and antigen-based detection tests (AgDT) negative predictive value after 3 months of massive use as a diagnostic tool for COVID-19 in Guatemala Methods The study period included nasopharyngeal swabs taken between March 12 and August 31, 2020, which results were entered in the national COVID-19 information system Proportional increase in testing between one month before and one month after the introduction of AgDT (May 9–June 8 vs June 9–July 8) was measured Results After AgDT introduction, there was a 139% increase in SARS-CoV-2 testing Between June 9 and August 31, 7 8% of 110 657 AgDT-negative patients had follow-up RT-PCR testing Of them, 30% were RT-PCR positive Conclusions While introducing AgDT improved access to diagnostics, ensuring the availability of timely RT-PCR capacities to confirm diagnosis is also key © 2020 Pan American Health Organization All rights reserved

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The timely release of SARS-CoV-2 first genomic sequences allowed the identification of the etiologic agent and development of diagnostic protocols. Genomic sequencing was a crucial step in generating data for driving laboratory response and detections of SARS-CoV-2 since the start of the COVID-19 pandemic. Because of all the progression and achievements that timely release of genetic sequence data represents in the public health response, the Pan American Health Organization (PAHO) in collaboration with countries’ public health laboratories, started implementation of a network for strengthening the Latin America and Caribbean (LAC) region on timely generation of SARS-CoV-2 genomic data. Here we describe the implementation of the COVID-19 Genomic Surveillance Regional Network in the Americas region during the beginning of the pandemic. The establishment of this network has strengthened laboratory response capacity at the country level, as well as facilitated timely release of SARS-CoV-2 genomic information to be used to complement the multiple response strategies for COVID-19 pandemic mitigation. As genomic epidemiology is useful for guiding public health decisions on outbreak and response, we also analysed the first SARS-CoV-2 genomic sequence data from countries of the Latin America and Caribbean Region.

By the time the etiologic agent of the COVID-19 was identified as a novel coronavirus, no country in the Americas Region had laboratory capacity for detecting this new virus. A strategic multilevel approach with specific reagent purchase and delivery, regional trainings, in-country missions, and the provision of technical support was established for timely preparedness of national reference laboratories for SARS-CoV-2 detection. All countries should be prepared to timely detect any potential pandemic emerging agent. The rapid SARS-CoV-2 molecular detection implementation throughout the Americas showed the importance of an efficient and coordinated laboratory response for preparedness. Here we present how in 25 days the Americas Region went from no SARS-CoV-2 diagnostic capacity, to molecular detection fully implemented in 28 Member States, under the coordinated strategy of the Pan American Health Organization and collaborative work at regional and country level with national authorities and public health laboratories.

Yellow fever (YF), an arboviral disease, affects an estimated 200,000 people and causes 30,000 deaths per year and recently has caused major epidemics in Africa and South America. Timely and accurate diagnosis of YF is critical for managing outbreaks and implementing vaccination campaigns. A YF immunoglobulin M (IgM) antibody-capture (MAC) enzyme-linked immunosorbent assay (ELISA) kit, the YF MAC-HD, was successfully introduced starting in 2018 to laboratories in Africa and South America. The YF MAC-HD kit can be performed in 3.5 hours, test up to 24 samples, and includes all reagents necessary to perform the test, except for water used to dilute wash buffer. In 2018 and 2019, a total of 56 laboratory personnel from 39 countries in Africa and South America were trained to use the kit during workshops, followed by take-home YF IgM proficiency testing (PT) exercises. Participants received either a 10- or 20-sample YF PT panel and performed testing using the YF MAC-HD kit. All countries obtained 90% or higher correct results. These results verified the technical viability and transferability of YF MAC-HD kit use for laboratories in YF-endemic countries., Author summary Yellow fever is a vaccine-preventable disease transmitted by mosquitoes that annually affects an estimated 200,000 people and causes 30,000 deaths. Being able to quickly and accurately identify people infected with yellow fever virus by laboratory confirmation is critical for managing outbreaks and vaccination campaigns. A test developed by the Centers for Disease Control and Prevention can identify yellow fever antibodies in a person’s blood within approximately four hours. In order to assure this test could be used in laboratories located in regions with yellow fever transmission, workshops were held to train laboratorians from Africa and South America on how to use the test. Laboratorians were then given a panel of samples and performed the test in their own laboratories. Of the 39 countries that performed testing, all countries scored 90% or higher concordant results, demonstrating the successful transfer of this yellow fever antibody detection test.

Summary Background A Zika virus epidemic emerged in northeast Brazil in 2015 and was followed by a striking increase in congenital microcephaly cases, triggering a declaration of an international public health emergency. This is the final report of the first case-control study evaluating the potential causes of microcephaly: congenital Zika virus infection, vaccines, and larvicides. The published preliminary report suggested a strong association between microcephaly and congenital Zika virus infection. Methods We did a case-control study in eight public maternity hospitals in Recife, Brazil. Cases were neonates born with microcephaly, defined as a head circumference of 2 SD below the mean. Two controls without microcephaly were matched to each case by expected date of delivery and area of residence. We tested the serum of cases and controls and the CSF of cases for detection of Zika virus genomes with quantitative RT-PCR and for detection of IgM antibodies with capture-IgM ELISA. We also tested maternal serum with plaque reduction neutralisation assays for Zika and dengue viruses. We estimated matched crude and adjusted odds ratios with exact conditional logistic regression to determine the association between microcephaly and Zika virus infection. Findings We screened neonates born between Jan 15 and Nov 30, 2016, and prospectively recruited 91 cases and 173 controls. In 32 (35%) cases, congenital Zika virus infection was confirmed by laboratory tests and no controls had confirmed Zika virus infections. 69 (83%) of 83 cases with known birthweight were small for gestational age, compared with eight (5%) of 173 controls. The overall matched odds ratio was 73·1 (95% CI 13·0–∞) for microcephaly and Zika virus infection after adjustments. Neither vaccination during pregnancy or use of the larvicide pyriproxyfen was associated with microcephaly. Results of laboratory tests for Zika virus and brain imaging results were available for 79 (87%) cases; within these cases, ten were positive for Zika virus and had cerebral abnormalities, 13 were positive for Zika infection but had no cerebral abnormalities, and 11 were negative for Zika virus but had cerebral abnormalities. Interpretation The association between microcephaly and congenital Zika virus infection was confirmed. We provide evidence of the absence of an effect of other potential factors, such as exposure to pyriproxyfen or vaccines (tetanus, diphtheria, and acellular pertussis, measles and rubella, or measles, mumps, and rubella) during pregnancy, confirming the findings of an ecological study of pyriproxyfen in Pernambuco and previous studies on the safety of Tdap vaccine administration during pregnancy. Funding Brazilian Ministry of Health, Pan American Health Organization, and Enhancing Research Activity in Epidemic Situations.

OBJECTIVE: To describe the epidemiology of respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) in Colombia from 2000 - 2011, including seasonal trends. METHODS: Nasopharyngeal aspirates and/or throat swabs from 14 870 patients with acute respiratory infections (ARI) were studied. Two subgroups were analyzed using molecular biology techniques. The first consisted of 264 RSV indirect fluorescence assay (IFA)-positive samples, the second of 264 RSV IFA-negative samples. RSV and hMPV were detected using reverse transcription polymerase chain reaction (RT-PCR). RESULTS: 2 799 samples (18.8%) contained a respiratory virus. RSV was detected by IFA in 1 333 samples (8.9%). RSV was detected by RT-PCR in 192 samples from the RSV IFA-positive subgroup and in 25 samples from the RSV IFA-negative subgroup. hMPV was detected in eight samples from the RSV IFA-positive subgroup and in 11 samples from the RSV IFA-negative subgroup. Among the RSV infections, subtype A was dominant in two-year intervals, subtype B was dominant in one-year intervals. 85.3% of RSV and 74% of hMPV infections occurred in children younger than 5 years old. RSV and hMPV infections were associated with rainy seasons. Co-infection with RSV A and RSV B was detected in two patients. Five cases of co-infection with RSV and hMPV were detected. CONCLUSIONS: This report is the first to examine the epidemiology of ARIs in Colombia, with an emphasis on RSV and hMPV. The samples studied here were obtained over a 12-year period and represent all age groups and both genders.

Objectives Our objective was to estimate the incidence of influenza-associated hospitalizations and in-hospital deaths in Central American Region. Design and setting We used hospital discharge records, influenza surveillance virology data, and population projections collected from Costa Rica, El Salvador, Guatemala, Honduras, and Nicaragua to estimate influenza-associated hospitalizations and in-hospital deaths. We performed a meta-analysis of influenza-associated hospitalizations and in-hospital deaths. Main outcome measures The highest annual incidence was observed among children aged

To describe the epidemiology of respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) in Colombia from 2000 - 2011, including seasonal trends.Nasopharyngeal aspirates and/or throat swabs from 14 870 patients with acute respiratory infections (ARI) were studied. Two subgroups were analyzed using molecular biology techniques. The first consisted of 264 RSV indirect fluorescence assay (IFA)-positive samples, the second of 264 RSV IFA-negative samples. RSV and hMPV were detected using reverse transcription polymerase chain reaction (RT-PCR).2 799 samples (18.8%) contained a respiratory virus. RSV was detected by IFA in 1 333 samples (8.9%). RSV was detected by RT-PCR in 192 samples from the RSV IFA-positive subgroup and in 25 samples from the RSV IFA-negative subgroup. hMPV was detected in eight samples from the RSV IFA-positive subgroup and in 11 samples from the RSV IFA-negative subgroup. Among the RSV infections, subtype A was dominant in two-year intervals, subtype B was dominant in one-year intervals. 85.3% of RSV and 74% of hMPV infections occurred in children younger than 5 years old. RSV and hMPV infections were associated with rainy seasons. Co-infection with RSV A and RSV B was detected in two patients. Five cases of co-infection with RSV and hMPV were detected.This report is the first to examine the epidemiology of ARIs in Colombia, with an emphasis on RSV and hMPV. The samples studied here were obtained over a 12-year period and represent all age groups and both genders.