Evolution, Medicine, and Public Health最新文献

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Antigenic evolution of SARS-CoV-2 in immunocompromised hosts. 免疫力低下的宿主体内 SARS-CoV-2 的抗原进化。
IF 3.3 3区 医学
Evolution, Medicine, and Public Health Pub Date : 2022-11-11 eCollection Date: 2023-01-01 DOI: 10.1093/emph/eoac037
Cameron A Smith, Ben Ashby
{"title":"Antigenic evolution of SARS-CoV-2 in immunocompromised hosts.","authors":"Cameron A Smith, Ben Ashby","doi":"10.1093/emph/eoac037","DOIUrl":"10.1093/emph/eoac037","url":null,"abstract":"<p><strong>Objectives/aims: </strong>Prolonged infections of immunocompromised individuals have been proposed as a crucial source of new variants of SARS-CoV-2 during the COVID-19 pandemic. In principle, sustained within-host antigenic evolution in immunocompromised hosts could allow novel immune escape variants to emerge more rapidly, but little is known about how and when immunocompromised hosts play a critical role in pathogen evolution.</p><p><strong>Materials and methods: </strong>Here, we use a simple mathematical model to understand the effects of immunocompromised hosts on the emergence of immune escape variants in the presence and absence of epistasis.</p><p><strong>Conclusions: </strong>We show that when the pathogen does not have to cross a fitness valley for immune escape to occur (no epistasis), immunocompromised individuals have no qualitative effect on antigenic evolution (although they may accelerate immune escape if within-host evolutionary dynamics are faster in immunocompromised individuals). But if a fitness valley exists between immune escape variants at the between-host level (epistasis), then persistent infections of immunocompromised individuals allow mutations to accumulate, therefore, facilitating rather than simply speeding up antigenic evolution. Our results suggest that better genomic surveillance of infected immunocompromised individuals and better global health equality, including improving access to vaccines and treatments for individuals who are immunocompromised (especially in lower- and middle-income countries), may be crucial to preventing the emergence of future immune escape variants of SARS-CoV-2.</p>","PeriodicalId":12156,"journal":{"name":"Evolution, Medicine, and Public Health","volume":"11 1","pages":"90-100"},"PeriodicalIF":3.3,"publicationDate":"2022-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10061940/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9240283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Early life adversity, reproductive history and breast cancer risk. 早期生活逆境、生育史和乳腺癌风险。
IF 3.7 3区 医学
Evolution, Medicine, and Public Health Pub Date : 2022-08-23 eCollection Date: 2022-01-01 DOI: 10.1093/emph/eoac034
Amy M Boddy, Shawn Rupp, Zhe Yu, Heidi Hanson, Athena Aktipis, Ken Smith
{"title":"Early life adversity, reproductive history and breast cancer risk.","authors":"Amy M Boddy, Shawn Rupp, Zhe Yu, Heidi Hanson, Athena Aktipis, Ken Smith","doi":"10.1093/emph/eoac034","DOIUrl":"10.1093/emph/eoac034","url":null,"abstract":"<p><strong>Background and objectives: </strong>Individuals who experience early life adversity are at an increased risk for chronic disease later in life. Less is known about how early life factors are associated with cancer susceptibility. Here, we use a life history framework to test whether early life adversity increases the risk of breast cancer. We predict that early life adversity can shift investment in somatic maintenance and accelerate the timing of reproduction, which may mediate or interact with the risk of breast cancer.</p><p><strong>Methodology: </strong>We use population-wide data from the Utah Population Database (UPDB) and Utah Cancer Registry, leading to 24 957 cases of women diagnosed with breast cancer spanning 20 years (1990-2010) and 124 785 age-matched controls. We generated a cumulative early life adversity summation score to evaluate the interaction (moderation) and mediation between early life adversity, reproductive history and their association with breast cancer risk.</p><p><strong>Results: </strong>Our analyses led to three key findings: (i) more early life adversity, when considered as a main effect, accelerates the time to first birth and death, (ii) early age at first birth and high parity decreases the risk of breast cancer and (iii) we find no association between early adversity and breast cancer risk either as a main effect or in its interaction with reproductive history.</p><p><strong>Conclusion and implications: </strong>Early adversity elevates the risk of overall mortality through mechanisms other than breast cancer risk. This suggests early life factors can generate different effects on health. Future work should incorporate more complex view of life history patterns, including multiple life stages, when making predictions about cancer susceptibility.</p>","PeriodicalId":12156,"journal":{"name":"Evolution, Medicine, and Public Health","volume":"10 1","pages":"429-438"},"PeriodicalIF":3.7,"publicationDate":"2022-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9464099/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9953211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Implications of leg length for metabolic health and fitness. 腿长对代谢健康和体能的影响。
IF 3.7 3区 医学
Evolution, Medicine, and Public Health Pub Date : 2022-07-21 eCollection Date: 2022-01-01 DOI: 10.1093/emph/eoac023
Meghan K Shirley, Owen J Arthurs, Kiran K Seunarine, Tim J Cole, Simon Eaton, Jane E Williams, Chris A Clark, Jonathan C K Wells
{"title":"Implications of leg length for metabolic health and fitness.","authors":"Meghan K Shirley, Owen J Arthurs, Kiran K Seunarine, Tim J Cole, Simon Eaton, Jane E Williams, Chris A Clark, Jonathan C K Wells","doi":"10.1093/emph/eoac023","DOIUrl":"10.1093/emph/eoac023","url":null,"abstract":"<p><strong>Background and objectives: </strong>Several studies have linked longer legs with favorable adult metabolic health outcomes and greater offspring birth weight. A recent Mendelian randomization study suggested a causal link between height and cardiometabolic risk; however, the underlying reasons remain poorly understood.</p><p><strong>Methodology: </strong>Using a cross-sectional design, we tested in a convenience sample of 70 healthy young women whether birth weight and tibia length as markers of early-life conditions associated more strongly with metabolically beneficial traits like organ size and skeletal muscle mass (SMM) than a statistically derived height-residual variable indexing later, more canalized growth.</p><p><strong>Results: </strong>Consistent with the 'developmental origins of health and disease' hypothesis, we found relatively strong associations of tibia length-but not birth weight-with adult organ size, brain size, SMM and resting energy expenditure measured by magnetic resonance imaging (MRI), dual-energy X-ray absorptiometry and indirect calorimetry, respectively.</p><p><strong>Conclusions and implications: </strong>Building on prior work, these results suggest that leg length is a sensitive marker of traits directly impacting metabolic and reproductive health. Alongside findings in the same sample relating tibia length and height-residual to MRI-measured pelvic dimensions, we suggest there may exist a degree of coordination in the development of long bone, lean mass and pelvic traits, possibly centered on early, pre-pubertal growth periods. Such phenotypic coordination has important implications for fitness, serving to benefit both adult health and the health of offspring in subsequent generations.</p>","PeriodicalId":12156,"journal":{"name":"Evolution, Medicine, and Public Health","volume":"10 1","pages":"316-324"},"PeriodicalIF":3.7,"publicationDate":"2022-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9326181/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10701439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Evolved resistance to a novel cationic peptide antibiotic requires high mutation supply. 对一种新型阳离子肽抗生素产生耐药性需要高突变供应。
IF 3.3 3区 医学
Evolution, Medicine, and Public Health Pub Date : 2022-05-30 eCollection Date: 2022-01-01 DOI: 10.1093/emph/eoac022
Alfonso Santos-Lopez, Melissa J Fritz, Jeffrey B Lombardo, Ansen H P Burr, Victoria A Heinrich, Christopher W Marshall, Vaughn S Cooper
{"title":"Evolved resistance to a novel cationic peptide antibiotic requires high mutation supply.","authors":"Alfonso Santos-Lopez, Melissa J Fritz, Jeffrey B Lombardo, Ansen H P Burr, Victoria A Heinrich, Christopher W Marshall, Vaughn S Cooper","doi":"10.1093/emph/eoac022","DOIUrl":"10.1093/emph/eoac022","url":null,"abstract":"<p><strong>Background and objectives: </strong>A key strategy for resolving the antibiotic resistance crisis is the development of new drugs with antimicrobial properties. The engineered cationic antimicrobial peptide WLBU2 (also known as PLG0206) is a promising broad-spectrum antimicrobial compound that has completed Phase I clinical studies. It has activity against Gram-negative and Gram-positive bacteria including infections associated with biofilm. No definitive mechanisms of resistance to WLBU2 have been identified.</p><p><strong>Methodology: </strong>Here, we used experimental evolution under different levels of mutation supply and whole genome sequencing (WGS) to detect the genetic pathways and probable mechanisms of resistance to this peptide. We propagated populations of wild-type and hypermutator <i>Pseudomonas aeruginosa</i> in the presence of WLBU2 and performed WGS of evolved populations and clones.</p><p><strong>Results: </strong>Populations that survived WLBU2 treatment acquired a minimum of two mutations, making the acquisition of resistance more difficult than for most antibiotics, which can be tolerated by mutation of a single target. Major targets of resistance to WLBU2 included the <i>orfN</i> and <i>pmrB</i> genes, previously described to confer resistance to other cationic peptides. More surprisingly, mutations that increase aggregation such as the <i>wsp</i> pathway were also selected despite the ability of WLBU2 to kill cells growing in a biofilm.</p><p><strong>Conclusions and implications: </strong>The results show how experimental evolution and WGS can identify genetic targets and actions of new antimicrobial compounds and predict pathways to resistance of new antibiotics in clinical practice.</p>","PeriodicalId":12156,"journal":{"name":"Evolution, Medicine, and Public Health","volume":"10 1","pages":"266-276"},"PeriodicalIF":3.3,"publicationDate":"2022-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9198447/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71520954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Which 'imperfect vaccines' encourage the evolution of higher virulence? 哪些 "不完善的疫苗 "会促使病毒进化出更强的毒性?
IF 3.3 3区 医学
Evolution, Medicine, and Public Health Pub Date : 2022-04-26 eCollection Date: 2022-01-01 DOI: 10.1093/emph/eoac015
James J Bull, Rustom Antia
{"title":"Which 'imperfect vaccines' encourage the evolution of higher virulence?","authors":"James J Bull, Rustom Antia","doi":"10.1093/emph/eoac015","DOIUrl":"10.1093/emph/eoac015","url":null,"abstract":"<p><strong>Background and objectives: </strong>Theory suggests that some types of vaccines against infectious pathogens may lead to the evolution of variants that cause increased harm, particularly when they infect unvaccinated individuals. This theory was supported by the observation that the use of an imperfect vaccine to control Marek's disease virus in chickens resulted in the virus evolving to be more lethal to unvaccinated birds. This raises the concern that the use of some other vaccines may lead to similar pernicious outcomes. We examine that theory with a focus on considering the regimes in which such outcomes are expected.</p><p><strong>Methodology: </strong>We evaluate the plausibility of assumptions in the original theory. The previous theory rested heavily on a particular form of transmission-mortality-recovery trade-off and invoked other assumptions about the pathways of evolution. We review alternatives to mortality in limiting transmission and consider evolutionary pathways that were omitted in the original theory.</p><p><strong>Results: </strong>The regime where the pernicious evolutionary outcome occurs is narrowed by our analysis but remains possible in various scenarios. We propose a more nuanced consideration of alternative models for the within-host dynamics of infections and for factors that limit virulence. Our analysis suggests imperfect vaccines against many pathogens will not lead to the evolution of pathogens with increased virulence in unvaccinated individuals.</p><p><strong>Conclusions and implications: </strong>Evolution of greater pathogen mortality driven by vaccination remains difficult to predict, but the scope for such outcomes appears limited. Incorporation of mechanistic details into the framework, especially regarding immunity, may be requisite for prediction accuracy.</p><p><strong>Lay summary: </strong>A virus of chickens appears to have evolved high mortality in response to a vaccine that merely prevented disease symptoms. Theory has predicted this type of evolution in response to a variety of vaccines and other interventions such as drug treatment. Under what circumstances is this pernicious result likely to occur? Analysis of the theory in light of recent changes in our understanding of viral biology raises doubts that medicine-driven, pernicious evolution is likely to be common. But we are far from a mechanistic understanding of the interaction between pathogen and host that can predict when vaccines and other medical interventions will lead to the unwanted evolution of more virulent pathogens. So, while the regime where a pernicious result obtains may be limited, caution remains warranted in designing many types of interventions.</p>","PeriodicalId":12156,"journal":{"name":"Evolution, Medicine, and Public Health","volume":"10 1","pages":"202-213"},"PeriodicalIF":3.3,"publicationDate":"2022-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9081871/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9381216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The evolution of the human healthcare system and implications for understanding our responses to COVID-19. 人类医疗保健系统的演变及其对了解我们应对 COVID-19 的影响。
IF 3.3 3区 医学
Evolution, Medicine, and Public Health Pub Date : 2022-02-12 eCollection Date: 2022-01-01 DOI: 10.1093/emph/eoac004
Sharon E Kessler, Robert Aunger
{"title":"The evolution of the human healthcare system and implications for understanding our responses to COVID-19.","authors":"Sharon E Kessler, Robert Aunger","doi":"10.1093/emph/eoac004","DOIUrl":"10.1093/emph/eoac004","url":null,"abstract":"<p><p>The COVID-19 pandemic has revealed an urgent need for a comprehensive, multidisciplinary understanding of how healthcare systems respond successfully to infectious pathogens-and how they fail. This study contributes a novel perspective that focuses on the selective pressures that shape healthcare systems over evolutionary time. We use a comparative approach to trace the evolution of care-giving and disease control behaviours across species and then map their integration into the contemporary human healthcare system. Self-care and pro-health environmental modification are ubiquitous across animals, while derived behaviours like care for kin, for strangers, and group-level organizational responses have evolved via different selection pressures. We then apply this framework to our behavioural responses to COVID-19 and demonstrate that three types of conflicts are occurring: (1) conflicting selection pressures on individuals, (2) evolutionary mismatches between the context in which our healthcare behaviours evolved and our globalized world of today and (3) evolutionary displacements in which older forms of care are currently dispensed through more derived forms. We discuss the significance of understanding how healthcare systems evolve and change for thinking about the role of healthcare systems in society during and after the time of COVID-19-and for us as a species as we continue to face selection from infectious diseases.</p>","PeriodicalId":12156,"journal":{"name":"Evolution, Medicine, and Public Health","volume":"10 1","pages":"87-107"},"PeriodicalIF":3.3,"publicationDate":"2022-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8908543/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10265044","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
An orally administered drug prevents selection for antibiotic-resistant bacteria in the gut during daptomycin therapy. 口服药物可防止在达托霉素治疗期间肠道中抗生素耐药细菌的选择。
IF 3.7 3区 医学
Evolution, Medicine, and Public Health Pub Date : 2022-01-01 DOI: 10.1093/emph/eoac035
Valerie J Morley, Derek G Sim, Aline Penkevich, Robert J Woods, Andrew F Read
{"title":"An orally administered drug prevents selection for antibiotic-resistant bacteria in the gut during daptomycin therapy.","authors":"Valerie J Morley,&nbsp;Derek G Sim,&nbsp;Aline Penkevich,&nbsp;Robert J Woods,&nbsp;Andrew F Read","doi":"10.1093/emph/eoac035","DOIUrl":"https://doi.org/10.1093/emph/eoac035","url":null,"abstract":"<p><strong>Background and objectives: </strong>Previously, we showed proof-of-concept in a mouse model that oral administration of cholestyramine prevented enrichment of daptomycin-resistant <i>Enterococcus faecium</i> in the gastrointestinal (GI) tract during daptomycin therapy. Cholestyramine binds daptomycin in the gut, which removes daptomycin selection pressure and so prevents the enrichment of resistant clones. Here, we investigated two open questions related to this approach: (i) can cholestyramine prevent the enrichment of diverse daptomycin mutations emerging <i>de novo</i> in the gut? and (ii) how does the timing of cholestyramine administration impact its ability to suppress resistance?</p><p><strong>Methodology: </strong>Mice with GI <i>E. faecium</i> were treated with daptomycin with or without cholestyramine, and <i>E. faecium</i> was cultured from feces to measure changes in daptomycin susceptibility. A subset of clones was sequenced to investigate the genomic basis of daptomycin resistance.</p><p><strong>Results: </strong>Cholestyramine prevented the enrichment of diverse resistance mutations that emerged <i>de novo</i> in daptomycin-treated mice. Whole-genome sequencing revealed that resistance emerged through multiple genetic pathways, with most candidate resistance mutations observed in the <i>clsA</i> gene. In addition, we observed that cholestyramine was most effective when administration started prior to the first dose of daptomycin. However, beginning cholestyramine after the first daptomycin dose reduced the frequency of resistant <i>E. faecium</i> compared to not using cholestyramine at all.</p><p><strong>Conclusions and implications: </strong>Cholestyramine prevented the enrichment of diverse daptomycin-resistance mutations in intestinal <i>E. faecium</i> populations during daptomycin treatment, and it is a promising tool for managing the transmission of daptomycin-resistant <i>E. faecium</i>.</p>","PeriodicalId":12156,"journal":{"name":"Evolution, Medicine, and Public Health","volume":"10 1","pages":"439-446"},"PeriodicalIF":3.7,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9472784/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10336334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Cesarean section and breastfeeding outcomes in an Indigenous Qom community with high breastfeeding support. 高母乳喂养支持的库姆土著社区剖宫产和母乳喂养结果。
IF 3.7 3区 医学
Evolution, Medicine, and Public Health Pub Date : 2022-01-01 DOI: 10.1093/emph/eoab045
Melanie Martin, Monica Keith, Sofía Olmedo, Deja Edwards, Alicia Barrientes, Anwesha Pan, Claudia Valeggia
{"title":"Cesarean section and breastfeeding outcomes in an Indigenous Qom community with high breastfeeding support.","authors":"Melanie Martin,&nbsp;Monica Keith,&nbsp;Sofía Olmedo,&nbsp;Deja Edwards,&nbsp;Alicia Barrientes,&nbsp;Anwesha Pan,&nbsp;Claudia Valeggia","doi":"10.1093/emph/eoab045","DOIUrl":"https://doi.org/10.1093/emph/eoab045","url":null,"abstract":"<p><strong>Background and objectives: </strong>Cesarean section may lead to suboptimal breastfeeding outcomes, though evidence has been mixed. Factors, such as premature birth, birth weight and maternal age may independently increase risk of cesarean and hinder breastfeeding initiation, while maternal preferences, support and sociostructural barriers may influence breastfeeding practices beyond the immediate postpartum period.</p><p><strong>Methodology: </strong>We assessed impacts of cesarean section and gestational factors on breastfeeding duration among Indigenous Qom mothers in Argentina who have strong traditional breastfeeding support. We modeled transitions from exclusive breastfeeding to complementary feeding and from complementary feeding to full weaning in a Bayesian time-to-event framework with birth mode and gestational covariates (<i>n</i> = 89 infants).</p><p><strong>Results: </strong>Estimated median time to full weaning was 30 months. Cesarean-delivered babies were weaned an average of 5 months later adjusting for gestational age, maternal parity and infant sex. No factors were associated with time-to-complementary feeding, and time-to-complementary feeding was not associated with time-to-full weaning.</p><p><strong>Conclusions and implications: </strong>Among Indigenous Qom mothers in Argentina, cesarean section was not associated with suboptimal breastfeeding outcomes. Although some Qom mothers do experience early breastfeeding problems, particularly following first birth, problems are not more frequent following cesarean delivery. Traditional postpartum kin and community support during prolonged postpartum periods may be instrumental in helping mothers to overcome early breastfeeding problems due to cesarean or other risk factors.</p>","PeriodicalId":12156,"journal":{"name":"Evolution, Medicine, and Public Health","volume":"10 1","pages":"36-46"},"PeriodicalIF":3.7,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8830290/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10335233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution. 实验进化过程中SARS-CoV-2的突变率及突变体的出现
IF 3.7 3区 医学
Evolution, Medicine, and Public Health Pub Date : 2022-01-01 DOI: 10.1093/emph/eoac010
Massimo Amicone, Vítor Borges, Maria João Alves, Joana Isidro, Líbia Zé-Zé, Sílvia Duarte, Luís Vieira, Raquel Guiomar, João Paulo Gomes, Isabel Gordo
{"title":"Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution.","authors":"Massimo Amicone,&nbsp;Vítor Borges,&nbsp;Maria João Alves,&nbsp;Joana Isidro,&nbsp;Líbia Zé-Zé,&nbsp;Sílvia Duarte,&nbsp;Luís Vieira,&nbsp;Raquel Guiomar,&nbsp;João Paulo Gomes,&nbsp;Isabel Gordo","doi":"10.1093/emph/eoac010","DOIUrl":"https://doi.org/10.1093/emph/eoac010","url":null,"abstract":"<p><strong>Background and objectives: </strong>To understand how organisms evolve, it is fundamental to study how mutations emerge and establish. Here, we estimated the rate of mutation accumulation of SARS-CoV-2 <i>in vitro</i> and investigated the repeatability of its evolution when facing a new cell type but no immune or drug pressures.</p><p><strong>Methodology: </strong>We performed experimental evolution with two strains of SARS-CoV-2, one carrying the originally described spike protein (CoV-2-D) and another carrying the D614G mutation that has spread worldwide (CoV-2-G). After 15 passages in Vero cells and whole genome sequencing, we characterized the spectrum and rate of the emerging mutations and looked for evidences of selection across the genomes of both strains.</p><p><strong>Results: </strong>From the frequencies of the mutations accumulated, and excluding the genes with signals of selection, we estimate a spontaneous mutation rate of 1.3 × 10 <sup><i>-</i>6</sup> ± 0.2 × 10<sup>-6</sup> per-base per-infection cycle (mean across both lineages of SARS-CoV-2 ± 2SEM). We further show that mutation accumulation is larger in the CoV-2-D lineage and heterogeneous along the genome, consistent with the action of positive selection on the spike protein, which accumulated five times more mutations than the corresponding genomic average. We also observe the emergence of mutators in the CoV-2-G background, likely linked to mutations in the RNA-dependent RNA polymerase and/or in the error-correcting exonuclease protein.</p><p><strong>Conclusions and implications: </strong>These results provide valuable information on how spontaneous mutations emerge in SARS-CoV-2 and on how selection can shape its genome toward adaptation to new environments. <b>Lay Summary:</b> Each time a virus replicates inside a cell, errors (mutations) occur. Here, via laboratory propagation in cells originally isolated from the kidney epithelium of African green monkeys, we estimated the rate at which the SARS-CoV-2 virus mutates-an important parameter for understanding how it can evolve within and across humans. We also confirm the potential of its Spike protein to adapt to a new environment and report the emergence of mutators-viral populations where mutations occur at a significantly faster rate.</p>","PeriodicalId":12156,"journal":{"name":"Evolution, Medicine, and Public Health","volume":"10 1","pages":"142-155"},"PeriodicalIF":3.7,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8996265/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10514328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 81
How a pregnant woman's relationships with her siblings relate to her mental health: a prenatal allocare perspective. 孕妇与兄弟姐妹的关系如何影响其心理健康:产前分配的视角。
IF 3.3 3区 医学
Evolution, Medicine, and Public Health Pub Date : 2021-12-20 eCollection Date: 2022-01-01 DOI: 10.1093/emph/eoab044
Molly Fox, Kyle S Wiley
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