Mutation rate and genotype variation of Ebola virus from Mali case sequences

Science ◽  
2015 ◽  
Vol 348 (6230) ◽  
pp. 117-119 ◽  
Author(s):  
T. Hoenen ◽  
D. Safronetz ◽  
A. Groseth ◽  
K. R. Wollenberg ◽  
O. A. Koita ◽  
...  
Keyword(s):  
Public Health ◽  
Molecular Diagnostics ◽  
Substitution Rate ◽  
Ebola Virus ◽  
Nucleotide Substitution ◽  
Rapid Evolution ◽  
Nucleotide Substitution Rate ◽  
Outbreak Response ◽  
Genotype Variation ◽  
Current Outbreak

The occurrence of Ebola virus (EBOV) in West Africa during 2013–2015 is unprecedented. Early reports suggested that in this outbreak EBOV is mutating twice as fast as previously observed, which indicates the potential for changes in transmissibility and virulence and could render current molecular diagnostics and countermeasures ineffective. We have determined additional full-length sequences from two clusters of imported EBOV infections into Mali, and we show that the nucleotide substitution rate (1.3 × 10–3 substitutions per site per year) is consistent with rates observed in Central African outbreaks. In addition, overall variation among all genotypes observed remains low. Thus, our data indicate that EBOV is not undergoing rapid evolution in humans during the current outbreak. This finding has important implications for outbreak response and public health decisions and should alleviate several previously raised concerns.

scholarly journals Anthropology in public health emergencies:what is anthropology good for?

2018 ◽  
Vol 3 (2) ◽  
pp. e000534 ◽  
Author(s):  
Darryl Stellmach ◽  
Isabel Beshar ◽  
Juliet Bedford ◽  
Philipp du Cros ◽  
Beverley Stringer
Keyword(s):  
Public Health ◽  
Disease Transmission ◽  
Ebola Virus ◽  
Virus Disease ◽  
Disease Outbreak ◽  
Outbreak Response ◽  
Public Health Response ◽  
Health Crisis ◽  
Health Response ◽  
Increasing Demand

Recent outbreaks of Ebola virus disease (2013–2016) and Zika virus (2015–2016) bring renewed recognition of the need to understand social pathways of disease transmission and barriers to care. Social scientists, anthropologists in particular, have been recognised as important players in disease outbreak response because of their ability to assess social, economic and political factors in local contexts. However, in emergency public health response, as with any interdisciplinary setting, different professions may disagree over methods, ethics and the nature of evidence itself. A disease outbreak is no place to begin to negotiate disciplinary differences. Given increasing demand for anthropologists to work alongside epidemiologists, clinicians and public health professionals in health crises, this paper gives a basic introduction to anthropological methods and seeks to bridge the gap in disciplinary expectations within emergencies. It asks: ‘What can anthropologists do in a public health crisis and how do they do it?’ It argues for an interdisciplinary conception of emergency and the recognition that social, psychological and institutional factors influence all aspects of care.

scholarly journals Genomic diversity of SARS-CoV-2 can be accelerated by a mutation in the nsp14 gene

2020 ◽  
Author(s):  
Kosuke Takada ◽  
Mahoko Takahashi Ueda ◽  
Tokiko Watanabe ◽  
So Nakagawa
Keyword(s):  
Amino Acid ◽  
Substitution Rate ◽  
Nucleotide Substitution ◽  
Acid Sites ◽  
Genomic Diversity ◽  
Nucleotide Substitution Rate ◽  
Structural Protein ◽  
Wild Type ◽  
Gamma Delta ◽  
Evolutionarily Conserved

AbstractNucleotide substitution rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is relatively low compared to the other RNA viruses because coronaviruses including SARS-CoV-2 encode non-structural protein 14 (nsp14) that is an error-correcting exonuclease protein. In this study, to understand genome evolution of SARS-CoV-2 in the current pandemic, we examined mutations of SARS-CoV-2 nsp14 which could inhibit its error-correcting function. First, to obtain functionally important sites of nsp14, we examined 62 representative coronaviruses belonging to alpha, beta, gamma, delta, and unclassified coronaviruses. As a result, 99 out of 527 amino acid sites of nsp14 were evolutionarily conserved. We then examined nsp14 sequences obtained from 28,082 SARS-CoV-2 genomes and identified 6 amino acid changes in nsp14 mutants that were not detected in the 62 representative coronaviruses. We examined genome substitution rates of these mutants and found that an nsp14 mutant with a proline to leucine change at position 203 (P203L) showed a higher substitution rate (35.9 substitutions/year) than SARS-CoV-2 possessing wild-type nsp14 (19.8 substitutions/year). We confirmed that the substitution rate of the P203L is significantly higher than those of other variants containing mutations in structural proteins. Although the number of SARS-CoV-2 variants containing P203L mutation of nsp14 is limited (26), these mutants appeared at least 10 times independently in the current pandemic. These results indicated that the molecular function of nsp14 is important for survival of various coronaviruses including SARS-CoV-2 and that some mutations such as P203L of nsp14 inhibiting its error-correcting function are removed rapidly due to their deleterious effects.

scholarly journals High Variability and Rapid Evolution of a Nanovirus

2010 ◽  
Vol 84 (18) ◽  
pp. 9105-9117 ◽  
Author(s):  
Ioana Grigoras ◽  
Tatiana Timchenko ◽  
Ana Grande-Pérez ◽  
Lina Katul ◽  
Heinrich-Josef Vetten ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Nucleotide Substitution ◽  
Rapid Evolution ◽  
Plant Viruses ◽  
High Variability ◽  
Nucleotide Substitution Rate ◽  
Virus Propagation ◽  
The Family ◽  
Leguminous Crops ◽  
Ssdna Viruses

ABSTRACT Nanoviruses are multipartite single-stranded DNA (ssDNA) plant viruses that cause important diseases of leguminous crops and banana. Little has been known about the variability and molecular evolution of these viruses. Here we report on the variability of faba bean necrotic stunt virus (FBNSV), a nanovirus from Ethiopia. We found mutation frequencies of 7.52 × 10−4 substitutions per nucleotide in a field population of the virus and 5.07 × 10−4 substitutions per nucleotide in a laboratory-maintained population derived thereof. Based on virus propagation for a period of more than 2 years, we determined a nucleotide substitution rate of 1.78 × 10−3 substitutions per nucleotide per year. This high molecular evolution rate places FBNSV, as a representative of the family Nanoviridae, among the fastest-evolving ssDNA viruses infecting plants or vertebrates.

scholarly journals Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12106
Author(s):  
Mikhail I. Schelkunov ◽  
Maxim S. Nuraliev ◽  
Maria D. Logacheva
Keyword(s):  
Substitution Rate ◽  
Nucleotide Substitution ◽  
Nucleotide Substitution Rate ◽  
Genomic Comparison ◽  
Plant Family ◽  
Plastid Genomes ◽  
The Family ◽  
Unknown Reason ◽  
Order Of Magnitude ◽  
Insight Into

The plant family Balanophoraceae consists entirely of species that have lost the ability to photosynthesize. Instead, they obtain nutrients by parasitizing other plants. Recent studies have revealed that plastid genomes of Balanophoraceae exhibit a number of interesting features, one of the most prominent of those being a highly elevated AT content of nearly 90%. Additionally, the nucleotide substitution rate in the plastid genomes of Balanophoraceae is an order of magnitude greater than that of their photosynthetic relatives without signs of relaxed selection. Currently, there are no definitive explanations for these features. Given these unusual features, we hypothesised that the nuclear genomes of Balanophoraceae may also provide valuable information in regard to understanding the evolution of non-photosynthetic plants. To gain insight into these genomes, in the present study we analysed the transcriptomes of two Balanophoraceae species (Rhopalocnemis phalloides and Balanophora fungosa) and compared them to the transcriptomes of their close photosynthetic relatives (Daenikera sp., Dendropemon caribaeus, and Malania oleifera). Our analysis revealed that the AT content of the nuclear genes of Balanophoraceae did not markedly differ from that of the photosynthetic relatives. The nucleotide substitution rate in the genes of Balanophoraceae is, for an unknown reason, several-fold larger than in the genes of photosynthetic Santalales; however, the negative selection in Balanophoraceae is likely stronger. We observed an extensive loss of photosynthesis-related genes in the Balanophoraceae family members. Additionally, we did not observe transcripts of several genes whose products function in plastid genome repair. This implies their loss or very low expression, which may explain the increased nucleotide substitution rate and AT content of the plastid genomes.

scholarly journals Increased evolutionary rate in the 2014 West African Ebola outbreak is due to transient polymorphism and not positive selection

2014 ◽  
Author(s):  
Stephanie J. Spielman ◽  
Austin G. Meyer ◽  
Claus O. Wilke
Keyword(s):  
Substitution Rate ◽  
Rapid Evolution ◽  
Sequence Divergence ◽  
West African ◽  
Evolutionary Analysis ◽  
Health Crisis ◽  
Public Health Crisis ◽  
Molecular Clock Model ◽  
Current Outbreak ◽  
Zaire Ebolavirus

Gire et al. (Science 345:1369-1372, 2014) analyzed 81 complete genomes sampled from the 2014 Zaire ebolavirus (EBOV) outbreak and reported "rapid accumulation of [...] genetic variation" and a substitution rate that was "roughly twice as high within the 2014 outbreak as between outbreaks." These findings have received widespread attention, and many have perceived Gire et al.'s results as implying rapid adaptation of EBOV to humans during the current outbreak. Here, we argue that, on the contrary, sequence divergence in EBOV is rather limited, and that the currently available data contain no robust signal of particularly rapid evolution or adaptation to humans. The doubled substitution rate can be attributed entirely to the application of a molecular-clock model to a population of sequences with minimal divergence and segregating polymorphisms. Our results highlight how subtle technical aspects of sophisticated evolutionary analysis methods may result in highly-publicized, misconstrued statements about an ongoing public health crisis.

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