Neutralizing responses in fully vaccinated with BNT162b2, CoronaVac, ChAdOx1, and Ad26.COV2.S against SARS-CoV-2 lineages in Colombia, 2020-2021 (preprint)

Background By March 2022, around 34 million people in Colombia had received a complete scheme of vaccines against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) including, mRNA-based vaccines, viral vectored coronavirus vaccines, or the inactivated whole virus vaccine. However, as several SARS CoV 2 variants of concern (VOC) and interest (VOI) cocirculate in the country, determining the resistance level to vaccine elicited neutralizing antibodies (nAbs) is useful to improve the efficacy of COVID-19 vaccination programs. Methods Microneutralization assays with the most prevalent SARS-CoV-2 lineages in Colombia during 2020-2021 were performed using serum samples from immunologically naive individuals between 9 and 13 weeks after receiving complete regimens of CoronaVac, BNT162b2, ChAdOx1, or Ad26.COV2.S. The mean neutralization titer (MN50) was calculated by the Reed-Muench method and used to determine differences in vaccine elicited nAbs against the SARS-CoV-2 lineages B.1.111, P.1 (Gamma), B.1.621 (Mu), and AY.25.1 (Delta). Results The most administered vaccines in the country, BNT162b2 and CoronaVac, elicited significantly different nAb responses against Mu, as the GMTs were 75.7 and 5.9 fold lower relative to the control lineage (B.1.111), while for Delta were 15.8 and 1.1-fold lower, respectively. In contrast, nAb responses against Mu and Delta were comparable between ChAd0x1-s and Ad26.COV2.S as the GMTs remained around 5 to 7 fold lower relative to B.1.111. Conclusions The emergence of SARS-CoV-2 variants in Colombia with a significant capacity to escape from vaccine elicited nAbs indicates that a booster dose is highly recommended. Furthermore, other non-pharmacological measures should be retained in the vaccinated population.

Low neutralizing antibody titers against the Mu variant of SARS-CoV-2 in BNT162b2 vaccinated individuals (preprint)

Summary Background Global surveillance programs for the virus that causes COVID-19 are showing the emergence of variants with mutations in the Spike protein, including the Mu variant, recently declared a Variant of Interest (VOI) by the World Health Organization. Genomic and laboratory surveillance is important in these types of variants because they may be more infectious or less susceptible to antiviral treatments and vaccine-induced antibodies. Objectives To evaluate the sensitivity of the Mu variant (B.1.621) to neutralizing antibodies induced by the BNT162b2 vaccine. Study design Three of the most predominant SARS-CoV-2 variants in Colombia during the epidemiological peaks of 2021 were isolated. Microneutralization assays were performed by incubating 120 TCDI 50 of each SARS-CoV-2 isolate with five 2-fold serial dilutions of sera from 14 BNT162b2 vaccinated volunteers. The MN 50 titer was calculated by the Reed-Muench formula Results The three isolated variants were Mu, a Variant of Interest (VOI), Gamma, a variant of concern (VOC), and B.1.111 that lacks genetic markers associated with greater virulence. At the end of August, the Mu and Gamma variants were widely distributed in Colombia. Mu was predominant (49%), followed by Gamma (25%). In contrast, B.1.111 became almost undetectable. The evaluation of neutralizing antibodies suggests that patients vaccinated with BNT162-2 generate neutralizing antibody titers against the Mu variant at significantly lower concentrations relative to B.1.111 and Gamma. Conclusions This study shows the importance of continuing with surveillance programs of emerging variants as well as the need to evaluate the neutralizing antibody response induced by other vaccines circulating in the country against Mu and other variants with high epidemiological impact. Highlights Mu and Gamma variants represented 49% and 25% of cases in Colombia by August 2021. Increased proportion of SARS-COV-2 cases were mostly associated with Mu variant, despite being detected simultaneously with the VOC Gamma The Mu variant remarkably escapes from neutralizing antibodies elicited by the BNT162b2-vaccine Laboratory studies of neutralizing antibodies are useful to determine the efficacy of SARS-CoV-2 vaccines against VOC and VOI.

Seroprevalence of Anti-Sars-Cov-2 Antibodies in Colombia, 2020: A Population-Based Study (preprint)

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to cause very high morbidity and mortality throughout Latin American countries. However, few population-based seroprevalence surveys have been conducted to quantify attack rates and characterize drivers of transmission.Methods: We conducted a population-based cross-sectional study to assess the seroprevalence of antibodies against SARS-CoV-2 in ten cities in Colombia between September and December, 2020. The study involved multi-stage cluster sampling at each city. Participants provided a serum sample and answered a demographic and risk factor questionnaire. Prior infection by SARS-CoV-2 was ascertained using the "SARS-CoV-2 Total (COV2T) Advia Centaur - Siemens" chemiluminescence assay.Findings: A total of 17863 participants from 7075 households participated in the study. Seroprevalence varied substantially between cities, ranging from 21% (95%CI 16-25%) in Medellín to 78% (95%CI 65-91%) in Guapi. There were no differences in seroprevalence by sex, but seropositivity was lower in adults 60 years or older and higher in certain ethnic groups. There was substantial heterogeneity in seroprevalence within cities, driven to a large extent by a strong association between socio-economic stratum and seropositivity.Interpretation: Colombia has been one of the Latin American countries most affected by the COVID-19 pandemic. This study documented very high attack rates in several Colombian cities by the end of 2020 and identified key drivers of heterogeneities including ethnicity and socio-economic stratum. Few studies of seroprevalence of SARS-CoV-2 have been conducted in Latin America, and therefore this study contributes to the fundamental understanding of the pandemic in the region.

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

The SARS-CoV-2 genetic diversification has a potential impact in the virus escape from natural infection- or vaccine-elicited neutralizing antibodies and higher transmissibility. Here we report the emergence of novel B.1.621 variant of interest with the insertion 145N in the N-terminal domain and amino acid change N501Y, E484K, and P681H in the Receptor Binding Domain of the Spike protein. Further studies in vitro biological assays and epidemiologic analysis will allow evaluating the public health impact of B.1.621 variant.

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

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 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. (preprint)

The COVID-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. The test was standardized using an antigenic epitopes 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, 34 positive sera were used, including sera from asymptomatic and symptomatic patients (mild and severe) and 68 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. The 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% for both parameters. The ELIPSE-COL assay was developed as an ELISA test using synthetic peptides for the study of the seroprevalence of SARS-CoV-2 infection in Colombia.

Genomic epidemiology of SARS-CoV-2 in Colombia (preprint)

Coronavirus disease 2019 (COVID-19) was first diagnosed in Colombia from a traveler arriving from Italy on February 26, 2020. To date, available data on the origins and number or introductions of SARS-CoV-2 into the country are limited. Here, we sequenced SARS-CoV-2 from 43 clinical samples and-together with another 73 genomes sequences available from the country-we investigated the emergence and the routes of importation of COVID-19 into Colombia using epidemiological, historical air travel and phylogenetic observations. Our study provided evidence of multiple introductions, mostly from Europe, with at least 12 lineages being documented. Phylogenetic findings validated the linkage of epidemiologically-linked transmission chains. Our results demonstrate the advantages of genome sequencing to complement COVID-19 outbreak investigation and underscores that human mobility and genetic data are relevant to complete epidemiological investigation and better characterize virus transmission dynamics at local scales.

Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in Colombia (preprint)

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

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. (preprint)

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.