scholarly journals Human endemic coronavirus emergence in the context of past and recent zoonotic outbreaks

2021 ◽  
Author(s):  
Diego Forni ◽  
Rachele Cagliani ◽  
Federica Arrigoni ◽  
Martino Benvenuti ◽  
Chiara Pontremoli ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Viral Disease ◽  
Time Frame ◽  
Antigenic Drift ◽  
Molecular Dating ◽  
Viral Diseases ◽  
Human Interferon ◽  
Human Populations ◽  
Influenza Pandemics ◽  
Temporal Succession

Abstract Understanding the evolutionary dynamics of the four human endemic coronaviruses might provide insight into the future trajectories of SARS-CoV-2 evolution. We re-assessed the timing of endemic coronavirus emergence and we show that all viruses entered human populations in a time-frame ranging from ~500 to 55 years ago. Because the three highly pathogenic coronaviruses (SARS-CoV, MERS-CoV, and SARS-CoV-2) spilled-over in tight temporal succession, the pattern of coronavirus emergence, in analogy to that of influenza pandemics, is highly irregular. To contextualize this observation in a wider perspective of viral diseases emergence since 1945, we mined epidemiology database information. After controlling for reporting bias, we find that, contrary to widespread beliefs, the occurrence of viral diseases (either zoonotic or not) has not increased over the last decades. Analysis of the recent and ongoing evolution of HCoV-229E and HCoV-OC43 indicated that positive selection most likely contributed to fine-tune the interaction with the human interferon/inflammatory response. Conversely, integration of evolutionary inference and molecular dating provided evidence that these viruses are not undergoing antigenic drift and the temporal emergence of spike protein variants is best explained by optimization of receptor binding affinity. These data provide a fresh look on viral disease emergence and on coronavirus evolution.

scholarly journals You Will Never Walk Alone: Codispersal of JC Polyomavirus with Human Populations

2019 ◽  
Vol 37 (2) ◽  
pp. 442-454 ◽  
Author(s):  
Diego Forni ◽  
Rachele Cagliani ◽  
Mario Clerici ◽  
Uberto Pozzoli ◽  
Manuela Sironi
Keyword(s):  
Geographic Distribution ◽  
Human Population ◽  
Strong Support ◽  
Time Frame ◽  
Genetic Distances ◽  
The Philippines ◽  
Molecular Dating ◽  
Human Populations ◽  
Jc Polyomavirus ◽  
Reconciliation Analysis

Abstract JC polyomavirus (JCPyV) is one of the most prevalent human viruses. Findings based on the geographic distribution of viral subtypes suggested that JCPyV codiverged with human populations. This view was however challenged by data reporting a much more recent origin and expansion of JCPyV. We collected information on ∼1,100 worldwide strains and we show that their geographic distribution roughly corresponds to major human migratory routes. Bayesian phylogeographic analysis inferred a Subsaharan origin for JCPyV, although with low posterior probability. High confidence inference at internal nodes provided strong support for a long-standing association between the virus and human populations. In line with these data, pairwise FST values for JCPyV and human mtDNA sampled from the same areas showed a positive and significant correlation. Likewise, very strong relationships were found when node ages in the JCPyV phylogeny were correlated with human population genetic distances (nuclear-marker based FST). Reconciliation analysis detected a significant cophylogenetic signal for the human population and JCPyV trees. Notably, JCPyV also traced some relatively recent migration events such as the expansion of people from the Philippines/Taiwan area into Remote Oceania, the gene flow between North-Eastern Siberian and Ainus, and the Koryak contribution to Circum-Arctic Americans. Finally, different molecular dating approaches dated the origin of JCPyV in a time frame that precedes human out-of-Africa migration. Thus, JCPyV infected early human populations and accompanied our species during worldwide dispersal. JCPyV typing can provide reliable geographic information and the virus most likely adapted to the genetic background of human populations.

scholarly journals The evolutionary dynamics of Oropouche Virus (OROV) in South America

2019 ◽  
Author(s):  
Bernardo Gutierrez ◽  
Emma Wise ◽  
Steven Pullan ◽  
Christopher Logue ◽  
Thomas A. Bowden ◽  
...  
Keyword(s):  
Viral Genome ◽  
Amazon Basin ◽  
Evolutionary Dynamics ◽  
Surface Proteins ◽  
Human Populations ◽  
Evolutionary Processes ◽  
Viral Pathogens ◽  
Viral Genomes ◽  
Glycosylation Sites ◽  
Variable Evolutionary Rates

AbstractThe Amazon basin is host to numerous arthropod-borne viral pathogens that cause febrile disease in humans. Among these,Oropouche orthobunyavirus(OROV) is a relatively understudied member of the Peribunyavirales that causes periodic outbreaks in human populations in Brazil and other South American countries. Although several studies have described the genetic diversity of the virus, the evolutionary processes that shape the viral genome remain poorly understood. Here we present a comprehensive study of the genomic dynamics of OROV that encompasses phylogenetic analysis, evolutionary rate estimates, inference of natural selective pressures, recombination and reassortment, and structural analysis of OROV variants. Our study includes all available published sequences, as well as a set of new OROV genomes sequences obtained from patients in Ecuador, representing the first set of viral genomes from this country. Our results show that differing evolutionary processes on the three segments that encompass the viral genome lead to variable evolutionary rates and TMRCAs that could be explained by cryptic reassortment. We also present the discovery of previously unobserved putative N-linked glycosylation sites, and codons which evolve under positive selection on the viral surface proteins, and discuss the potential role of these features in the evolution of the virus through a combined phylogenetic and structural approach.

Predicting evolution in diverse communities

2019 ◽  
pp. 167-188
Author(s):  
Timothy G. Barraclough
Keyword(s):  
Microbial Community ◽  
Ecosystem Functioning ◽  
Evolutionary Dynamics ◽  
Control Measures ◽  
Living Systems ◽  
Human Populations ◽  
Focal Species ◽  
Diverse Communities ◽  
Challenges And Opportunities ◽  
Disease Agent

Following the outline of basic theory and evidence in chapters 7 and 8, this chapter sets the challenge of attempting to predict evolutionary dynamics in realistically diverse communities. Many challenges and opportunities facing human populations rely on being able to predict living systems. Even when a single focal species such as a pest or disease agent is of particular concern, its dynamics and responses to control measures always depend on interactions with a diverse set of other species. Even when the focus is on whole-ecosystem functioning, that depends on trait responses of constituent species. The chapter outlines several case studies where a multispecies evolutionary approach is required, including managing marine fisheries, controlling crop pests, and managing human microbiomes for improved health. To illustrate possible ways forwards, a model of evolution in a microbial community is presented, and possible methods for tracking evolution in diverse communities are discussed.

Sexually Transmitted, Urinary Tract, and Gastrointestinal Tract Infections

2016 ◽  
pp. 521-538
Author(s):  
M. Rizwan Sohail
Keyword(s):  
Influenza A ◽  
The United States ◽  
Antigenic Drift ◽  
Influenza B ◽  
Sexually Transmitted ◽  
Influenza Pandemics ◽  
Population Immunity ◽  
Large Numbers ◽  
Seasonal Epidemics ◽  
Tract Infections

Influenza causes annual, seasonal epidemics that lead to tens of thousands of deaths each year in the United States. Two influenza A strains (H3N2 and H1N1) and 1 or 2 influenza B strains typically circulate during winter months and undergo minor antigenic mutations (antigenic drift) resulting in annual seasonal epidemics. Influenza pandemics occur more rarely (every 20-30 years) and are the result of major antigenic changes (antigenic shift) leading to large numbers of infections due to low levels of population immunity. In seasonal epidemics, 80% to 90% of deaths due to influenza occur in persons older than 65 years.

scholarly journals Evolutionary dynamics of culturally transmitted, fertility-reducing traits

2020 ◽  
Vol 287 (1925) ◽  
pp. 20192468
Author(s):  
Dominik Wodarz ◽  
Shaun Stipp ◽  
David Hirshleifer ◽  
Natalia L. Komarova
Keyword(s):  
Demographic Transition ◽  
Cultural Transmission ◽  
Western Europe ◽  
Evolutionary Dynamics ◽  
Transition Process ◽  
Low Fertility ◽  
Human Populations ◽  
Demographic Transitions ◽  
Cultural Evolutionary ◽  
Fertility Traits

Human populations in many countries have undergone a phase of demographic transition, characterized by a major reduction in fertility at a time of increased resource availability. A key stylized fact is that the reduction in fertility is preceded by a reduction in mortality and a consequent increase in population density. Various theories have been proposed to account for the demographic transition process, including maladaptation, increased parental investment in fewer offspring, and cultural evolution. None of these approaches, including formal cultural evolutionary models of the demographic transitions, have addressed a possible direct causal relationship between a reduction in mortality and the subsequent decline in fertility. We provide mathematical models in which low mortality favours the cultural selection of low-fertility traits. This occurs because reduced mortality slows turnover in the model, which allows the cultural transmission advantage of low-fertility traits to outrace their reproductive disadvantage. For mortality to be a crucial determinant of outcome, a cultural transmission bias is required where slow reproducers exert higher social influence. Computer simulations of our models that allow for exogenous variation in the death rate can reproduce the central features of the demographic transition process, including substantial reductions in fertility within only one to three generations. A model assuming continuous evolution of reproduction rates through imitation errors predicts fertility to fall below replacement levels if death rates are sufficiently low. This can potentially explain the very low preferred family sizes in Western Europe.

Viral Disease in Hematology

Hematology ◽  
2000 ◽  
Vol 2000 (1) ◽  
pp. 409-423 ◽  
Author(s):  
Genoveffa Franchini ◽  
Richard F. Ambinder ◽  
Michèle Barry
Keyword(s):  
Leukemia Virus ◽  
Antiviral Treatment ◽  
Basic Research ◽  
Epidemiological Data ◽  
Viral Disease ◽  
Human Populations ◽  
Genetic Characteristics ◽  
Barr Virus ◽  
Ebv Infection ◽  
Human T Cell

As part of the international outreach of the American Society of Hematology, this review addresses some aspects of the genetics, biology, epidemiology, and clinical relevance of viruses that cause a variety of hematopoietic disorders in human populations. The viruses described here have a different pattern of geographical distribution, and the disease manifestations may vary according to environmental and/or genetic characteristics of the host. Epstein-Barr virus, a linear double-stranded DNA virus (herpesvirus), and the human T-cell leukemia virus, a retrovirus with a single-stranded diploid RNA genome, are associated among other diseases with lymphoma and leukemia/lymphoma, respectively. Both viruses cause a lifelong infection, but only a small percentage of infected individuals develop hematopoietic neoplasms. Epidemiological data suggest that the time of infection may be important in determining disease outcome in both HTLV-I and EBV infection. The pathogenic mechanisms used by these viruses are of most interest since they may recapitulate growth dysregulation steps also occurring in other hematopoietic malignancies.In Section I Dr. Franchini reviews the biology, genetics and diseases associated with HTLV-I and HTLV-II. In Section II, Dr. Ambinder reviews the biology of EBV infection and its relationship to the pathogenesis of Hodgkin's disease and other malignancies.In Section III, Dr. Barry reviews the viral hemorrhagic fevers caused by RNA viruses such as Arenaviridae, Bunyaviridae, Filoviridae, and Flaviviridae, which can lead to acute syndromes that can be fatal. However, prompt diagnosis is key for patient management as well as for limiting their spread to others. These syndromes have become the focus of public concern and represent not only a clinical challenge, since in most cases no specific antiviral treatment is available, but also a challenge for future basic research on their biology and pathogenesis since little is known at present.

scholarly journals 60 million years of co-divergence in the fig–wasp symbiosis

2005 ◽  
Vol 272 (1581) ◽  
pp. 2593-2599 ◽  
Author(s):  
Nina Rønsted ◽  
George D Weiblen ◽  
James M Cook ◽  
Nicolas Salamin ◽  
Carlos A Machado ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Time Frame ◽  
Molecular Dating ◽  
Fig Wasp ◽  
Geological Time ◽  
Molecular Phylogenetic ◽  
Pollinator Specialization ◽  
Phylogenetic Hypotheses ◽  
Fossil Data ◽  
Plant Pollinator

Figs ( Ficus ; ca 750 species) and fig wasps (Agaoninae) are obligate mutualists: all figs are pollinated by agaonines that feed exclusively on figs. This extraordinary symbiosis is the most extreme example of specialization in a plant–pollinator interaction and has fuelled much speculation about co-divergence. The hypothesis that pollinator specialization led to the parallel diversification of fig and pollinator lineages (co-divergence) has so far not been tested due to the lack of robust and comprehensive phylogenetic hypotheses for both partners. We produced and combined the most comprehensive molecular phylogenetic trees to date with fossil data to generate independent age estimates for fig and pollinator lineages, using both non-parametric rate smoothing and penalized likelihood dating methods. Molecular dating of ten pairs of interacting lineages provides an unparalleled example of plant–insect co-divergence over a geological time frame spanning at least 60 million years.

scholarly journals Evolutionary dynamics of human and avian metapneumoviruses

2008 ◽  
Vol 89 (12) ◽  
pp. 2933-2942 ◽  
Author(s):  
Miranda de Graaf ◽  
Albert D. M. E. Osterhaus ◽  
Ron A. M. Fouchier ◽  
Edward C. Holmes
Keyword(s):  
Genetic Diversity ◽  
Evolutionary Dynamics ◽  
Recent Common Ancestor ◽  
Human Populations ◽  
Population Bottlenecks ◽  
Genetic Lineages ◽  
The Past ◽  
Most Recent Common Ancestor ◽  
Large Sets ◽  
Respiratory Tract Illnesses

Human (HMPV) and avian (AMPV) metapneumoviruses are closely related viruses that cause respiratory tract illnesses in humans and birds, respectively. Although HMPV was first discovered in 2001, retrospective studies have shown that HMPV has been circulating in humans for at least 50 years. AMPV was first isolated in the 1970s, and can be classified into four subgroups, A–D. AMPV subgroup C is more closely related to HMPV than to any other AMPV subgroup, suggesting that HMPV has emerged from AMPV-C upon zoonosis. Presently, at least four genetic lineages of HMPV circulate in human populations – A1, A2, B1 and B2 – of which lineages A and B are antigenically distinct. We used a Bayesian Markov Chain Monte Carlo (MCMC) framework to determine the evolutionary and epidemiological dynamics of HMPV and AMPV-C. The rates of nucleotide substitution, relative genetic diversity and time to the most recent common ancestor (TMRCA) were estimated using large sets of sequences of the nucleoprotein, the fusion protein and attachment protein genes. The sampled genetic diversity of HMPV was found to have arisen within the past 119–133 years, with consistent results across all three genes, while the TMRCA for HMPV and AMPV-C was estimated to have existed around 200 years ago. The relative genetic diversity observed in the four HMPV lineages was low, most likely reflecting continual population bottlenecks, with only limited evidence for positive selection.

scholarly journals Effective and Simple Methods of Preventing the Transmission of Viral Diseases

2020 ◽  
pp. 46-56
Author(s):  
A. Taqaddas
Keyword(s):  
Health Care ◽  
Virus Infection ◽  
Care Setting ◽  
Viral Infections ◽  
Viral Disease ◽  
Therapeutic Strategies ◽  
Viral Transmission ◽  
Viral Diseases ◽  
Policy Makers ◽  
Health Care Settings

Viral infections have always been of major concern in communities, health care settings and medical fields including radiotherapy and Radiology. Recently corona virus infection has attained global attention in the wake of covid-19 outbreak and consequently highlighted importance of viral prevention, diagnostic and therapeutic strategies to control and treat viral disease. In view of the recent events, the author reviewed the current and past literature to discuss contagious versus infectious viral transmission, as well as simple and effective ways of preventing the spread of viral diseases in community and health care setting so that this information can be used for preventing viral transmission at all levels. The article is written for a wide variety of audiences i.e. scientific and medical communities policy makers and general public.

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