| Literature DB >> 35411706 |
Walter A Boeger1, Daniel R Brooks2,3,4, Valeria Trivellone5, Salvatore J Agosta3,6, Eric P Hoberg7,8.
Abstract
The unusual genetic diversity of the Omicron strain has led to speculation about its origin. The mathematical modelling platform developed for the Stockholm Paradigm (SP) indicates strongly that it has retro-colonized humans from an unidentified nonhuman mammal, likely originally infected by humans. The relationship between Omicron and all other SARS-CoV-2 variants indicates oscillations among hosts, a core part of the SP. Such oscillations result from the emergence of novel variants following colonization of new hosts, replenishing and expanding the risk space for disease emergence. The SP predicts that pathogens colonize new hosts using pre-existing capacities. Those events are thus predictable to a certain extent. Novel variants emerge after a colonization and are not predictable. This makes it imperative to take proactive measures for anticipating emerging infectious diseases (EID) and mitigating their impact. The SP suggests a policy protocol, DAMA, to accomplish this goal. DAMA comprises: DOCUMENT to detect pathogens before they emerge in new places or colonize new hosts; ASSESS to determine risk; MONITOR to detect changes in pathogen populations that increase the risk of outbreaks and ACT to prevent outbreaks when possible and minimize their impact when they occur.Entities:
Keywords: evolution; mutation; oscillations; risk space; wildlife
Mesh:
Year: 2022 PMID: 35411706 PMCID: PMC9115439 DOI: 10.1111/tbed.14557
Source DB: PubMed Journal: Transbound Emerg Dis ISSN: 1865-1674 Impact factor: 4.521
FIGURE 1The putative dynamics of host oscillation associated with the origin and emergence of the Omicron strain of SARS‐COV‐2. (left) and the phylogeny of the putative pathway of differentiation (accumulation of mutations of the S1 protein derived from Nextstrain – www.nextrain.com ) of the variant Omicron (pink area and visual regression area in red) compared to the pathway recovered for all lineages of SARS‐COV‐2 (grey area and regression area in black). We postulate that the differences in the pathways between the above lineages are associated to distinct selective regimes, likely determined by differences in the ACE2 receptor of different host species. (a,b) Colonization of humans from original wildlife host species, directly or by steppingstone, resulting in a new population – e.g., the lineage of the 19A strain – composed by a limited portion of the genotypic diversity of the precursor of the virus (bottleneck, blue curve with short amplitude). (b,c) In humans, the virus diversifies under the pressure of the new selection and differentiates (blue curve with wide amplitude) from the original ancestral population. (c,d) Subsequent colonization of a new unknown host species with associated bottleneck (red curve with narrow amplitude) of the newly formed viral population. (d,e) In isolation, the new population – i.e., the lineage of the Omicron strain – diversifies under the new host pressure (red curve with wide amplitude). (e,f) Recolonization of humans resulting in the unique features of the Omicron strain. Background panels represent oscillation among putative potential host species of mammals
FIGURE 2Maximum likelihood phylogeny of the Spike protein (S1) of selected sequences of SARS‐CoV‐2 from distinct host species, variants and geographic location. Black = strains detected in humans; Red = strains detected in other nonhuman mammals. Boxplot of branch lengths is depicted in the inset – outliers are identified according to the labelled branches in the phylogeny – yellow ovate label; red outlier numbers refer to branches associated with nonhuman mammals. The basal long branch (branch 80) leading to Omicron suggests evolution under a distinct selective regime (a nonhuman host species) and the retro‐colonization and subsequent change in the selective regime in humans (branches 81, 82); despite the recent origin of the variant, long branch is also associated to expansion into dogs (branch 86). Other instances of potential retro‐colonization are suggested in the phylogeny (e.g., many of the remaining outliers indicated by question marks, in special branches 25, 93)
FIGURE 3Humans as ecological super‐spreaders. Movements of humans and anthropogenic activities provide the opportunity for the dissemination of the virus worldwide to other human populations and local wild, peri‐urban and urban assemblage of nonhuman animals. This drives host oscillation, virus divergence and diversification – renewing the risk space of new variants and emergences