Human respiratory syncytial virus and metapneumovirus in patients with acute respiratory infection in Colombia, 2000 - 2011.

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.

Predictors of poor outcomes of respiratory syncytial virus acute lower respiratory infections in children under 5 years of age in a middle-income tropical country based on the National Public Health Surveillance System.

OBJECTIVES: The aim of the present study is to gain insight into the identification of region-specific factors associated with poor outcomes in children under 5 years of age with confirmed respiratory syncytial virus acute lower respiratory infection (RSV-ALRI) living in Colombia, a middle-income country, based on the National Public Health Surveillance System of the country. METHODS: An analytical cross-sectional study was conducted using epidemiological data from the records of morbidity and mortality of respiratory infections as registered in the surveillance system report of the National Institute of Health of Colombia 2018, including children under 5 years of age with confirmed RSV-ALRI. Predictor variables included demographic and clinical variables, as well as variables measured after hospital attendance. Outcome variables analyzed were respiratory failure, the need for pediatric intensive care unit admission, and mortality. RESULTS: Of a total of 8470 patients with a diagnosis of ALRI, we selected 1215 (14.3%) that were under 5 years of age and were positive for RSV. After controlling for potential confounders, it was found that age, gender, socioeconomic stratum, incomplete pneumococcal conjugate vaccine 13 immunization for age, cardiac disease, and malnutrition as comorbidities, chest X-ray findings, and development of sepsis independently predicted poor outcomes among the patients analyzed. CONCLUSIONS: The identified predictors for poor outcomes in RSV-affected children may be helpful for guiding efficient and targeted national and/or regional programs and public policies to assist in achieving Goal 3 of the Sustainable Development Goals adopted by the United Nations in 2015.

Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America.

SARS-CoV-2 is a new member of the genus Betacoronavirus, responsible for the COVID-19 pandemic. The virus crossed the species barrier and established in the human population taking advantage of the spike protein high affinity for the ACE receptor to infect the lower respiratory tract. The Nucleocapsid (N) and Spike (S) are highly immunogenic structural proteins and most commercial COVID-19 diagnostic assays target these proteins. In an unpredictable epidemic, it is essential to know about their genetic variability. The objective of this study was to describe the substitution frequency of the S and N proteins of SARS-CoV-2 in South America. A total of 504 amino acid and nucleotide sequences of the S and N proteins of SARS-CoV-2 from seven South American countries (Argentina, Brazil, Chile, Ecuador, Peru, Uruguay, and Colombia), reported as of June 3, and corresponding to samples collected between March and April 2020, were compared through substitution matrices using the Muscle algorithm. Forty-three sequences from 13 Colombian departments were obtained in this study using the Oxford Nanopore and Illumina MiSeq technologies, following the amplicon-based ARTIC network protocol. The substitutions D614G in S and R203K/G204R in N were the most frequent in South America, observed in 83% and 34% of the sequences respectively. Strikingly, genomes with the conserved position D614 were almost completely replaced by genomes with the G614 substitution between March to April 2020. A similar replacement pattern was observed with R203K/G204R although more marked in Chile, Argentina and Brazil, suggesting similar introduction history and/or control strategies of SARS-CoV-2 in these countries. It is necessary to continue with the genomic surveillance of S and N proteins during the SARS-CoV-2 pandemic as this information can be useful for developing vaccines, therapeutics and diagnostic tests.

Molecular analysis of several in-house rRT-PCR protocols for SARS-CoV-2 detection in the context of genetic variability of the virus in Colombia.

The COVID-19 pandemic caused by SARS-CoV-2 is a public health problem unprecedented in the recent history of humanity. Different in-house real-time RT-PCR (rRT-PCR) methods for SARS-CoV-2 diagnosis and the appearance of genomes with mutations in primer regions have been reported. Hence, whole-genome data from locally-circulating SARS-CoV-2 strains contribute to the knowledge of its global variability and the development and fine tuning of diagnostic protocols. To describe the genetic variability of Colombian SARS-CoV-2 genomes in hybridization regions of oligonucleotides of the main in-house methods for SARS-CoV-2 detection, RNA samples with confirmed SARS-CoV-2 molecular diagnosis were processed through next-generation sequencing. Primers/probes sequences from 13 target regions for SARS-CoV-2 detection suggested by 7 institutions and consolidated by WHO during the early stage of the pandemic were aligned with Muscle tool to assess the genetic variability potentially affecting their performance. Finally, the corresponding codon positions at the 3' end of each primer, the open reading frame inspection was identified for each gene/protein product. Complete SARS-CoV-2 genomes were obtained from 30 COVID-19 cases, representative of the current epidemiology in the country. Mismatches between at least one Colombian sequence and five oligonucleotides targeting the RdRP and N genes were observed. The 3' end of 4 primers aligned to the third codon position, showed high risk of nucleotide substitution and potential mismatches at this critical position. Genetic variability was detected in Colombian SARS-CoV-2 sequences in some of the primer/probe regions for in-house rRT-PCR diagnostic tests available at WHO COVID-19 technical guidelines; its impact on the performance and rates of false-negative results should be experimentally evaluated. The genomic surveillance of SARS-CoV-2 is highly recommended for the early identification of mutations in critical regions and to issue recommendations on specific diagnostic tests to ensure the coverage of locally-circulating genetic variants.

Human respiratory syncytial virus and metapneumovirus in patients with acute respiratory infection in Colombia, 2000 - 2011 / Virus sincitial respiratorio y metapneumovirus humano en pacientes con infección respiratoria aguda en Colombia, 2000 - 2011

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.

OBJETIVO: Describir la epidemiología y tendencias estacionales del virus sincitial respiratorio (VSR) y metapneumovirus humano (MPVh) en Colombia durante el período 2000 - 2011. MÉTODOS: Se recolectaron aspirados nasofaríngeos o hisopados faríngeos de 14 870 pacientes con infección respiratoria aguda. Se analizaron dos subgrupos por técnicas de biología molecular. El primero estuvo compuesto por 264 muestras positivas para el VSR por inmunofluorescencia indirecta (IFI), y el segundo estuvo compuesto por 264 muestras negativas para el VSR por IFI. La técnica utilizada para la detección del VSR y el MPVh en ambos subgrupos fue la transcripción inversa asociada a la reacción en cadena de la polimerasa (RT-PCR). RESULTADOS: 2 799 muestras (18,8%) contenían algún virus respiratorio. Se detectó VSR por IFI en 1 333 muestras (8,9%), e igualmente fue detectado por RT-PCR en 192 muestras en el subgrupo de muestras positivas para el VSR por IFI y en 25 muestras en el subgrupo de muestras negativas para el VSR por IFI. Se detectó MPVh en 8 muestras en el subgrupo de muestras positivas para el VSR por IFI, y en 11 muestras en el subgrupo de muestras negativas para el VSR por IFI. De las infecciones causadas por el VSR, el subtipo A fue dominante en períodos bianuales; en contraste, el subtipo B fue dominante en períodos anuales. El 85,3% de las infecciones por el VSR y 74% de las infecciones por el MPVh ocurrieron en niños menores de 5 años de edad. Las infecciones causadas por el VSR y el MPVh se asociaron con las estaciones de lluvia. Se encontró coinfección con VSR A y VSR B en 2 pacientes, y coinfección con VSR y MPVh en 5 pacientes. CONCLUSIONES: Esta investigación es la primera en estudiar la epidemiología de las infecciones respiratorias agudas en Colombia, con énfasis en las causadas por el VSR y el MPVh. Las muestras estudiadas fueron recolectadas durante un período de 12 años y representan todos los grupos etarios de ambos sexos.