The seasonal behaviour of COVID-19 and its galectin-like culprit of the viral spike

Caetano-Anollés, Kelsey; Hernandez, Nicolas; Mughal, Fizza; Tomaszewski, Tre; Caetano‐Anollés, Gustavo

doi:10.1016/bs.mim.2021.10.002

Cited by 10 publications

(28 citation statements)

References 175 publications

(212 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Markers of VOC constellations confirmed the recruitment patterns we previously uncovered in Australia ( Tomaszewski et al , 2022 ). Haplotype constitution was relatively conserved but also showed it was subject to the increasing trend of marker and haplotype accretion we highlighted worldwide ( Caetano-Anollés et al , 2022 ) and in Australia ( Tomaszewski et al , 2022 ). Indeed, we found five haplotypes holding 23 markers for the early VOC Alpha, six haplotypes holding 28 markers for VOC Delta, and 16 haplotypes holding 78 markers for the ongoing VOC Omicron.…”

Section: Resultsmentioning

confidence: 85%

“…The existence of a cloud of viral variants exploring a combinatorial landscape of mutations predicts that mutations and their combinations should precede the rise of VOC constellations. In a previous study we showed that VOC haplotypes recruited marker combinations already present in individual protein sequences before VOC emergence during late 2020 ( Caetano-Anollés et al , 2022 ; Tomaszewski et al , 2022 ). Here, we illustrate again the reuse of marker combinations in haplotypes by studying their presence in a dataset of 137,605 sequences of the S-protein retrieved worldwide on November 14, 2020 by Showers et al (2022) , exactly one month earlier than the announcement of VOC Alpha in the United Kingdom ( Public Health England, 2020 ).…”

Section: Resultsmentioning

confidence: 93%

“…Note the early arrival of VOC Alpha, followed by VOC Delta and then VOC Omicron. The timeline of clades and VOCs shows three successive phases driven by proteome flexibility and rigidity, environmental sensing, and vaccine-driven immune escape, which are shaded in light yellow, blue, and salmon, respectively ( Caetano-Anollés et al , 2022 ). (B).…”

Section: Resultsmentioning

confidence: 99%

“…Regions included ‘Tropics’, ‘Northern Temperate’, ‘Southern Temperate’, and “Arctic” (latitude boundaries defined by 30°, 60° and 90° N and S); no ‘Antarctic’ sequences were available. Given background knowledge, latitude-delimited regions were expected to uncover seasonal effects in the global viral population ( Caetano-Anollés et al , 2022 ). From these sequences, a total of 183,276 unique amino acid substitutions and insertion/deletions (variants) were identified and subsequently filtered with a “relevancy” heuristic that only kept those with a prevalence of greater or equal to one standard deviation over the mean of the entire sequence set.…”

Section: Resultsmentioning

confidence: 99%

“…While too many deleterious mutations can push viral populations close to an ‘error threshold’ and the catastrophic possibility of extinction ( Domingo et al , 2012 ), mutations that are not advantageous are generally eliminated. Instead, beneficial mutations often combine with each other to collectively increase the fitness of the viral ‘quasispecies’ ( Domingo et al , 1978 ), structuring this dynamic ‘cloud’ of viral variants by linkage and collective effects on function and fitness ( Caetano-Anollés et al , 2022 ).…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Seasonal effects decouple SARS-CoV-2 haplotypes worldwide

et al. 2023

Self Cite

View full text Add to dashboard Cite

Background: Variants of concern (VOCs) have been replacing each other during the still rampant COVID-19 pandemic. As a result, SARS-CoV-2 populations have evolved increasingly intricate constellations of mutations that often enhance transmissibility, disease severity, and other epidemiological characteristics. The origin and evolution of these constellations remain puzzling. Methods: Here we study the evolution of VOCs at the proteome level by analyzing about 12 million genomic sequences retrieved from GISAID on July 23, 2022. A total 183,276 mutations were identified and filtered with a relevancy heuristic. The prevalence of haplotypes and free-standing mutations was then tracked monthly in various latitude corridors of the world. Results: A chronology of 22 haplotypes defined three phases driven by protein flexibility-rigidity, environmental sensing, and immune escape. A network of haplotypes illustrated the recruitment and coalescence of mutations into major VOC constellations and seasonal effects of decoupling and loss. Protein interaction networks mediated by haplotypes predicted communications impacting the structure and function of proteins, showing the increasingly central role of molecular interactions involving the spike (S), nucleocapsid (N), and membrane (M) proteins. Haplotype markers either affected fusogenic regions while spreading along the sequence of the S-protein or clustered around binding domains. Modeling of protein structure with AlphaFold2 showed that VOC Omicron and one of its haplotypes were major contributors to the distortion of the M-protein endodomain, which behaves as a receptor of other structural proteins during virion assembly. Remarkably, VOC constellations acted cooperatively to balance the more extreme effects of individual haplotypes. Conclusions: Our study uncovers seasonal patterns of emergence and diversification occurring amid a highly dynamic evolutionary landscape of bursts and waves. The mapping of genetically-linked mutations to structures that sense environmental change with powerful ab initio modeling tools demonstrates the potential of deep-learning for COVID-19 predictive intelligence and therapeutic intervention.

show abstract

Section: Resultsmentioning

confidence: 85%