Monitoring acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity and emerging mutations in this ongoing pandemic is crucial for understanding its evolution and assuring the performance of diagnostic tests, vaccines, and therapies against coronavirus disease (COVID-19). This study reports on the amino acid (aa) conservation degree and the global and regional temporal evolution by epidemiological week for each residue of the following four structural SARS-CoV-2 proteins: spike, envelope, membrane, and nucleocapsid. All, 105,276 worldwide SARS-CoV-2 complete and partial sequences from 117 countries available in the Global Initiative on Sharing All Influenza Data (GISAID) from 29 December 2019 to 12 September 2020 were downloaded and processed using an in-house bioinformatics tool. Despite the extremely high conservation of SARS-CoV-2 structural proteins (>99%), all presented aa changes, i.e., 142 aa changes in 65 of the 75 envelope aa, 291 aa changes in 165 of the 222 membrane aa, 890 aa changes in 359 of the 419 nucleocapsid aa, and 2671 changes in 1132 of the 1273 spike aa. Mutations evolution differed across geographic regions and epidemiological weeks (epiweeks). The most prevalent aa changes were D614G (81.5%) in the spike protein, followed by the R203K and G204R combination (37%) in the nucleocapsid protein. The presented data provide insight into the genetic variability of SARS-CoV-2 structural proteins during the pandemic and highlights local and worldwide emerging aa changes of interest for further SARS-CoV-2 structural and functional analysis.

Monitoring SARS-CoV-2’s genetic diversity and emerging mutations in this ongoing pandemic is crucial to understanding its evolution and ensuring the performance of COVID-19 diagnostic tests, vaccines, and therapies. Spain has been one of the main epicenters of COVID-19, reaching the highest number of cases and deaths per 100,000 population in Europe at the beginning of the pandemic. This study aims to investigate the epidemiology of SARS-CoV-2 in Spain and its 18 Autonomous Communities across the six epidemic waves established from February 2020 to January 2022. We report on the circulating SARS-CoV-2 variants in each epidemic wave and Spanish region and analyze the mutation frequency, amino acid (aa) conservation, and most frequent aa changes across each structural/non-structural/accessory viral protein among the Spanish sequences deposited in the GISAID database during the study period. The overall SARS-CoV-2 mutation frequency was 1.24 × 10⁻⁵. The aa conservation was >99% in the three types of protein, being non-structural the most conserved. Accessory proteins had more variable positions, while structural proteins presented more aa changes per sequence. Six main lineages spread successfully in Spain from 2020 to 2022. The presented data provide an insight into the SARS-CoV-2 circulation and genetic variability in Spain during the first two years of the pandemic.

HIV variants carry natural polymorphisms related to drug resistance (R-markers) fixed during viral evolution in the absence of antiretroviral therapy (ART) that may impact on drug susceptibility and resistance pathways. We aimed to identify the HIV type 2 (HIV-2) variant-specific R-markers at Pol in all available sequences from ART-naive subjects deposited in Los Alamos database according to reported HIV-2 drug resistance-associated mutations (DRMs) and report the performance of two online HIV-2 resistance interpretation tools (HIV2EU Tool and Stanford HIVdb Program for HIV-2) to detect them. From a total of 587 sequences, we found 23 R-markers in low frequency, in groups A, B, and G. Four were present in >10% of the sequences with no direct impact on antiretroviral susceptibility. HIV2EU Tool detected one, whereas Stanford program all four. Stanford new tool, although still under development, seems effective in detecting HIV-2 DRMs and may prove a useful tool for HIV-2 resistance interpretation when fully developed.

There are 39 million people infected by the human immunodeficiency virus (HIV) and 1.3 million new annually infections with more than 150 variants circulating. Early HIV detection is crucial for timely antiretroviral therapy and transmission prevention, but no technique can detect HIV before 10 days of infection. Aptamers, single-stranded oligonucleotides, can recognize specific proteins with high affinity and specificity. New molecular assays based on aptamers selected against highly-conserved peptides in HIV proteins could help to detect the virus earlier. We have selected and characterized the first two aptamers against a highly-conserved and exposed peptide in the HIV protease (PR) after analyzing 236,240/6,436 HIV-1/HIV-2 PR sequences of nearly 150 HIV variants (types/groups/subtypes/circulating recombinants) by new bioinformatics tools. The selected aptamers were characterized by bioinformatics analysis, exploring their affinity, sensitivity, specificity, and best combination by Enzyme-Linked-Oligonucleotide-Assays (ELONA). Different strategies were explored to increase sensitivity for HIV PR detection, and the best one could detect viral PR (3.13 ng, 3.76·10⁸ virions/well) and also HIV in infected samples with viraemia >8 log. Our anti-HIV PR aptamers are a promissing tool to be incorporated into new nanotechnologies for an ultrasensitive detection of HIV proteins in clinical samples for an early diagnosis of all virus variants.

Purpose: Genetic sequence analysis has become essential in many fields of medicine, biology, and epidemiology. However, the currently available tools can pose a challenge for users without advanced computational skills. Results: We present EpiMolBio ( https://www.epimolbio.com ), a free-to-use software designed with an intuitive, user-friendly interface that enables a broad spectrum of users to explore genetic variability. Its diverse toolkit encompasses sequence processing, conservation and variability analysis, consensus sequence generation, and identification of genome mutation or amino acid changes, including specialized tools for HIV and SARS-CoV-2 analysis.

Motivation: Genetic sequence analysis has become essential in many medicine, biology, and epidemiology fields. However, the currently available tools can pose a challenge for users without advanced computational skills. Results: We present EpiMolBio, a free-to-use software designed with an intuitive, user-friendly interface that enables a broad spectrum of users to explore genetic variability. Its diverse toolkit encompasses sequence processing, conservation and variability analysis, consensus sequence generation, and genome mutation or amino acid changes identification, including specialized tools for HIV and SARS-CoV-2 analysis. Availability: Freely available on the web at https://www.epimolbio.com and https://github.com/EpiMolBio/EpiMolBio . Contact: africa.holguin@salud.madrid.org ; roberto117343@gmail.com Supplementary information: Supplementary Table 1, 2, and Supplementary Text 1.