Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean.

Latin America and Caribbean (LAC) regions were an important epicenter of the COVID-19 pandemic and SARS-CoV-2 evolution. Through the COVID-19 Genomic Surveillance Regional Network (COVIGEN), LAC countries produced an important number of genomic sequencing data that made possible an enhanced SARS-CoV-2 genomic surveillance capacity in the Americas, paving the way for characterization of emerging variants and helping to guide the public health response. In this study we analyzed approximately 300,000 SARS-CoV-2 sequences generated between February 2020 and March 2022 by multiple genomic surveillance efforts in LAC and reconstructed the diffusion patterns of the main variants of concern (VOCs) and of interest (VOIs) possibly originated in the Region. Our phylogenetic analysis revealed that the spread of variants Gamma, Lambda and Mu reflects human mobility patterns due to variations of international air passenger transportation and gradual lifting of social distance measures previously implemented in countries. Our results highlight the potential of genetic data to reconstruct viral spread and unveil preferential routes of viral migrations that are shaped by human mobility patterns.

Etiology of Acute Lower Respiratory Illness Hospitalizations Among Infants in 4 Countries.

Background: Recent studies explored which pathogens drive the global burden of pneumonia hospitalizations among young children. However, the etiology of broader acute lower respiratory tract infections (ALRIs) remains unclear. Methods: Using a multicountry study (Albania, Jordan, Nicaragua, and the Philippines) of hospitalized infants and non-ill community controls between 2015 and 2017, we assessed the prevalence and severity of viral infections and coinfections. We also estimated the proportion of ALRI hospitalizations caused by 21 respiratory pathogens identified via multiplex real-time reverse transcription polymerase chain reaction with bayesian nested partially latent class models. Results: An overall 3632 hospitalized infants and 1068 non-ill community controls participated in the study and had specimens tested. Among hospitalized infants, 1743 (48.0%) met the ALRI case definition for the etiology analysis. After accounting for the prevalence in non-ill controls, respiratory syncytial virus (RSV) was responsible for the largest proportion of ALRI hospitalizations, although the magnitude varied across sites-ranging from 65.2% (95% credible interval, 46.3%-79.6%) in Albania to 34.9% (95% credible interval, 20.0%-49.0%) in the Philippines. While the fraction of ALRI hospitalizations caused by RSV decreased as age increased, it remained the greatest driver. After RSV, rhinovirus/enterovirus (range, 13.4%-27.1%) and human metapneumovirus (range, 6.3%-12.0%) were the next-highest contributors to ALRI hospitalizations. Conclusions: We observed substantial numbers of ALRI hospitalizations, with RSV as the largest source, particularly in infants aged <3 months. This underscores the potential for vaccines and long-lasting monoclonal antibodies on the horizon to reduce the burden of ALRI in infants worldwide.

Development of in-house serological methods for diagnosis and surveillance of chikungunya / Desarrollo de métodos serológicos propios para el diagnóstico y la vigilancia del chikungunya

ABSTRACT Objective To develop and evaluate serological methods for chikungunya diagnosis and research in Nicaragua. Methods Two IgM ELISA capture systems (MAC-ELISA) for diagnosis of acute chikungunya virus (CHIKV) infections, and two Inhibition ELISA Methods (IEM) to measure total antibodies against CHIKV were developed using monoclonal antibodies (mAbs) and hyperimmune serum at the National Virology Laboratory of Nicaragua in 2014-2015. The sensitivity, specificity, predictive values, and agreement of the MAC-ELISAs were obtained by comparing the results of 198 samples (116 positive; 82 negative) with the Centers for Disease Control and Prevention's IgM ELISA (Atlanta, Georgia, United States; CDC-MAC-ELISA). For clinical evaluation of the four serological techniques, 260 paired acute and convalescent phase serum samples of suspected chikungunya cases were used. Results All four assays were standardized by determining the optimal concentrations of the different reagents. Processing times were substantially reduced compared to the CDC-MAC-ELISA. For the MAC-ELISA systems, a sensitivity of 96.6% and 97.4%, and a specificity of 98.8% and 91.5% were obtained using mAb and hyperimmune serum, respectively, compared with the CDC method. Clinical evaluation of the four serological techniques versus the CDC real-time RT-PCR assay resulted in a sensitivity of 95.7% and a specificity of 88.8%-95.9%. Conclusion Two MAC-ELISA and two IEM systems were standardized, demonstrating very good quality for chikungunya diagnosis and research demands. This will achieve more efficient epidemiological surveillance in Nicaragua, the first country in Central America to produce its own reagents for serological diagnosis of CHIKV. The methods evaluated here can be applied in other countries and will contribute to sustainable diagnostic systems to combat the disease.

RESUMEN Objetivo Elaborar y evaluar métodos serológicos para el diagnóstico y la investigación del chikungunya. Métodos Se elaboraron dos sistemas de ELISA de captura de IgM (MAC-ELISA por sus siglas en inglés) para el diagnóstico de la infección aguda por el virus de (CHIKV) y dos métodos de ELISA de inhibición (MEI) para determinar el valor cuantitativo de los anticuerpos totales contra el CHIKV, en el Laboratorio Nacional de Virología de Nicaragua en 2014-2015, para lo cual se utilizaron anticuerpos monoclonales (AcMo) y sueros hiperinmunes. Se determinó la sensibilidad, la especificidad y los valores predictivos, así como la concordancia de los MAC-ELISA, comparando los resultados de 198 muestras (116 positivas y 82 negativas) con el ELISA de los Centros para el Control y la Prevención de Enfermedades de los Estados Unidos (Atlanta; MAC-ELISA-CDC). Para la evaluación clínica de las cuatro técnicas serológicas, se emplearon 260 muestras de suero obtenidas en la fase aguda y en la fase de convalecencia de presuntos casos de chikungunya. Resultados Se estandarizaron los cuatro métodos analíticos determinando las concentraciones óptimas de los diferentes reactivos. La duración del procesamiento se redujo sustancialmente en comparación con el MAC-ELISA-CDC. Con los sistemas de MAC-ELISA, se obtuvo una sensibilidad del 96,6% y del 97,4% y una especificidad del 98,8% y del 91,5% al utilizar AcMo y suero hiperinmune, respectivamente, en comparación con el método de los CDC. La evaluación clínica de las cuatro técnicas serológicas, en comparación con la PCR en tiempo real de los CDC, arrojó una sensibilidad del 95,7% y una especificidad del 88,8%-95,9%. Conclusiones Se estandarizaron dos sistemas de ELISA-MAC y dos de MEI y se comprobó que poseen la calidad adecuada para el diagnóstico y las investigaciones del chikungunya, con lo cual mejorará la eficiencia de la vigilancia epidemiológica en Nicaragua, el primer país centroamericano que produce sus propios reactivos para el diagnóstico serológico del CHIKV. Los métodos estudiados en este trabajo pueden aplicarse en otros países y contribuyen al desarrollo de sistemas de diagnóstico sostenibles para combatir la enfermedad.