bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolutionary dynamics of pre- and postzygotic reproductive isolation in cichlid fishes
Authors: Rometsch Sina J. , Torres-Dowdall Julián , Meyer Axel
Published: July 2020

Cichlid fishes are exceptionally species-rich, speciated at explosive rates and, hence, are a model system in speciation research. Yet, their reproductive isolating barriers have, so far, not been comprehensively studied. Here, we review current knowledge on pre- and postzygotic mechanisms in cichlids. While premating isolation is the norm in cichlids, its strength varies across lineages and with the geographical setting. Moreover, manipulations of ambient conditions tended to reduce assortative mating among closely related species, suggesting that premating isolation in cichlids is often fragile and context dependent. The observed lack of complete reproductive isolation is supported by past and present hybridization events that have contributed to diversity by creating novel allelic combinations. On the other hand, our meta-analysis highlights that intrinsic postzygotic isolation might accumulate faster than assumed. Mild forms of genetic incompatibilities, such as sex ratio distortion, can already be observed among closely related species. Therefore, cessation of gene flow by strong reproductive isolation in cichlids requires a combination of premating prezygotic isolation supplemented with intrinsic and extrinsic postzygotic barriers. Further, we suggest crucial next steps to improve our knowledge about reproductive barriers in cichlids to understand the evolutionary dynamics of pre- and postzygotic isolation mechanisms during adaptive radiations.

This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
Speciation through chromosomal fusion and fission in Lepidoptera
Authors: de Vos Jurriaan M. , Augustijnen Hannah , Bätscher Livio , Lucek Kay
Published: July 2020

Changes in chromosome numbers may strongly affect reproductive barriers, because individuals heterozygous for distinct karyotypes are typically expected to be at least partially sterile or to show reduced recombination. Therefore, several classic speciation models are based on chromosomal changes. One import mechanism generating variation in chromosome numbers is fusion and fission of existing chromosomes, which is particularly likely in species with holocentric chromosomes, i.e. chromosomes that lack a single centromere. Holocentric chromosomes evolved repeatedly across the tree of life, including in Lepidoptera
.
Although changes in chromosome numbers are hypothesized to be an important driver of the spectacular diversification of Lepidoptera, comparative studies across the order are lacking. We performed the first comprehensive literature survey of karyotypes for Lepidoptera species since the 1970s and tested if, and how, chromosomal variation might affect speciation. Even though a meta-analysis of karyological differences between closely related taxa did not reveal an effect on the degree of reproductive isolation, phylogenetic diversification rate analyses across the 16 best-covered genera indicated a strong, positive association of rates of chromosome number evolution and speciation. These findings suggest a macroevolutionary impact of varying chromosome numbers in Lepidoptera and likely apply to other taxonomic groups, especially to those with holocentric chromosomes.

This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.
The role of copy-number variation in the reinforcement of sexual isolation between the two European subspecies of the house mouse
Authors: North Henry L. , Caminade Pierre , Severac Dany , Belkhir Khalid , Smadja Carole M.
Published: July 2020

Reinforcement has the potential to generate strong reproductive isolation through the evolution of barrier traits as a response to selection against maladaptive hybridization, but the genetic changes associated with this process remain largely unexplored. Building upon the increasing evidence for a role of structural variants in adaptation and speciation, we addressed the role of copy-number variation in the reinforcement of sexual isolation evidenced between the two European subspecies of the house mouse. We characterized copy-number divergence between populations ofMus musculus musculusthat display assortative mate choice, and those that do not, using whole-genome resequencing data. Updating methods to detect deletions and tandem duplications (collectively: copy-number variants, CNVs) in Pool-Seq data, we developed an analytical pipeline dedicated to identifying genomic regions showing the expected pattern of copy-number displacement under a reinforcement scenario. This strategy allowed us to detect 1824 deletions and seven tandem duplications that showed extreme differences in frequency between behavioural classes across replicate comparisons. A subset of 480 deletions and four tandem duplications were specifically associated with the derived trait of assortative mate choice. These ‘Choosiness-associated’ CNVs occur in hundreds of genes. Consistent with our hypothesis, such genes included olfactory receptors potentially involved in the olfactory-based assortative mate choice in this system as well as one gene,Sp110, that is known to show patterns of differential expression between behavioural classes in an organ used in mate choice—the vomeronasal organ. These results demonstrate that fine-scale structural changes are common and highly variable within species, despite being under-studied, and may be important targets of reinforcing selection in this system and others.

This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.
Adaptive zones shape the magnitude of premating reproductive isolation in
Timema
stick insects
Authors: Muschick Moritz , Soria-Carrasco Víctor , Feder Jeffrey L. , Gompert Zach , Nosil Patrik
Published: July 2020

Simpson's fossil-record inspired model of ‘adaptive zones’ proposes that evolution is dominated by small fluctuations within adaptive zones, occasionally punctuated by larger shifts between zones. This model can help explain why the process of population divergence often results in weak or moderate reproductive isolation (RI), rather than strong RI and distinct species. Applied to the speciation process, the adaptive zones hypothesis makes two inter-related predictions: (i) large shifts between zones are relatively rare, (ii) when large shifts do occur they generate stronger RI than shifts within zones. Here, we use ecological, phylogenetic and behavioural data to test these predictions in
Timema
stick insects. We show that host use in
Timema
is dominated by moderate shifts within the systematic divisions of flowering plants and conifers, with only a few extreme shifts between these divisions. However, when extreme shifts occur, they generate greater RI than do more moderate shifts. Our results support the adaptive zones model, and suggest that the net contribution of ecological shifts to diversification is dependent on both their magnitude and frequency. We discuss the generality of our findings in the light of emerging evidence from diverse taxa that the evolution of RI is not always the only factor determining the origin of species diversity.

This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.
Multi-locus interactions and the build-up of reproductive isolation
Authors: Satokangas I. , Martin S. H. , Helanterä H. , Saramäki J. , Kulmuni J.
Published: July 2020

All genes interact with other genes, and their additive effects and epistatic interactions affect an organism's phenotype and fitness. Recent theoretical and empirical work has advanced our understanding of the role of multi-locus interactions in speciation. However, relating different models to one another and to empirical observations is challenging. This review focuses on multi-locus interactions that lead to reproductive isolation (RI) through reduced hybrid fitness. We first review theoretical approaches and show how recent work incorporating a mechanistic understanding of multi-locus interactions recapitulates earlier models, but also makes novel predictions concerning the build-up of RI. These include high variance in the build-up rate of RI among taxa, the emergence of strong incompatibilities producing localized barriers to introgression, and an effect of population size on the build-up of RI. We then review recent experimental approaches to detect multi-locus interactions underlying RI using genomic data. We argue that future studies would benefit from overlapping methods like ancestry disequilibrium scans, genome scans of differentiation and analyses of hybrid gene expression. Finally, we highlight a need for further overlap between theoretical and empirical work, and approaches that predict what kind of patterns multi-locus interactions resulting in incompatibilities will leave in genome-wide polymorphism data.

This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.
Evolution of strong reproductive isolation in plants: broad-scale patterns and lessons from a perennial model group
Authors: Shang Huiying , Hess Jaqueline , Pickup Melinda , Field David L. , Ingvarsson Pär K. , Liu Jianquan , Lexer Christian
Published: July 2020

Many recent studies have addressed the mechanisms operating during the early stages of speciation, but surprisingly few studies have tested theoretical predictions on the evolution of strong reproductive isolation (RI). To help address this gap, we first undertook a quantitative review of the hybrid zone literature for flowering plants in relation to reproductive barriers. Then, usingPopulusas an exemplary model group, we analysed genome-wide variation for phylogenetic tree topologies in both early- and late-stage speciation taxa to determine how these patterns may be related to the genomic architecture of RI. Our plant literature survey revealed variation in barrier complexity and an association between barrier number and introgressive gene flow. Focusing onPopulus,our genome-wide analysis of tree topologies in speciating poplar taxa points to unusually complex genomic architectures of RI, consistent with earlier genome-wide association studies. These architectures appear to facilitate the ‘escape’ of introgressed genome segments from polygenic barriers even with strong RI, thus affecting their relationships with recombination rates. Placed within the context of the broader literature, our data illustrate how phylogenomic approaches hold great promise for addressing the evolution and temporary breakdown of RI during late stages of speciation.

This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
The evolution of strong reproductive isolation between sympatric intertidal snails
Authors: Stankowski Sean , Westram Anja M. , Zagrodzka Zuzanna B. , Eyres Isobel , Broquet Thomas , Johannesson Kerstin , Butlin Roger K.
Published: July 2020

The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology,Littorina arcanaandLittorina saxatilisdiffer in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions.

This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
The ecological stage changes benefits of mate choice and drives preference divergence
Authors: Tinghitella Robin M. , Lackey Alycia C. R. , Durso Catherine , Koop Jennifer A. H. , Boughman Janette W.
Published: July 2020

Preference divergence is thought to contribute to reproductive isolation. Ecology can alter the way selection acts on female preferences, making them most likely to diverge when ecological conditions vary among populations. We present a novel mechanism for ecologically dependent sexual selection, termed ‘the ecological stage’ to highlight its ecological dependence. Our hypothesized mechanism emphasizes that males and females interact over mating in a specific ecological context, and different ecological conditions change the costs and benefits of mating interactions, selecting for different preferences in distinct environments and different male traits, especially when traits are condition dependent. We test key predictions of this mechanism in a sympatric three-spine stickleback species pair. We used a maternal half-sib split-clutch design for both species, mating females to attractive and unattractive males and raising progeny on alternate diets that mimic the specialized diets of the species in nature. We estimated the benefits of mate choice for an indicator trait (male nuptial colour) by measuring many fitness components across the lifetimes of both sons and daughters from these crosses. We analysed fitness data using a combination of aster and mixed models. We found that many benefits of mating with high-colour males depended on both species and diet. These results support the ecological stage hypothesis for sticklebacks. Finally, we discuss the potential role of this mechanism for other taxa and highlight its ability to enhance reproductive isolation as speciation proceeds, thus facilitating the evolution of strong reproductive isolation.

This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
Anthropogenic hybridization at sea: three evolutionary questions relevant to invasive species management
Authors: Viard Frédérique , Riginos Cynthia , Bierne Nicolas
Published: July 2020

Species introductions promote secondary contacts between taxa with long histories of allopatric divergence. Anthropogenic contact zones thus offer valuable contrasts to speciation studies in natural systems where past spatial isolations may have been brief or intermittent. Investigations of anthropogenic hybridization are rare for marine animals, which have high fecundity and high dispersal ability, characteristics that contrast to most terrestrial animals. Genomic studies indicate that gene flow can still occur after millions of years of divergence, as illustrated by invasive mussels and tunicates. In this context, we highlight three issues: (i) the effects of high propagule pressure and demographic asymmetries on introgression directionality, (ii) the role of hybridization in preventing introduced species spread, and (iii) the importance of postzygotic barriers in maintaining reproductive isolation. Anthropogenic contact zones offer evolutionary biologists unprecedented large scale hybridization experiments. In addition to breaking the highly effective reproductive isolating barrier of spatial segregation, they allow researchers to explore unusual demographic contexts with strong asymmetries. The outcomes are diverse, from introgression swamping to strong barriers to gene flow, and lead to local containment or widespread invasion. These outcomes should not be neglected in management policies of marine invasive species.

This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.
Genome-wide patterns of divergence and introgression after secondary contact betweenPungitiussticklebacks
Authors: Yamasaki Yo Y. , Kakioka Ryo , Takahashi Hiroshi , Toyoda Atsushi , Nagano Atsushi J. , Machida Yoshiyasu , Møller Peter R. , Kitano Jun
Published: July 2020

Speciation is a continuous process. Although it is known that differential adaptation can initiate divergence even in the face of gene flow, we know relatively little about the mechanisms driving complete reproductive isolation and the genomic patterns of divergence and introgression at the later stages of speciation. Sticklebacks contain many pairs of sympatric species differing in levels of reproductive isolation and divergence history. Nevertheless, most previous studies have focused on young species pairs. Here, we investigated two sympatric stickleback species,Pungitius pungitiusandP. sinensis, whose habitats overlap in eastern Hokkaido; these species show hybrid male sterility, suggesting that they may be at a late stage of speciation. Our demographic analysis using whole-genome sequence data showed that these species split 1.73 Ma and came into secondary contact 37 200 years ago after a period of allopatry. This long period of allopatry might have promoted the evolution of intrinsic incompatibility. Although we detected on-going gene flow and signatures of introgression, overall genomic divergence was high, with considerable heterogeneity across the genome. The heterogeneity was significantly associated with variation in recombination rate. This sympatric pair provides new avenues to investigate the late stages of the stickleback speciation continuum.

This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.
Sympatric ecological divergence with coevolution of niche preference
Authors: Payne Pavel , Polechová Jitka
Published: July 2020

Reinforcement, the increase of assortative mating driven by selection against unfit hybrids, is conditional on pre-existing divergence. Yet, for ecological divergence to precede the evolution of assortment, strict symmetries between fitnesses in niches must hold, and/or there must be low gene flow between the nascent species. It has thus been argued that conditions favouring sympatric speciation are rarely met in nature. Indeed, we show that under disruptive selection, violating symmetries in niche sizes and increasing strength of the trade-off in selection between the niches quickly leads to loss of genetic variation, instead of evolution of specialists. The region of the parameter space where polymorphism is maintained further narrows with increasing number of loci encoding the diverging trait and the rate of recombination between them. Yet, evolvable assortment and pre-existing assortment both substantially broaden the parameter space within which polymorphism is maintained. Notably, pre-existing niche preference speeds up further increase of assortment, thus facilitating reinforcement in the later phases of speciation. We conclude that in order for sympatric ecological divergence to occur, niche preference must coevolve throughout the divergence process. Even if populations come into secondary contact, having diverged in isolation, niche preference substantially broadens the conditions for coexistence in sympatry and completion of the speciation process.

This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
What cost decisiveness? A cost benefit analysis of the lockdown to contain COVID-19 in India
Authors: Dutta Mousumi , Husain Zakir
Published: July 2020

On 24th March, 2020 the Government of India announced a national level lockdown to contain the spread of COVID. The lockdown policy has generated considerable controversy, with critics arguing that it was done without adequate notice or planning, exposed vulnerable section of the population to a humanitarian crisis, and failed to contain the spread of COVID. In response, the Government has claimed that lockdown slowed the transmission process of COVID, thereby reducing the number of cases and deaths substantially. The consequent pressure on the health infrastructure was also much less. To judge between competing claims, this study has undertaken the first cost-benefit analysis of the world’s biggest lockdown. Although the data for a proper cost-benefit analysis is currently not available, we have made a ball point estimate of the net benefit of the lockdown under alternative scenarios. Our estimates reveal the net benefits of lockdown to be negative; moreover, the results are robust under all scenarios.
SARS-CoV-2 RNA extraction using magnetic beads for rapid large-scale testing by RT-qPCR and RT-LAMP
Authors: Klein Steffen , Müller Thorsten G. , Khalid Dina , Sonntag-Buck Vera , Heuser Anke-Mareil , Glass Bärbel , Meurer Matthias , Morales Ivonne , Schillak Angelika , Freistaedter Andrew , Ambiel Ina , Winter Sophie L. , Zimmermann Liv , Naumoska Tamara , Bubeck Felix , Kirrmaier Daniel , Ullrich Stephanie , Miranda Isabel Barreto , Anders Simon , Grimm Dirk , Schnitzler Paul , Knop Michael , Kräusslich Hans-Georg , Dao Thi Viet Loan , Börner Kathleen , Chlanda Petr
Published: July 2020

Rapid large-scale testing is essential for controlling the ongoing pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The standard diagnostic pipeline for testing SARS-CoV-2 presence in patients with an ongoing infection is predominantly based on pharyngeal swabs, from which the viral RNA is extracted using commercial kits followed by reverse transcription and quantitative PCR detection. As a result of the large demand for testing, commercial RNA extraction kits may be limited and alternative, non-commercial protocols are needed. Here, we provide a magnetic bead RNA extraction protocol that is predominantly based on in-house made reagents and is performed in 96-well plates supporting large-scale testing. Magnetic bead RNA extraction was benchmarked against the commercial QIAcube extraction platform. Comparable viral RNA detection sensitivity and specificity were obtained by fluorescent and colorimetric RT-LAMP using N primers, as well as RT-qPCR using E gene primers showing that the here presented RNA extraction protocol can be combined with a variety of detection methods at high throughput. Importantly, the presented diagnostic workflow can be quickly set up in a laboratory without access to an automated pipetting robot.
Default(y) Mode Network: Important regions of DMN do not survive alterations in flip angles
Authors: Singhal Ishan , Soni Abhishek K. , Srinivasan Narayanan
Published: July 2020

The default mode network (DMN) is thought to capture intrinsic activity of the brain and has been instrumental in understanding the dynamics of the brain. However, the DMN has not been without critics; both conceptual and empirical. The empirical criticisms caution against physiological noise as a source for the reported connectivity in the DMN. Smaller flip angles (FAs) have been modelled and shown to reduce physiological noise in BOLD signal recordings. A previous functional MRI (fMRI) study with flickering checkerboard stimuli, manipulated FAs to show that activity in the posterior-cingulate cortex (PCC) and precuneus is prone to physiological noise. This raises questions about studies that show activations in these areas (PCC and precuneus) with a fixed FA and the role of these areas in brain networks like DMN. Given the prominent role of PCC and precuneus in DMN, we studied the effect of FAs on the resting-state functional connectivity involving these areas in DMN. We used four FAs and recorded resting-state activity in a 3-T scanner. The results show PCC and precuneus BOLD functional connectivity is inconsistent. We lend support to previous empirical criticisms of DMN, linking its activity to physiological noise. Our results add to concerns about PCC and precuneus related BOLD activity and their putative role in DMN. Alongside previous studies we advocate using smaller flip angles as an empirical tool to investigate physiological noise in fMRI studies.
The impact of the variation of imaging factors on the robustness of Computed Tomography Radiomic Features: A review
Authors: Reiazi Reza , Abbas Engy , Famiyeh Petra , Rezaie Aria , Kwan Jennifer Y. Y. , Patel Tirth , Bratman Scott V , Tadic Tony , Liu Fei-Fei , Haibe-Kains Benjamin
Published: July 2020

The field of radiomics is at the forefront of personalized medicine. However, there are concerns regarding the robustness of its features against multiple medical imaging parameters and the performance of the predictive models built upon them. Therefore, our review aims to identify image perturbation factors (IPF) that most influence the robustness of radiomic features in biomedical research. We also provide insights into the validity and discrepancy of different methodologies applied to investigate the robustness of radiomic features. We selected 527 papers based on the primary criterion that the papers had imaging parameters that affected the reproducibility of radiomic features extracted from computed tomography (CT) images. We compared the reported performance of these parameters along with IPF in the eligible studies. We then proceeded to divide our studies into three groups based on the type of their IPF: (i) scanner parameters, (ii) acquisition parameters and (iii) reconstruction parameters. Our review highlighted that the reconstruction algorithm was the most reproducible factor and shape along with intensity histogram (IH) were the most robust radiomic features against variation in imaging parameters. This review identified substantial inconsistencies related to the methodology and the reporting style of the reviewed studies such as type of study performed, the metrics used for robustness, the feature extraction techniques, the image perturbation factors, the reporting style and their outcome inclusion. Finally, we hope the IPFs and the methodology inconsistencies identified will aid the scientific community in conducting research in a way that is more reproducible and avoids the pitfalls of previous analyses.
A novel Sporothrix brasiliensis genomic variant in Midwestern Brazil: evidence for an older and wider sporotrichosis outbreak
Authors: Filho João Eudes , Santos Isabele Barbieri , Reis Carmélia Matos Santiago , Patané José Salvatori , Paredes Verenice , Romualdo João Paulo , Poggianni Sabrina Santos Costa , Castro Talita de Cássia Borges , Gomez Oscar Mauricio , Pereira Sandro Antonio , Pacheco Schubach Edvar Yuri , Gomes Kamila Peres , Mavengere Heidi , Alves Lucas Gomes de Brito , Lucas Joaquim , Paes Hugo Costa , Albuquerque Patricia , Cruz Laurício Monteiro , McEwen Juan G. , Stajich Jason E. , Almeida-Paes Rodrigo , Zancopé-Oliveira Rosely Maria , Matute Daniel R. , Barker Bridget , Felipe Maria Sueli Soares , Teixeira Marcus de Melo , Nicola André Moraes
Published: July 2020

Sporotrichosis is a subcutaneous infection caused by fungi from the genus Sporothrix. The disease is transmitted by inoculation of infective particles found in plant-contaminated material or diseased animals, characterizing the classic sapronotic and emerging zoonotic transmission, respectively. Since 1998, Brazil has experienced a zoonotic sporotrichosis epidemic due to S. brasiliensis, centered in the state of Rio de Janeiro. Our observation of feline sporotrichosis cases in Brasília (Midwestern Brazil), around 900 km away from Rio de Janeiro, led us to question whether the epidemic caused by S. brasiliensis has spread from the epicenter in Rio de Janeiro, emerged independently in the two locations, or whether the disease has been present and unrecognized in Midwestern Brazil. A retrospective analysis of 91 human and 4 animal cases from Brasília, ranging from 1993 to 2018, suggests the occurrence of both sapronotic and zoonotic transmission. Molecular typing identified S. schenckii as the agent in two animals and all seven human patients from which we were able to recover clinical isolates. However, in two animals, the disease was caused by S. brasiliensis. Whole-genome sequence typing of seven S. brasiliensis strains suggests that isolates from Brasília are genetically distinct from those obtained at the epicenter of the outbreak in Rio de Janeiro, both in phylogenomic and population genomic analyses. The two S. brasiliensis populations seem to have separated 2.24 - 3.09 million years ago, indicating independent outbreaks or that the zoonotic S. brasiliensis outbreak might have started earlier and be spread wider in South America than previously recognized.
Huge Excess Mortality due to the delta strain of COVID-19 in Japan in August and September, 2021
Authors: Kurita Junko , Sugawara Tamie , Ohkusa Yasushi
Published: July 2020

Background

No remarkable mortality attributable to COVID-19 confirmed by PCR test has been observed in Japan.

Object

We sought to quantify excess mortality using the National Institute of Infectious Diseases (NIID) model.

Method

We applied the NIID model to deaths of all causes from 1987 up through October, 2021 for the whole of Japan and up through August, 2021 for Tokyo.

Results

Results in Japan show huge number of excess mortality, up to 10 thousands in the two months, in August and September, 2021. On the other hand, in Tokyo, 1323 excess mortality was detected

Discussion and Conclusion

We detected substantial excess mortality in Japan in August and September, 2021 and in Tokyo in August, 2021. It might be important to continue to monitor excess mortality of COVID-19 carefully hereafter.
Improving pandemic mitigation policies across communities through coupled dynamics of risk perception and infection
Authors: Silk Matthew J , Carrignon Simon , Bentley R. Alexander , Fefferman Nina H
Published: July 2020

Decisions to adhere to health-protective behaviors (e.g. mask-wearing, social distancing, etc.) that impact the spread of COVID-19 are not made in isolation by each individual. They are instead the result of the social construction of perceived risks and resulting community norms. In populations in which disease is unlikely to spread throughout all communities simultaneously, community-driven perception of risk can drastically alter collective outcomes. A community could respond to a few infections by becoming fearful and adopting anticipatory behaviors that protect them from disease spread. Similarly, there could be false reassurance, in which low disease incidence over time leads to community consensus that protective actions are unnecessary (even if they are the reason cases remains rare). We therefore model COVID-19 spread with three synergistic dynamics governing individual behavioral choices: (1) Social construction of concern, (2) Awareness of disease incidence, and (3) Reassurance by lack of disease. We use a multiplex network approach that captures social communication and epidemiological spread. We find that effective protective policies enacted too early may backfire by allowing a community to become reassured and therefore unwilling to adopt or maintain further protective behaviors. Based on these insights, we propose that public health policies for which success relies on collective action should be designed to exploit thebehaviourally receptive phase; the period between the generation of sufficient concern as to foster adoption of novel protective behaviors and the relaxation of adherence driven by reassurance fostered by avoidance of negative outcomes over time.
Assessing the impact of preventive mass vaccination campaigns on yellow fever outbreaks in Africa : a population-level self-controlled case-series study
Authors: Jean Kévin , Raad Hanaya , Gaythorpe Katy A. M. , Hamlet Arran , Mueller Judith E. , Hogan Dan , Mengistu Tewodaj , Whitaker Heather J. , Garske Tini , Hocine Mounia N.
Published: July 2020

Introduction

The Eliminate Yellow fever Epidemics (EYE) strategy was launched in 2017 in response to the resurgence of yellow fever in Africa and the Americas. The strategy relies on several vaccination activities, including preventive mass vaccination campaigns (PMVCs). However, by how much PMVCs decrease the risk of outbreak to occur has not yet been quantified.

Methods

We used the self-controlled case series (SCCS) method to assess the association between the occurrence of yellow fever outbreaks and the implementation of PMVCs at the province level in the African endemic region. As all time-invariant confounders are implicitly controlled for, the SCCS method is an alternative to classical cohort or case-control study designs when the risk of residual confounding is high.

The location and dates of outbreaks were identified from international epidemiological records, and information on PMVCs was provided by coordinators of vaccination activities and international funders. The study sample consisted of provinces that were both affected by an outbreak and targeted for a PMVC between 2005 and 2018. We compared the relative incidence of outbreaks before and after the implementation of a PMVC. The sensitivity of our estimates to a range of assumptions was explored, and the results of the SCCS method were compared to those obtained through a retrospective cohort study design. We further derived the number of yellow fever outbreaks that have been prevented by PMVCs.

Results

The study sample consisted of 33 African provinces. Among these, outbreaks occurred during the pre-PMVC period in 26 (78.8%) provinces versus 7 (21.2%) occurring in the post-PMVC period. This corresponded to a significantly reduced incidence rate ratio of 0.14 (95% Confidence interval 0.06 to 0.34) for the post-PMVC versus pre-PMVC period. This estimate was robust across a range of sensitivity analyses, while the results of the cohort-style analyses were highly sensitive to the choice of covariates included in the model. Based on the SCCS results, we estimated that PMVCs have reduced the number of outbreaks by 34% (22% to 45%) in Africa over the study period.

Conclusion

Our estimates provide new empirical evidence of the high preventive impact of PMVCs on yellow fever outbreaks. This study illustrates that the SCCS method can be advantageously applied at the population level in order to evaluate a public health intervention.
In search of “hepatic factor:” Lack of evidence for ALK1 ligands BMP9 and BMP10
Authors: Capasso Teresa L. , Trucco Sara M. , Hindes Morgan , Schwartze Tristin , Bloch Jamie L. , Kreutzer Jacqueline , Cook Stephen C. , Hinck Cynthia S. , Treggiari Davide , Feingold Brian , Hinck Andrew P. , Roman Beth L.
Published: July 2020

In children with single ventricle physiology, the Glenn procedure is performed to redirect venous return from the superior vena cava directly to the pulmonary arteries and route venous return from the inferior vena cava exclusively to the systemic circulation. Although this surgery successfully palliates the hemodynamic stress experienced by the single ventricle, patients frequently develop pulmonary arteriovenous malformations (PAVMs). Interestingly, PAVMs may regress upon rerouting of hepatic venous effluent to the pulmonary vasculature, suggesting the presence of a circulating “hepatic factor” that is required to prevent PAVMs. Here, we test the hypothesis that hepatic factor is bone morphogenetic protein 9 (BMP9) and/or BMP10. These circulating ligands are produced by the liver and activate endothelial endoglin (ENG)/ALK1 signaling, and mutations in ENG and ALK1 cause hereditary hemorrhagic telangiectasia, a genetic disease associated with AVM development. However, we found no within-subject variation in BMP9, BMP10, or BMP9/10 plasma concentrations when sampled from five cardiovascular sites, failing to support the idea that the Glenn would limit access of these ligands to the lung vasculature. Unexpectedly, however, we found a significant decrease in all three ligand concentrations in Glenn cases versus controls. Our findings suggest that BMP9/BMP10/ENG/ALK1 signaling may be decreased in the Glenn vasculature but fail to implicate these ligands as hepatic factor.
Lockdown measures in response to COVID-19 in Sub-Saharan Africa: A rapid study of nine countries
Authors: Haider Najmul , Osman Abdinasir Yusuf , Gadzekpo Audrey , Akpede George O. , Asogun Danny , Ansumana Rashid , Lessells Richard , Khan Palwasha , Hamid Muzamil Mahdi Abdel , Yeboah-Manu Dorothy , Mboera Leonard , Shayo Elizabeth H , Mbaga Blandina T , Urassa Mark , Musoke David , Kapata Nathan , Ferrand Rashida Abbas , Chanda-Kapata Pascalina , Stigler Florian , Czypionka Thomas , Kock Richard , McCoy David
Published: July 2020

Lockdown measures have been introduced worldwide to contain the transmission of COVID-19. This paper defines the term lockdown and describes the design, timing and implementation of lockdown in nine countries in Sub Saharan Africa: Ghana, Nigeria, South Africa, Sierra Leone, Sudan, Tanzania, Uganda, Zambia and Zimbabwe. It also discusses the manner in which lockdown is enforced, the need to mitigate the harms of lockdown, and the association between lockdown and the reported number of COVID-19 cases and deaths. While there are some commonalities in the implementation of lockdown, a more notable finding is the variation in the design, timing and implementation of lockdown measures across the nine countries. We found that the number of reported cases is heavily dependent on the number of tests done, and that testing rates ranged from 9 to 21,261 per million population. The reported number of COVID-19 deaths per million population also varies, but is generally low when compared to countries in Europe and North America. While lockdown measures may have helped inhibit some community transmission, the pattern and nature of the epidemic remains unclear. Of concern are signs of lockdown harming health by affecting the functioning of the health system and causing social and economic harms. This paper highlights the need for inter-sectoral and trans-disciplinary research capable of providing a rigorous and holistic assessment of the harms and benefits of lockdown.
Negative impact of the COVID-19 pandemic on sleep quantitative parameters, quality, and circadian alignment: Implications for psychological well-being and emotional regulation
Authors: Salehinejad Mohammad Ali , Majidinezhad Maryam , Ghanavati Elham , Kouestanian Sahar , Vicario Carmelo M. , Nitsche Michael A. , Nejati Vahid
Published: July 2020

Background

The COVID-19 pandemic has spread worldwide, affecting millions of people and exposing them to home quarantine, isolation, and social distancing. While recent reports showed increased distress and depressive/anxiety state related to COVID-19 crisis, we investigated how home quarantine affected sleep parameters in healthy individuals.

Methods

160 healthy individuals who were in home quarantine in April 2020 for at least one month participated in this study. Participants rated and compared their quantitative sleep parameters (time to go to bed, sleep duration, getting-up time) and sleep quality factors, pre-and during home quarantine due to the COVID-19 pandemic. Furthermore, participants’ chronotype was determined to see if sleep parameters are differentially affected in different chronotypes.

Results

The time to fall asleep and get-up in the morning were significantly delayed in all participants, indicating a significant circadian misalignment. Sleep quality was reported to be significantly poorer in all participants and chronotypes, and included more daily disturbances (more sleep disturbances, higher daily dysfunctions due to low quality of sleep) and less perceived sleep quality (lower subjective sleep quality, longer time taken to fall asleep at night, more use of sleep medication for improving sleep quality) during home quarantine.

Conclusions

Home quarantine due to COVID-19 pandemic has a detrimental impact on sleep quality. Online interventions including self-help sleep programs, stress management, relaxation practices, stimulus control, sleep hygiene, and mindfulness training are available interventions in the current situation.
Dynamics of RT-qPCR SARS-CoV-2 Detection Rates Prior to and After Symptom Onset
Authors: Sherrill-Mix Scott
Published: July 2020

Effective RT-qPCR testing for SARS-CoV-2 is essential for treatment, surveillance and control of the COVID-19 pandemic. A recent meta-analysis 1 suggested that testing prior to the onset of symptoms is likely to miss the majority of infected individuals. These findings cast severe doubts on the effectiveness of mass screening efforts intended to detect SARS-CoV-2 prior to the onset of symptoms and decrease community transmissions from pre-/asymptomatic individuals2–4. However, alternative analyses and additional data described herein refine these estimates and suggest that many SARS-CoV-2 infections could potentially be detected prior to symptom onset.
Health coverage for people without social security in Mexico: a retrospective cohort to assess childhood acute lymphoblastic leukaemia survival
Authors: Muñoz-Aguirre P , Huerta-Gutierrez R , Zamora S , Mohar A , Vega-Vega L , Hernández-Ávila JE , Morales-Carmona E , Zapata-Tarres M , Bautista-Arredondo S , Perez-Cuevas R , Rivera-Luna R , Reich MR , Lajous M
Published: July 2020

We aimed to measure survival of children with acute lymphoblastic leukaemia (ALL) under Mexico’s public health insurance for the population without social security, and explore patient groups that may be at risk for increased mortality.

We conducted a retrospective cohort study using claims data from Mexico’s Seguro Popular program, covering cancer treatment in people without social security, 2005-15. We estimated 5-year national and state-specific survival for children with ALL across Mexico who initiated cancer treatment under this public healthcare insurance scheme.

8,977 children with ALL were treated under Seguro Popular in 2005-15. Under this financing scheme, treated children doubled from 535 in 2005 to 1,070 in 2015, and their 5-year survival was 61.8% (95%CI 60.8, 62.9). Estimates for 5-year survival remained constant over time. We observed wide gaps in risk-standardized 5-year survival among states ranging from 74.7% to 43.7%. We found a higher risk of mortality for children who received treatment in a non-paediatric specialty hospital (Hazards Ratio, HR=1.18; 95%CI 1.09, 1.26), facilities without a paediatric oncology/haematology specialist (HR=2.17; 95%CI 1.62, 2.90), and hospitals with low patient volume (HR=1.22; 95%CI 1.13, 1.32).

In a decade Mexico’s Seguro Popular doubled access to ALL treatment for children without social security and by 2015 financed the vast majority of estimated ALL cases for that population. While some progress in ALL survival may have been achieved, nationwide 5-year survival was unsatisfactory and did not improve over time.

Our results provide lessons for Mexico’s evolving health system and for countries moving towards universal health coverage.

Novelty and impact

There has been no comprehensive assessment of the health outcomes of Mexico’s policy for financing high-cost cancer treatments that was part of Seguro Popular, health reform aimed at providing care to the population without social security. The study identified several factors amenable to intervention that could improve survival for childhood ALL in Mexico and reduce the observed disparities.

Decision could consider administrative databases as a source of clinical outcomes to ensure the quality their systems.
Pre-diagnostic circulating concentrations of insulin-like growth factor-1 and risk of COVID-19 mortality: results from UK Biobank
Authors: Fan Xikang , Yin Cheng , Wang Jiayu , Yang Mingjia , Ma Hongxia , Jin Guangfu , Song Mingyang , Hu Zhibin , Shen Hongbing , Hang Dong
Published: July 2020

Background

Coronavirus disease 2019 (COVID-19) deteriorates suddenly primarily due to excessive inflammatory injury, and insulin-like growth factor-1 (IGF-1) is implicated in endocrine control of the immune system. However, the effect of IGF-1 levels on COVID-19 prognosis remains unknown.

Objective

To investigate the association between circulating IGF-1 concentrations and mortality risk among COVID-19 patients.

Design

Prospective analysis.

Setting

UK Biobank.

Participants

1425 COVID-19 patients who had pre-diagnostic serum IGF-1 measurements at baseline (2006-2010).

Main outcome measures

COVID-19 mortality (available death data updated to 22 May 2020). Unconditional logistic regression was performed to estimate the odds ratio (OR) and 95% confidence intervals (CIs) of mortality across the IGF-1 quartiles.

Results

Among 1425 COVID-19 patients, 365 deaths occurred due to COVID-19. Compared to the lowest quartile of IGF-1 concentrations, the highest quartile was associated with a 37% lower risk of mortality (OR: 0.63, 95% CI: 0.43-0.93, P-trend=0.03). The association was stronger in women and nonsmokers (both P-interaction=0.01).

Conclusions

Higher IGF-1 concentrations are associated with a lower risk of COVID-19 mortality. Further studies are required to determine whether and how targeting IGF-1 pathway might improve COVID-19 prognosis.
Bibliometric Analysis of COVID-19 in the Context of Migration Health: A Study Protocol
Authors: Pernitez-Agan Sweetmavourneen , Bautista Mary Ann , Lopez Janice , Sampson Margaret , Wickramage Kolitha
Published: July 2020

Introduction

Human mobility has been pivotal to the spread of COVID-19 through travel and migration. To mitigate the spread, most countries have imposed strict travel restrictions that have severely affected both the wellbeing and livelihoods of many migrant and mobile populations (both internally and internationally), particularly those from impoverished communities, those affected by humanitarian crises, including populations displaced and/or living in camps and camp-like settings. The need to include migrants (both regular and irregular or ‘undocumented’) in national strategic response plans for disease prevention and control has been increasingly recognized. Better understanding of the existing scientific evidence in migration health is crucial in designing effective response measures. In this paper, we present a protocol for a bibliometric analysis of scientific publications on COVID-19 and migration health. Expected study findings aim to provide valuable information to support evidence mapping on COVID-19 and migration health, particularly the identification of important research gaps.

Methods and analysis

Using Elsevier’s Scopus abstract and citation database, a comprehensive search strategy will be applied to map scientific publications on COVID-19 and migration health. The current analysis will focus on research published from 1 January 2020 to 4 May 2020. The search query on migration health will largely focus on migration, migrant and human mobility-related terms. Three reviewers will screen publications for eligibility. The extracted bibliographic information will be analysed to determine the dominant research themes, country coverage and migrant groups. Collaboration networks will be analysed using VosViewer, a network analysis software. A deep dive on dominant research themes or migrant health-related topics will be done by creating visualization network maps of keywords from the retrieved publications.

Ethics and dissemination

This analysis will draw on publicly available data and does not directly involve human participants; ethics review is not required.