@article {766, title = {Detection of High Level of Co-Infection and the Emergence of Novel SARS CoV-2 Delta-Omicron and Omicron-Omicron Recombinants in the Epidemiological Surveillance of Andalusia.}, journal = {Int J Mol Sci}, volume = {24}, year = {2023}, month = {2023 Jan 26}, abstract = {

Recombination is an evolutionary strategy to quickly acquire new viral properties inherited from the parental lineages. The systematic survey of the SARS-CoV-2 genome sequences of the Andalusian genomic surveillance strategy has allowed the detection of an unexpectedly high number of co-infections, which constitute the ideal scenario for the emergence of new recombinants. Whole genome sequence of SARS-CoV-2 has been carried out as part of the genomic surveillance programme. Sample sources included the main hospitals in the Andalusia region. In addition to the increase of co-infections and known recombinants, three novel SARS-CoV-2 delta-omicron and omicron-omicron recombinant variants with two break points have been detected. Our observations document an epidemiological scenario in which co-infection and recombination are detected more frequently. Finally, we describe a family case in which co-infection is followed by the detection of a recombinant made from the two co-infecting variants. This increased number of recombinants raises the risk of emergence of recombinant variants with increased transmissibility and pathogenicity.

}, issn = {1422-0067}, doi = {10.3390/ijms24032419}, author = {Perez-Florido, Javier and Casimiro-Soriguer, Carlos S and Ortuno, Francisco and Fernandez-Rueda, Jose L and Aguado, Andrea and Lara, Mar{\'\i}a and Riazzo, Cristina and Rodriguez-Iglesias, Manuel A and Camacho-Martinez, Pedro and Merino-Diaz, Laura and Pupo-Ledo, Inmaculada and de Salazar, Adolfo and Vi{\~n}uela, Laura and Fuentes, Ana and Chueca, Natalia and Garc{\'\i}a, Federico and Dopazo, Joaquin and Lepe, Jose A} } @article {801, title = {Evaluation of a combined detection of SARS-CoV-2 and its variants using real-time allele-specific PCR strategy: an advantage for clinical practice.}, journal = {Epidemiol Infect}, volume = {151}, year = {2023}, month = {2023 Nov 24}, pages = {e201}, abstract = {

This study aimed to assess the ability of a real-time reverse transcription polymerase chain reaction (RT-PCR) with multiple targets to detect SARS-CoV-2 and its variants in a single test. Nasopharyngeal specimens were collected from patients in Granada, Spain, between January 2021 and December 2022. Five allele-specific RT-PCR kits were used sequentially, with each kit designed to detect a predominant variant at the time. When the Alpha variant was dominant, the kit included the HV69/70 deletion, E and N genes. When Delta replaced Alpha, the kit incorporated the L452R mutation in addition to E and N genes. When Omicron became dominant, L452R was replaced with the N679K mutation. Before incorporating each variant kit, a comparative analysis was carried out with SARS-CoV-2 whole genome sequencing (WGS). The results demonstrated that RT-PCR with multiple targets can provide rapid and effective detection of SARS-CoV-2 and its variants in a single test. A very high degree of agreement (96.2\%) was obtained between the comparison of RT-PCR and WGS. Allele-specific RT-PCR assays make it easier to implement epidemiological surveillance systems for effective public health decision making.

}, keywords = {Alleles, COVID-19, COVID-19 Testing, Humans, Real-Time Polymerase Chain Reaction, SARS-CoV-2, Sensitivity and Specificity}, issn = {1469-4409}, doi = {10.1017/S095026882300184X}, author = {Chaves-Blanco, Luc{\'\i}a and de Salazar, Adolfo and Fuentes, Ana and Vi{\~n}uela, Laura and Perez-Florido, Javier and Dopazo, Joaquin and Garc{\'\i}a, Federico} } @article {744, title = {Highly accurate whole-genome imputation of SARS-CoV-2 from partial or low-quality sequences.}, journal = {Gigascience}, volume = {10}, year = {2021}, month = {2021 12 02}, abstract = {

BACKGROUND: The current SARS-CoV-2 pandemic has emphasized the utility of viral whole-genome sequencing in the surveillance and control of the pathogen. An unprecedented ongoing global initiative is producing hundreds of thousands of sequences worldwide. However, the complex circumstances in which viruses are sequenced, along with the demand of urgent results, causes a high rate of incomplete and, therefore, useless sequences. Viral sequences evolve in the context of a complex phylogeny and different positions along the genome are in linkage disequilibrium. Therefore, an imputation method would be able to predict missing positions from the available sequencing data.

RESULTS: We have developed the impuSARS application, which takes advantage of the enormous number of SARS-CoV-2 genomes available, using a reference panel containing 239,301 sequences, to produce missing data imputation in viral genomes. ImpuSARS was tested in a wide range of conditions (continuous fragments, amplicons or sparse individual positions missing), showing great fidelity when reconstructing the original sequences, recovering the lineage with a 100\% precision for almost all the lineages, even in very poorly covered genomes (<20\%).

CONCLUSIONS: Imputation can improve the pace of SARS-CoV-2 sequencing production by recovering many incomplete or low-quality sequences that would be otherwise discarded. ImpuSARS can be incorporated in any primary data processing pipeline for SARS-CoV-2 whole-genome sequencing.

}, keywords = {Genome, Viral, Phylogeny, SARS-CoV-2, Whole Genome Sequencing}, issn = {2047-217X}, doi = {10.1093/gigascience/giab078}, author = {Ortuno, Francisco M and Loucera, Carlos and Casimiro-Soriguer, Carlos S and Lepe, Jose A and Camacho Martinez, Pedro and Merino Diaz, Laura and de Salazar, Adolfo and Chueca, Natalia and Garc{\'\i}a, Federico and Perez-Florido, Javier and Dopazo, Joaquin} }