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

Pérez-Florido, Javier; Casimiro-Soriguer, Carlos S.; Ortuño, Francisco; Fernandez-Rueda, Jose L.; Aguado, Ana M.; Lara, María Pía; Riazzo, Cristina; Rodríguez-Iglesias, Manuel; Camacho‐Martínez, Pedro; Merino-Díaz, Laura; Pupo-Ledo, Inmaculada; Salazar, Adolfo de; Viñuela, Laura; Fuentes, Ana Yara Postigo; Chueca, Natalia; García, Féderico; Dopazo, Joaquı́n; Lepe, José Antonio

doi:10.3390/ijms24032419

Cited by 5 publications

(5 citation statements)

References 23 publications

(27 reference statements)

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“…10.3389/fmicb. 2023.1228128 Frontiers in Microbiology 09 frontiersin.org (Perez-Florido et al, 2023). Immunodeficient individuals are considered incubators for punctuated evolutionary events, possibly due to their vulnerability to chronic and co-infections (Rockett et al, 2022).…”

Section: Co-infection In Immunocompromised Population Accelerates Rec...mentioning

confidence: 99%

“…In Brazil, nine co-infection events (0.61%) were identified in the investigated samples from May 2020 to April 2021, although this data is likely an underestimation due to sample limitations. Recombination has been found to occur more frequently in immunodeficient individuals at high risk of severe COVID-19 ( Perez-Florido et al, 2023 ). Immunodeficient individuals are considered incubators for punctuated evolutionary events, possibly due to their vulnerability to chronic and co-infections ( Rockett et al, 2022 ).…”

Section: Recombinant Mutations Complement Variants With New Propertiesmentioning

confidence: 99%

See 1 more Smart Citation

The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2

Fang

Zhao

et al. 2023

Front. Microbiol.

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Over three years’ pandemic of 2019 novel coronavirus disease (COVID-19), multiple variants and novel subvariants have emerged successively, outcompeted earlier variants and become predominant. The sequential emergence of variants reflects the evolutionary process of mutation-selection-adaption of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Amino acid substitution/insertion/deletion in the spike protein causes altered viral antigenicity, transmissibility, and pathogenicity of SARS-CoV-2. Early in the pandemic, D614G mutation conferred virus with advantages over previous variants and increased transmissibility, and it also laid a conservative background for subsequent substantial mutations. The role of genomic recombination in the evolution of SARS-CoV-2 raised increasing concern with the occurrence of novel recombinants such as Deltacron, XBB.1.5, XBB.1.9.1, and XBB.1.16 in the late phase of pandemic. Co-circulation of different variants and co-infection in immunocompromised patients accelerate the emergence of recombinants. Surveillance for SARS-CoV-2 genomic variations, particularly spike protein mutation and recombination, is essential to identify ongoing changes in the viral genome and antigenic epitopes and thus leads to the development of new vaccine strategies and interventions.

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Section: Co-infection In Immunocompromised Population Accelerates Rec...mentioning

confidence: 99%

Section: Recombinant Mutations Complement Variants With New Propertiesmentioning

confidence: 99%

The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2

Fang

Zhao

et al. 2023

Front. Microbiol.

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“…The identification of recombination events between the Delta and Omicron (BA.1 and BA.2) lineages justifies the investigation of SARS-CoV-2 co-infections. However, most existing studies are restricted to co-infections involving these two divergent lineages and to late phases of the pandemic when they co-circulated [1][2][3][4]. Only a few studies have analysed co-infections at earlier stages of the pandemic [5][6][7].…”

Section: Introductionmentioning

confidence: 99%

Mining genomic repositories to further our knowledge of the extent of SARS-CoV-2 co-infections

Peñas-Utrilla,

Muñóz,

Pérez-Lago

et al. 2024

Microbial Genomics

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Recombination events between Delta and Omicron SARS-CoV-2 lineages highlight the need for co-infection research. Existing studies focus on late-phase co-infections, with few examining earlier pandemic stages. This new study aims to globally identify and characterize co-infections using a bioinformatic pipeline to analyse genomic data from diverse locations and pandemic phases. Among 26988 high-quality SARS-CoV-2 isolates from 11 diverse project databases, we identified 141 potential co-infection cases (0.52%), surpassing previous prevalence estimates. These co-infections were observed throughout the pandemic timeline, with an increase noted after the emergence of the Omicron variant. Co-infections involving the Omicron variant were the most prevalent, potentially influenced by the high level of diversity within this lineage and its impact on the viral landscape. Additionally, we found co-infections involving the pre-Alpha/Alpha lineages, which have been rarely described, raising possibilities of contributing to new lineage emergence through recombination events. The analysis revealed co-infection cases involving both different and the same lineages/sublineages. Our study showcases the potential of our pipeline to leverage valuable information stored in global sequence repositories, advancing our understanding of SARS-CoV-2 co-infections. The prevalence of co-infections highlights the importance of monitoring viral diversity and its potential implications on disease dynamics. Integrating clinical data with genomic findings can further shed light on the clinical implications and outcomes of co-infections.

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“…Epidemiological evidence in Andalusian genomic surveillance indicates a correlation between an increase in co-infection cases and a higher number of circulating recombinant variants. The unexpectedly high number of co-infection cases led to the emergence of new recombinant variants (Perez-Florido et al, 2023). Detection of co-infection is probably underestimated (Combes et al, 2022), and it is, therefore, crucial to detect these cases during genomic surveillance as early as possible for clinical management and treatment strategies, elucidation of transmission dynamics and appropriate public health measures, and surveillance of genomic diversity and evolution.…”

Section: Introductionmentioning

confidence: 99%

Developing a bioinformatics pipeline to detect Delta and Omicron co-infection cases in the Philippines during SARS-CoV-2 genomic surveillance

L. Realingo,

M. Polotan,

B. Abulencia

et al. 2024

Preprint

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Co-infection with two SARS-CoV-2 variants is rarely detected, but may have clinical implications and is hypothesized to be a precursor to SARS-CoV-2 variant recombination. It is therefore important to rapidly identify co-infection cases. Here, we report two cases of co-infection detected during routine genomic surveillance. Both samples were initially suspected to have been cross-contaminated due to the unusual number of private mutations identified by Nextclade and positions flagged for nucleotide mixtures by Bammix. To rule out cross-contamination, we decontaminated the workspaces and resequenced the samples. However, the anomalies remained and the samples were therefore investigated for co-infection. To validate this hypothesis, we created a bioinformatics pipeline to determine the lineages present in the samples, performedde novoassembly, and investigated the alternative allele fraction of mutations mapping to both variants. Freyja was used and showed an estimated lineage abundance of 49.81% and 48.09% for Delta and Omicron, respectively, in the first sample. For the second sample, Delta had 82.76% abundance and Omicron had 4.99% abundance, with the presence of 12.24% abundance for other variants. Our findings support that the first sample is a case of co-infection of Delta and Omicron variants while the second sample is a cryptic co-infection of both variants, potentially undergoing recombination events. This study highlights the importance of developing a more stringent bioinformatics workflow to identify co-infection cases in genomic surveillance.

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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

Cited by 5 publications

References 23 publications

The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2

The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2

Mining genomic repositories to further our knowledge of the extent of SARS-CoV-2 co-infections

Developing a bioinformatics pipeline to detect Delta and Omicron co-infection cases in the Philippines during SARS-CoV-2 genomic surveillance

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