RESUMO
The healthcare workers are considered as a high-risk group for infection with SARS-CoV-2, so they were included in the first stage of the National Plan for Vaccination against COVID-19 in Colombia. An ongoing prospective cohort study to evaluate immune response to vaccination included 490 workers from health institutions in Bogota, Colombia, vaccinated between March and June 2021 with BNT162b2 (Pfizer-BioNtech). Multiple samples were collected during a follow-up period of 6 months after immunization. We report cases of asymptomatic and symptomatic SARS-CoV-2 infections detected in this cohort. For each participant demographic data, vaccination dates, results for SARS-CoV-2 RT-PCR, and detection of antibody (IgG) tests during the follow-up period were collected. SARS-CoV-2 infection was detected in 38 (7.7 %) volunteers. Of these, 81.6% had a positive RT-PCR for SARS-CoV-2, and 18.4% were confirmed by detection of IgG anti-SARS-CoV-2 nucleoprotein; 76.3% of infections occurred after 7 days of second dose. A total of 57.9% of the cases were asymptomatic. No hospitalizations or deaths were registered. When infection occurred, 81.6% of infected participants had presence of IgG anti-S antibodies. In 12 samples in which genomic characterization was achieved, 83.4% corresponded to the variant Mu, 8.3% Gamma, and 8.3% Delta. All findings agree with other reports in different studies that show the benefit of COVID-19 vaccines, protecting specially against severe disease but not against infection or re-infection.
RESUMO
IntroductionSARS-CoV-2 is a new member of the genus Betacoronavirus, responsible for the COVID-19 pandemics. The virus crossed the species barrier and established in the human population due to its ability to exploit the ACE receptor for virus entry, which is present and abundant in several tissues, including the lung and respiratory tract, gastrointestinal tract and hearth. Virus interaction with the cellular receptor is mediated by the surface protein, known as Spike. Another structural protein of major importance in the Nucleocapsid, directly interacting with the viral RNA to form the ribonucleocapsid, considered a multifunctional protein, and being the target of the most molecular diagnostics assays. ObjectiveTo describe the frequency of substitutions in spike and nucleocapsid proteins of SARS-CoV-2 circulating in Colombia and evaluate the frequency of these substitutions in SARS-CoV-2 sequences from other countries of South America. Materials and methodsSamples of 43 patients were included for viral RNA detection by real-time RT-PCR using the Charite-Berlin protocol for the amplification of the SARS-CoV-2 E and RdRp genes. Genome sequences were obtained through the Oxford Nanopore and Illumina MiSeq technologies, following the artic.network "nCoV-2019 sequencing protocol". Available genomes were consulted from GISAID, GenBank, and Genome sequence archive (GSA) and a total of 371 genomes sequences from South America were included. The genome sequences were aligned with the Muscle tool using the MEGA X software. Substitution matrices of the Colombian sequences respect to the reference genome (NC_045512) at the nucleotide and amino acid levels were generated for the spike and nucleocapsid gene. Resultssubstitution D614G in the amino acid sequence of spike protein was found in 86.7% of the Colombian sequences; substitutions G181V and D936Y in 2.3%, respectively. Five substitutions were found in the nucleocapsid protein, with substitution R203K and G204R being the most frequent (13.95 %) in Colombia. The substitutions D614G in Spike and R203K-G204R in nucleocapsid have a frequency of 83% and 28% respectively in sequences from South America. ConclusionNon-synonymous substitutions were found in the spike and nucleocapsid proteins in Colombian genomes, the most frequent being D614G in Spike and R203K-G204R in nucleocapsid. These substitutions are frequent in the genomes reported for other South American countries. It is necessary to continue with genomic surveillance of the changes in Spike and Nucleocapsid proteins during the SARS-CoV-2 pandemic in Colombia and South America, even more considering that these proteins are the most commonly used antigen in serological tests. HighlightsO_LIThe spike and nucleocapsid proteins of SARS-CoV-2 circulating in Colombia and South-American countries have similar patterns of non-synonymous substitutions C_LIO_LISubstitutions D614G in Spike and R203K-G204R in Nucleocapsid are the most frequent in Colombia and South-American countries C_LI
RESUMO
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 inhouse 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. HIGHLIGHTSO_LIColombian SARS-CoV-2 sequences displayed genetic variability in some target regions used for COVID-19 diagnosis. C_LIO_LIMismatches in critical primer regions could impact their performance and the rate of false negative results. C_LI
