Incipient Parallel Evolution of SARS-CoV-2 Deltacron Variant in South Brazil

Sant’Anna, Fernando Hayashi; Andreis, Tiago Finger; Salvato, Richard Steiner; Varela, Ana Paula Muterle; Comerlato, Juliana; Gregianini, Tatiana Schäffer; Barcellos, Regina Bones; Godinho, Fernanda Marques de Souza; Resende, Paola Cristina; Wallau, Gabriel Luz; Castro, Thaís Regina y; Casarin, Bruna Campestrini; Vieira, Andressa de Almeida; Schwarzbold, Alexandre Vargas; Trindade, Priscila de Arruda; Giannini, Gabriela Luchiari Tumioto; Freese, Luana; Bristot, Giovana; Brasil, Carolina Serpa; Rocha, Bruna de Oliveira; Martins, Paloma Bortolini; Oliveira, Francine Hehn de; Oosterhout, Cock van; Wendland, Eliana Márcia

doi:10.3390/vaccines11020212

Cited by 1 publication

(4 citation statements)

References 44 publications

(57 reference statements)

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“…However, in a relatively short time, analogous Deltacron phenomena began to be documented across a multitude of nations, spanning from France, the Netherlands, Denmark, and the United Kingdom to Brazil and the United States, among others [ 77 , 78 , 79 , 80 , 81 , 82 , 83 , 84 , 85 , 86 , 87 ]. Specifically, occurrences of recombination between the Delta (AY.4, AY.x) and Omicron (BA.1, BA.1.1) variants were identified, and these recombinants were designated XD, XF, and XS, with the letter “X” denoting the recombination event itself.…”

Section: Discussionmentioning

confidence: 99%

“…XD, for instance, showcased the Omicron spike protein mutations in conjunction with a Delta backbone. In other instances, breakpoints within the ORF1ab region were observed, with the remainder of the genome reflecting Omicron characteristics [ 77 , 78 , 79 , 80 , 81 , 82 , 83 , 84 , 85 , 86 , 87 , 88 , 89 , 90 , 91 ]. These discoveries garnered considerable attention and were subsequently monitored by the World Health Organization (WHO).…”

Section: Discussionmentioning

confidence: 99%

“…Consequently, the evolution of the concept of Deltacron can be traced from the initial identification of Omicron signatures within Delta variants to a sequence of stages encompassing controversy, gradual acceptance, recognition as a potential threat, and eventually becoming a focal point for numerous scientific publications and a subject of mass and social media coverage [ 76 , 77 , 78 , 79 , 80 , 81 , 82 , 83 , 84 , 85 , 86 , 87 ]. Despite the inherent risk of social media’s propensity to amplify and propagate misinformation, a challenge that could inadvertently fuel hesitancy in promptly sharing time-sensitive scientific data, we decided to disseminate our initial findings [ 92 , 93 ].…”

Section: Discussionmentioning

confidence: 99%

“…Despite the inherent risk of social media’s propensity to amplify and propagate misinformation, a challenge that could inadvertently fuel hesitancy in promptly sharing time-sensitive scientific data, we decided to disseminate our initial findings [ 92 , 93 ]. This choice played a pivotal role in highlighting an important phenomenon, elevating awareness, and fostering heightened vigilance among relevant stakeholders [ 22 , 74 , 84 , 85 , 86 , 87 ]. Our commitment bore fruit, as the scientific community adeptly navigated through the noise and distortion generated by social media amplification, thereby effectively addressing the implications of the cocirculation of two of the most infectious and impactful variants that have emerged during this pandemic [ 79 , 80 , 94 , 95 ].…”

Section: Discussionmentioning

confidence: 99%

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Unraveling the Dynamics of Omicron (BA.1, BA.2, and BA.5) Waves and Emergence of the Deltacron Variant: Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus (Oct 2021–Oct 2022)

Chrysostomou,

Vrancken,

Haralambous

et al. 2023

Viruses

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Commencing in December 2019 with the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), three years of the coronavirus disease 2019 (COVID-19) pandemic have transpired. The virus has consistently demonstrated a tendency for evolutionary adaptation, resulting in mutations that impact both immune evasion and transmissibility. This ongoing process has led to successive waves of infections. This study offers a comprehensive assessment spanning genetic, phylogenetic, phylodynamic, and phylogeographic dimensions, focused on the trajectory of the SARS-CoV-2 epidemic in Cyprus. Based on a dataset comprising 4700 viral genomic sequences obtained from affected individuals between October 2021 and October 2022, our analysis is presented. Over this timeframe, a total of 167 distinct lineages and sublineages emerged, including variants such as Delta and Omicron (1, 2, and 5). Notably, during the fifth wave of infections, Omicron subvariants 1 and 2 gained prominence, followed by the ascendancy of Omicron 5 in the subsequent sixth wave. Additionally, during the fifth wave (December 2021–January 2022), a unique set of Delta sequences with genetic mutations associated with Omicron variant 1, dubbed “Deltacron”, was identified. The emergence of this phenomenon initially evoked skepticism, characterized by concerns primarily centered around contamination or coinfection as plausible etiological contributors. These hypotheses were predominantly disseminated through unsubstantiated assertions within the realms of social and mass media, lacking concurrent scientific evidence to validate their claims. Nevertheless, the exhaustive molecular analyses presented in this study have demonstrated that such occurrences would likely lead to a frameshift mutation—a genetic aberration conspicuously absent in our provided sequences. This substantiates the accuracy of our initial assertion while refuting contamination or coinfection as potential etiologies. Comparable observations on a global scale dispelled doubt, eventually leading to the recognition of Delta-Omicron variants by the scientific community and their subsequent monitoring by the World Health Organization (WHO). As our investigation delved deeper into the intricate dynamics of the SARS-CoV-2 epidemic in Cyprus, a discernible pattern emerged, highlighting the major role of international connections in shaping the virus’s local trajectory. Notably, the United States and the United Kingdom were the central conduits governing the entry and exit of the virus to and from Cyprus. Moreover, notable migratory routes included nations such as Greece, South Korea, France, Germany, Brazil, Spain, Australia, Denmark, Sweden, and Italy. These empirical findings underscore that the spread of SARS-CoV-2 within Cyprus was markedly influenced by the influx of new, highly transmissible variants, triggering successive waves of infection. This investigation elucidates the emergence of new waves of infection subsequent to the advent of highly contagious and transmissible viral variants, notably characterized by an abundance of mutations localized within the spike protein. Notably, this discovery decisively contradicts the hitherto hypothesis of seasonal fluctuations in the virus’s epidemiological dynamics. This study emphasizes the importance of meticulously examining molecular genetics alongside virus migration patterns within a specific region. Past experiences also emphasize the substantial evolutionary potential of viruses such as SARS-CoV-2, underscoring the need for sustained vigilance. However, as the pandemic’s dynamics continue to evolve, a balanced approach between caution and resilience becomes paramount. This ethos encourages an approach founded on informed prudence and self-preservation, guided by public health authorities, rather than enduring apprehension. Such an approach empowers societies to adapt and progress, fostering a poised confidence rooted in well-founded adaptation.

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