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1.
PLoS Biol ; 20(3): e3001587, 2022 Mar.
Article in English | MEDLINE | ID: covidwho-1793660

ABSTRACT

In a new paper published in PLOS Biology, Dudin and colleagues evolve simple multicellularity in Sphaeroforma arctica, a unicellular relative of animals. This work establishes a new and open-ended avenue for examining the evolution of multicellularity in an important but understudied group of organisms.


Subject(s)
Biological Evolution , Animals
2.
Viruses ; 12(5)2020 04 30.
Article in English | MEDLINE | ID: covidwho-1726009

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which first occurred in Wuhan (China) in December of 2019, causes a severe acute respiratory illness with a high mortality rate, and has spread around the world. To gain an understanding of the evolution of the newly emerging SARS-CoV-2, we herein analyzed the codon usage pattern of SARS-CoV-2. For this purpose, we compared the codon usage of SARS-CoV-2 with that of other viruses belonging to the subfamily of Orthocoronavirinae. We found that SARS-CoV-2 has a high AU content that strongly influences its codon usage, which appears to be better adapted to the human host. We also studied the evolutionary pressures that influence the codon usage of five conserved coronavirus genes encoding the viral replicase, spike, envelope, membrane and nucleocapsid proteins. We found different patterns of both mutational bias and natural selection that affect the codon usage of these genes. Moreover, we show here that the two integral membrane proteins (matrix and envelope) tend to evolve slowly by accumulating nucleotide mutations on their corresponding genes. Conversely, genes encoding nucleocapsid (N), viral replicase and spike proteins (S), although they are regarded as are important targets for the development of vaccines and antiviral drugs, tend to evolve faster in comparison to the two genes mentioned above. Overall, our results suggest that the higher divergence observed for the latter three genes could represent a significant barrier in the development of antiviral therapeutics against SARS-CoV-2.


Subject(s)
Betacoronavirus/genetics , Codon , Coronavirus/genetics , Genome, Viral , Base Composition , Betacoronavirus/chemistry , Betacoronavirus/physiology , Biological Evolution , Coronavirus/classification , Genes, Viral , Host Specificity , Mutation , Phylogeny , SARS-CoV-2
3.
Trends Immunol ; 43(2): 117-131, 2022 02.
Article in English | MEDLINE | ID: covidwho-1654629

ABSTRACT

The mammalian immune system packs serious punch against infection but can also cause harm: for example, coronavirus disease 2019 (COVID-19) made headline news of the simultaneous power and peril of human immune responses. In principle, natural selection leads to exquisite adaptation and therefore cytokine responsiveness that optimally balances the benefits of defense against its costs (e.g., immunopathology suffered and resources expended). Here, we illustrate how evolutionary biology can predict such optima and also help to explain when/why individuals exhibit apparently maladaptive immunopathological responses. Ultimately, we argue that the evolutionary legacies of multicellularity and life-history strategy, in addition to our coevolution with symbionts and our demographic history, together explain human susceptibility to overzealous, pathology-inducing cytokine responses. Evolutionary insight thereby complements molecular/cellular mechanistic insights into immunopathology.


Subject(s)
COVID-19 , Adaptation, Physiological , Animals , Biological Evolution , Cytokines/genetics , Humans , Immune System , SARS-CoV-2
4.
Biosystems ; 213: 104606, 2022 Mar.
Article in English | MEDLINE | ID: covidwho-1620508

ABSTRACT

The analysis of evolutionary data allows uncovering information about the organisms and how they have adapted and evolved. This information could provide us with new insights about the specialisation of organisms (or part of them), how they adapt, how similar they are with other species, among others. Unfortunately, this evolutionary history can only be estimated, and for that, several computational methods exist. Among the methods, optimisation methods are one of the main approaches to deal with this problem, with multiobjective optimisation producing promising results. In this paper, we deal with multiobjective phylogenetic inference, using a multi-modal metaheuristic approach that exploits the decision space in the multiobjective formulation of the problem. In particular, we incorporate a new metric based on a topological tree distance. We compare the method with state of the art algorithms in terms of performance. Additionally, we perform a thorough analysis of a study case on a yeast Saccharomyces cerevisiae dataset. Results show that our proposal is able to improve the diversity of solutions while improving or keeping the quality of solutions in terms of hypervolume.


Subject(s)
Algorithms , Biological Evolution , Computer Simulation , Phylogeny
6.
Immunity ; 54(12): 2681-2687, 2021 12 14.
Article in English | MEDLINE | ID: covidwho-1568762

ABSTRACT

Antigenic drift refers to the evolutionary accumulation of amino acid substitutions in viral proteins selected by host adaptive immune systems as the virus circulates in a population. Antigenic drift can substantially limit the duration of immunity conferred by infection and vaccination. Here, I explain the factors contributing to the rapid antigenic drift of the SARS-CoV-2 spike protein and receptor proteins of other viruses and discuss the implications for SARS-CoV-2 evolution and immunity.


Subject(s)
COVID-19/immunology , Mutation/genetics , SARS-CoV-2/physiology , Adaptive Immunity , Animals , Biological Evolution , Host-Pathogen Interactions , Humans , Spike Glycoprotein, Coronavirus/immunology , Vaccination
7.
J Med Virol ; 94(4): 1257-1260, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1568203

ABSTRACT

The ongoing discussion about the real origin of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) feeds acrimonious debates. Where did SARS-CoV-2 come from? Was SARS-CoV-2 transmitted in the wild from an animal to a person before exploding in Wuhan or was it an engineered virus that escaped from research or a laboratory in Wuhan? Right now, we still don't know enough whether SARS-CoV-2 is human-made or not, and lab-leak theories remain essentially speculative. Many recent studies have pointed out several plausible scenarios. Anyhow, currently, even if suspicions by some about the possibility of lab-leak hypothesis still remain, the consensus view is that the pandemic probably started from a natural source and, to determine the real origin of the SARS-CoV-2 virus, further research is needed.


Subject(s)
COVID-19/virology , SARS-CoV-2/genetics , Animals , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , Biological Evolution , COVID-19/epidemiology , COVID-19/transmission , Humans , Laboratories , SARS-CoV-2/isolation & purification , Viral Zoonoses/epidemiology , Viral Zoonoses/transmission , Viral Zoonoses/virology
8.
Nat Methods ; 18(12): 1477-1488, 2021 12.
Article in English | MEDLINE | ID: covidwho-1541247

ABSTRACT

Emergence of new viral agents is driven by evolution of interactions between viral proteins and host targets. For instance, increased infectivity of SARS-CoV-2 compared to SARS-CoV-1 arose in part through rapid evolution along the interface between the spike protein and its human receptor ACE2, leading to increased binding affinity. To facilitate broader exploration of how pathogen-host interactions might impact transmission and virulence in the ongoing COVID-19 pandemic, we performed state-of-the-art interface prediction followed by molecular docking to construct a three-dimensional structural interactome between SARS-CoV-2 and human. We additionally carried out downstream meta-analyses to investigate enrichment of sequence divergence between SARS-CoV-1 and SARS-CoV-2 or human population variants along viral-human protein-interaction interfaces, predict changes in binding affinity by these mutations/variants and further prioritize drug repurposing candidates predicted to competitively bind human targets. We believe this resource ( http://3D-SARS2.yulab.org ) will aid in development and testing of informed hypotheses for SARS-CoV-2 etiology and treatments.


Subject(s)
Angiotensin-Converting Enzyme 2/metabolism , COVID-19/virology , SARS-CoV-2/genetics , SARS-CoV-2/metabolism , Spike Glycoprotein, Coronavirus/genetics , Virus Attachment , Biological Evolution , COVID-19/immunology , Genetic Variation , Humans , Models, Molecular , Molecular Structure , Protein Conformation , Spike Glycoprotein, Coronavirus/physiology
9.
Int J Environ Res Public Health ; 18(21)2021 11 05.
Article in English | MEDLINE | ID: covidwho-1512304

ABSTRACT

Natural disasters have obvious cross-regional and compound characteristics. Cross-regional emergency cooperation for natural disasters deepens the diversification of coordination relations and the complexity of interaction modes among emergency response organizations, including horizontal and vertical organizational interactions. In order to clarify the cooperation mechanism of emergency organizations during cross-regional emergency cooperation for natural disasters and to explore the key factors that affect the cooperative relationships of emergency organizations, in this study, a game model is constructed based on evolutionary game theory, which is composed of local, neighboring, and central governments. Then, the stability of the emergency game strategy is analyzed. On this basis, a numerical simulation is used to simulate the dynamic evolution trajectory of the game system. The results show that there is an embedded mutual promotion mechanism that evolves towards a positive emergency strategy combination among the game subjects. The selection strategies of the game subjects show the characteristics of consistency and the following: enhanced cooperation efficiency between local and neighboring governments, emergency capital stock, and shared resources, therefore, guiding social emergency forces to actively participate in emergency operations. Strengthening the emergency dispatching strength of the central government and the effectiveness of central-local emergency dispatching, can support the performance of cross-regional emergency cooperation for natural disasters. Furthermore, the efficiency of cooperation between local and neighboring governments will be enhanced.


Subject(s)
Game Theory , Natural Disasters , Biological Evolution , Computer Simulation , Cooperative Behavior , Emergency Service, Hospital , Humans
10.
Elife ; 102021 09 21.
Article in English | MEDLINE | ID: covidwho-1513080

ABSTRACT

Researchers worldwide are repeatedly warning us against future zoonotic diseases resulting from humankind's insurgence into natural ecosystems. The same zoonotic pathogens that cause severe infections in a human host frequently fail to produce any disease outcome in their natural hosts. What precise features of the immune system enable natural reservoirs to carry these pathogens so efficiently? To understand these effects, we highlight the importance of tracing the evolutionary basis of pathogen tolerance in reservoir hosts, while drawing implications from their diverse physiological and life-history traits, and ecological contexts of host-pathogen interactions. Long-term co-evolution might allow reservoir hosts to modulate immunity and evolve tolerance to zoonotic pathogens, increasing their circulation and infectious period. Such processes can also create a genetically diverse pathogen pool by allowing more mutations and genetic exchanges between circulating strains, thereby harboring rare alive-on-arrival variants with extended infectivity to new hosts (i.e., spillover). Finally, we end by underscoring the indispensability of a large multidisciplinary empirical framework to explore the proposed link between evolved tolerance, pathogen prevalence, and spillover in the wild.


Subject(s)
Biological Evolution , Communicable Diseases, Emerging/transmission , Disease Reservoirs , Zoonoses/transmission , Animals , Communicable Diseases, Emerging/epidemiology , Communicable Diseases, Emerging/immunology , Host-Pathogen Interactions , Humans , Virulence , Zoonoses/epidemiology , Zoonoses/immunology
11.
Viruses ; 13(11)2021 10 29.
Article in English | MEDLINE | ID: covidwho-1488760

ABSTRACT

The SARS-CoV-2 pandemic is one of the most concerning health problems around the globe. We reported the emergence of SARS-CoV-2 variant B.1.1.519 in Mexico City. We reported the effective reproduction number (Rt) of B.1.1.519 and presented evidence of its geographical origin based on phylogenetic analysis. We also studied its evolution via haplotype analysis and identified the most recurrent haplotypes. Finally, we studied the clinical impact of B.1.1.519. The B.1.1.519 variant was predominant between November 2020 and May 2021, reaching 90% of all cases sequenced in February 2021. It is characterized by three amino acid changes in the spike protein: T478K, P681H, and T732A. Its Rt varies between 0.5 and 2.9. Its geographical origin remain to be investigated. Patients infected with variant B.1.1.519 showed a highly significant adjusted odds ratio (aOR) increase of 1.85 over non-B.1.1.519 patients for developing a severe/critical outcome (p = 0.000296, 1.33-2.6 95% CI) and a 2.35-fold increase for hospitalization (p = 0.005, 1.32-4.34 95% CI). The continuous monitoring of this and other variants will be required to control the ongoing pandemic as it evolves.


Subject(s)
COVID-19/epidemiology , COVID-19/virology , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Basic Reproduction Number/statistics & numerical data , Biological Evolution , Genome, Viral , Haplotypes , Humans , Mexico/epidemiology , Mutation , Nasopharynx/virology , Phylogeny , RNA, Viral , SARS-CoV-2/classification
12.
Viruses ; 13(10)2021 09 29.
Article in English | MEDLINE | ID: covidwho-1441884

ABSTRACT

Bats have been identified as natural reservoirs of a variety of coronaviruses. They harbor at least 19 of the 33 defined species of alpha- and betacoronaviruses. Previously, the bat coronavirus HKU10 was found in two bat species of different suborders, Rousettus leschenaultia and Hipposideros pomona, in south China. However, its geographic distribution and evolution history are not fully investigated. Here, we screened this viral species by a nested reverse transcriptase PCR in our archived samples collected over 10 years from 25 provinces of China and one province of Laos. From 8004 bat fecal samples, 26 were found to be positive for bat coronavirus HKU10 (BtCoV HKU10). New habitats of BtCoV HKU10 were found in the Yunnan, Guangxi, and Hainan Provinces of China, and Louang Namtha Province in Laos. In addition to H. pomona, BtCoV HKU10 variants were found circulating in Aselliscus stoliczkanus and Hipposideros larvatus. We sequenced full-length genomes of 17 newly discovered BtCoV HKU10 strains and compared them with previously published sequences. Our results revealed a much higher genetic diversity of BtCoV HKU10, particularly in spike genes and accessory genes. Besides the two previously reported lineages, we found six novel lineages in their new habitats, three of which were located in Yunnan province. The genotypes of these viruses are closely related to sampling locations based on polyproteins, and correlated to bat species based on spike genes. Combining phylogenetic analysis, selective pressure, and molecular-clock calculation, we demonstrated that Yunnan bats harbor a gene pool of BtCoV HKU10, with H. pomona as a natural reservoir. The cell tropism test using spike-pseudotyped lentivirus system showed that BtCoV HKU10 could enter cells from human and bat, suggesting a potential interspecies spillover. Continuous studies on these bat coronaviruses will expand our understanding of the evolution and genetic diversity of coronaviruses, and provide a prewarning of potential zoonotic diseases from bats.


Subject(s)
Alphacoronavirus/genetics , Chiroptera/virology , Alphacoronavirus/pathogenicity , Animals , Base Sequence/genetics , Biological Evolution , China , Chiroptera/genetics , Coronavirus/genetics , Coronavirus/pathogenicity , Coronavirus Infections/virology , Evolution, Molecular , Genetic Variation/genetics , Genome, Viral/genetics , Genotype , Phylogeny , Sequence Analysis, DNA/methods , Viral Proteins/genetics
13.
mBio ; 12(5): e0214421, 2021 10 26.
Article in English | MEDLINE | ID: covidwho-1440802

ABSTRACT

Ecology and evolution, especially of microbes, have never been more relevant than in our global fight against SARS-CoV-2, the virus that causes COVID-19. Understanding how populations of SARS-CoV-2 grow, disperse, and evolve is of critical importance to managing the COVID-19 pandemic, and these questions are fundamentally ecological and evolutionary in nature. We compiled data from bioRxiv and medRxiv preprint abstracts and US National Institutes of Health Research Project grant abstracts to visualize the impact that the pivot to COVID-19 research has had on the study of microbes across biological disciplines. Finding that the pivot appears weaker in ecology and evolutionary biology than in other areas of biology, we discuss why the ecology and evolution of microbes, both pathogenic and otherwise, need renewed attention and investment going forward.


Subject(s)
Biological Evolution , COVID-19/epidemiology , Ecology , Microbiota/physiology , Humans , Pandemics
15.
Viruses ; 13(9)2021 09 21.
Article in English | MEDLINE | ID: covidwho-1427003

ABSTRACT

The error rate displayed during template copying to produce viral RNA progeny is a biologically relevant parameter of the replication complexes of viruses. It has consequences for virus-host interactions, and it represents the first step in the diversification of viruses in nature. Measurements during infections and with purified viral polymerases indicate that mutation rates for RNA viruses are in the range of 10-3 to 10-6 copying errors per nucleotide incorporated into the nascent RNA product. Although viruses are thought to exploit high error rates for adaptation to changing environments, some of them possess misincorporation correcting activities. One of them is a proofreading-repair 3' to 5' exonuclease present in coronaviruses that may decrease the error rate during replication. Here we review experimental evidence and models of information maintenance that explain why elevated mutation rates have been preserved during the evolution of RNA (and some DNA) viruses. The models also offer an interpretation of why error correction mechanisms have evolved to maintain the stability of genetic information carried out by large viral RNA genomes such as the coronaviruses.


Subject(s)
Genome, Viral , Mutation , RNA Virus Infections/virology , RNA Viruses/genetics , RNA, Viral , Animals , Biological Evolution , Coronavirus/genetics , Exonucleases/metabolism , Genetic Variation , Humans , Mutation Rate , Virus Replication
16.
PLoS Pathog ; 17(9): e1009929, 2021 09.
Article in English | MEDLINE | ID: covidwho-1430555

ABSTRACT

Remdesivir (RDV), a broadly acting nucleoside analogue, is the only FDA approved small molecule antiviral for the treatment of COVID-19 patients. To date, there are no reports identifying SARS-CoV-2 RDV resistance in patients, animal models or in vitro. Here, we selected drug-resistant viral populations by serially passaging SARS-CoV-2 in vitro in the presence of RDV. Using high throughput sequencing, we identified a single mutation in RNA-dependent RNA polymerase (NSP12) at a residue conserved among all coronaviruses in two independently evolved populations displaying decreased RDV sensitivity. Introduction of the NSP12 E802D mutation into our SARS-CoV-2 reverse genetics backbone confirmed its role in decreasing RDV sensitivity in vitro. Substitution of E802 did not affect viral replication or activity of an alternate nucleoside analogue (EIDD2801) but did affect virus fitness in a competition assay. Analysis of the globally circulating SARS-CoV-2 variants (>800,000 sequences) showed no evidence of widespread transmission of RDV-resistant mutants. Surprisingly, we observed an excess of substitutions in spike at corresponding sites identified in the emerging SARS-CoV-2 variants of concern (i.e., H69, E484, N501, H655) indicating that they can arise in vitro in the absence of immune selection. The identification and characterisation of a drug resistant signature within the SARS-CoV-2 genome has implications for clinical management and virus surveillance.


Subject(s)
Adenosine Monophosphate/analogs & derivatives , Alanine/analogs & derivatives , Antiviral Agents/pharmacology , COVID-19 , Coronavirus RNA-Dependent RNA Polymerase/genetics , Drug Resistance, Microbial/genetics , SARS-CoV-2/drug effects , Adenosine Monophosphate/pharmacology , Alanine/pharmacology , Animals , Biological Evolution , COVID-19/drug therapy , Chlorocebus aethiops , Humans , Mutation , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/metabolism , Vero Cells
17.
Nat Rev Genet ; 22(12): 757-773, 2021 12.
Article in English | MEDLINE | ID: covidwho-1428829

ABSTRACT

The past several months have witnessed the emergence of SARS-CoV-2 variants with novel spike protein mutations that are influencing the epidemiological and clinical aspects of the COVID-19 pandemic. These variants can increase rates of virus transmission and/or increase the risk of reinfection and reduce the protection afforded by neutralizing monoclonal antibodies and vaccination. These variants can therefore enable SARS-CoV-2 to continue its spread in the face of rising population immunity while maintaining or increasing its replication fitness. The identification of four rapidly expanding virus lineages since December 2020, designated variants of concern, has ushered in a new stage of the pandemic. The four variants of concern, the Alpha variant (originally identified in the UK), the Beta variant (originally identified in South Africa), the Gamma variant (originally identified in Brazil) and the Delta variant (originally identified in India), share several mutations with one another as well as with an increasing number of other recently identified SARS-CoV-2 variants. Collectively, these SARS-CoV-2 variants complicate the COVID-19 research agenda and necessitate additional avenues of laboratory, epidemiological and clinical research.


Subject(s)
COVID-19/virology , Mutation , SARS-CoV-2/physiology , SARS-CoV-2/pathogenicity , Biological Evolution , COVID-19/epidemiology , Epitopes/immunology , Humans , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/immunology
18.
Curr Opin Psychol ; 44: 202-207, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1415334

ABSTRACT

High-cost cooperation directed towards strangers is difficult to explain from an evolutionary perspective. Here, it is argued that by studying the behaviours, motivations, and preferences of real-world high-cost cooperators - blood and organ donors - insights can be uncovered into the mechanisms supporting cooperation. In this respect, this article details two novel mechanisms to enhance cooperation in the face of free-riding, (1) 'reactive reluctant altruism' whereby people help because they do not trust others to help and (2) the 'Good Shepherd' effect whereby cooperation is enhanced when people observed others cooperate although the social norm is to free-ride. Finally, it is argued that repeated acts of high-cost cooperation are sustained by a self-selection process based on the reinforcing effect of warm-glow.


Subject(s)
Tissue and Organ Procurement , Altruism , Biological Evolution , Humans , Motivation , Trust
19.
Comput Biol Med ; 138: 104866, 2021 11.
Article in English | MEDLINE | ID: covidwho-1415328

ABSTRACT

With the increasing number of samples, the manual clustering of COVID-19 and medical disease data samples becomes time-consuming and requires highly skilled labour. Recently, several algorithms have been used for clustering medical datasets deterministically; however, these definitions have not been effective in grouping and analysing medical diseases. The use of evolutionary clustering algorithms may help to effectively cluster these diseases. On this presumption, we improved the current evolutionary clustering algorithm star (ECA*), called iECA*, in three manners: (i) utilising the elbow method to find the correct number of clusters; (ii) cleaning and processing data as part of iECA* to apply it to multivariate and domain-theory datasets; (iii) using iECA* for real-world applications in clustering COVID-19 and medical disease datasets. Experiments were conducted to examine the performance of iECA* against state-of-the-art algorithms using performance and validation measures (validation measures, statistical benchmarking, and performance ranking framework). The results demonstrate three primary findings. First, iECA* was more effective than other algorithms in grouping the chosen medical disease datasets according to the cluster validation criteria. Second, iECA* exhibited the lower execution time and memory consumption for clustering all the datasets, compared to the current clustering methods analysed. Third, an operational framework was proposed to rate the effectiveness of iECA* against other algorithms in the datasets analysed, and the results indicated that iECA* exhibited the best performance in clustering all medical datasets. Further research is required on real-world multi-dimensional data containing complex knowledge fields for experimental verification of iECA* compared to evolutionary algorithms.


Subject(s)
COVID-19 , Algorithms , Biological Evolution , Cluster Analysis , Humans , SARS-CoV-2
20.
Cell ; 184(20): 5247-5260.e19, 2021 09 30.
Article in English | MEDLINE | ID: covidwho-1415259

ABSTRACT

3' untranslated region (3'UTR) variants are strongly associated with human traits and diseases, yet few have been causally identified. We developed the massively parallel reporter assay for 3'UTRs (MPRAu) to sensitively assay 12,173 3'UTR variants. We applied MPRAu to six human cell lines, focusing on genetic variants associated with genome-wide association studies (GWAS) and human evolutionary adaptation. MPRAu expands our understanding of 3'UTR function, suggesting that simple sequences predominately explain 3'UTR regulatory activity. We adapt MPRAu to uncover diverse molecular mechanisms at base pair resolution, including an adenylate-uridylate (AU)-rich element of LEPR linked to potential metabolic evolutionary adaptations in East Asians. We nominate hundreds of 3'UTR causal variants with genetically fine-mapped phenotype associations. Using endogenous allelic replacements, we characterize one variant that disrupts a miRNA site regulating the viral defense gene TRIM14 and one that alters PILRB abundance, nominating a causal variant underlying transcriptional changes in age-related macular degeneration.


Subject(s)
3' Untranslated Regions/genetics , Biological Evolution , Disease/genetics , Genome-Wide Association Study , Algorithms , Alleles , Gene Expression Regulation , Genes, Reporter , Genetic Variation , Humans , Phenotype , Polymorphism, Single Nucleotide/genetics , Polyribosomes/metabolism , Quantitative Trait Loci/genetics , RNA/genetics
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