Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2

The genetic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has the potential to impact the virus transmissibility and the escape from natural infection- or vaccine-elicited neutralizing antibodies. Here, representative samples from circulating SARS-CoV-2 in Colombia between January and April 2021, were processed for genome sequencing and lineage determination following the nanopore amplicon ARTIC network protocol and PANGOLIN pipeline. This strategy allowed us to identify the emergence of the B.1.621 lineage, considered a variant of interest (VOI) with the accumulation of several substitutions affecting the Spike protein, including the amino acid changes T95I, Y144T, Y145S and the insertion 146N in the N-terminal domain, R346K, E484K and N501Y in the Receptor-binding Domain (RBD) and P681H1 in the S1/S2 cleavage site of the Spike protein. The rapid increase in frequency and fixation in a relatively short time in Magdalena, Atlantico, Bolivar, Bogota D.C, and Santander that were near the theoretical herd immunity suggests an epidemiologic impact. Further studies will be required to assess the biological and epidemiologic roles of the substitution pattern found in the B.1.621 lineage. HighlightsO_LIMonitoring the emergence of new variants of SARS-CoV-2 in real time is a worldwide priority. C_LIO_LIEmerging variants of SARS-CoV-2 may have high impact biological implications for public health C_LIO_LIThe SARS-CoV-2 B.1.621 variant of interest was characterized by several substitutions: T95I, Y144T, Y145S, ins146N, R346K, E484K, N501Y and P681H in spike protein. C_LI

Novel highly divergent SARS-CoV-2 lineage with the Spike substitutions L249S and E484K

COVID-19 pandemics has led to genetic diversification of SARS-CoV-2 and the appearance of variants with potential impact in transmissibility and viral escape from acquired immunity. We report a new lineage containing ten distinctive amino acid changes across the genome. Further studies are required for monitoring its epidemiologic impact.

ELIPSE-COL: A novel ELISA test based on rational envisioned synthetic peptides for detection of SARS-CoV-2 infection in Colombia.

BackgroundCOVID-19 pandemic caused by infection with the betacoronavirus SARS-CoV-2 is the greatest public health defiant on a global scale in the last 100 years. Governments and health Institutes face challenges during the pandemic, related to the diagnosis, mitigation, treatment, and timely detection after the epidemic peak for the prevention of new infections and the evaluation of the real impact of the COVID-19 disease in different geographic areas. To develop a valuable tool to study the seroprevalence of SARS-CoV-2 infection in Colombia, an "in-house" ELISA was achieved for the detection of IgG anti-SARS-CoV-2 antibodies in serum. MethodsThe test was standardized using an antigenic epitope "Pool" of the synthetic peptide as antigen derived from antigenic regions of the spike, nucleocapsid, envelope, and membrane structural proteins, which were designed, based on the genomic information of SARS-CoV-2 circulating in Colombia. In the ELISA standardization process, 94 positive sera were used, including sera from asymptomatic and symptomatic patients (mild and severe) and 123 negative sera, including pre-pandemic historical negatives originating from patients living in arbovirus endemic areas or patients with a history of respiratory diseases and sera from patients with a negative rRT-PCR test for SARS-CoV-2. ResultsThe in-house peptide ELIPSE-COL test showed promising performance, being able to detect reactivity in sera from asymptomatic and symptomatic patients. The sensitivity and specificity of the assay were 91.4% and 83.7% respectively. ConclusionELIPSE-COL assay was developed as an ELISA test using synthetic peptides for the study of the seroprevalence of SARS-CoV-2 infection in Colombia. SUMMARY BOXO_LIDetection of IgG anti-SARS-CoV-2 antibodies is required for the evaluation of the pandemic impact and vaccination strategies. C_LIO_LIELIPSE-COL is an in-house test based on synthetic peptides as antigen derived from antigenic regions of the spike, nucleocapsid, envelope, and membrane structural proteins. C_LIO_LIThe sensitivity and specificity of the assay were 91.4% and 83.7% respectively suggesting a promising performance. C_LIO_LIELIPSE-COL test is a valuable tool for the study of seroprevalence in Colombia. C_LI