scholarly journals Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses

2019 ◽  
Author(s):  
Nicola F. Müller ◽  
Ugnė Stolz ◽  
Gytis Dudas ◽  
Tanja Stadler ◽  
Timothy G. Vaughan
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Population Level ◽  
Influenza Viruses ◽  
Monte Carlo Algorithm ◽  
Full Genome Sequence ◽  
Full Genome ◽  
Human Influenza ◽  
Fitness Benefits

AbstractReassortment is an important source of genetic diversity in segmented viruses and is the main source of novel pathogenic influenza viruses. Despite this, studying the reassortment process has been constrained by the lack of a coherent, model-based inference framework. We here introduce a novel coalescent based model that allows us to explicitly model the joint coalescent and reassortment process. In order to perform inference under this model, we present an efficient Markov chain Monte Carlo algorithm to sample rooted networks and the embedding of phylogenetic trees within networks. Together, these provide the means to jointly infer coalescent and reassortment rates with the reassortment network and the embedding of segments in that network from full genome sequence data. Studying reassortment patterns of different human influenza datasets, we find large differences in reassortment rates across different human influenza viruses. Additionally, we find that reassortment events predominantly occur on selectively fitter parts of reassortment networks showing that on a population level, reassortment positively contributes to the fitness of human influenza viruses.

scholarly journals Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses

2020 ◽  
Vol 117 (29) ◽  
pp. 17104-17111
Author(s):  
Nicola F. Müller ◽  
Ugnė Stolz ◽  
Gytis Dudas ◽  
Tanja Stadler ◽  
Timothy G. Vaughan
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Population Level ◽  
Influenza Viruses ◽  
Monte Carlo Algorithm ◽  
Full Genome Sequence ◽  
Full Genome ◽  
Human Influenza ◽  
Fitness Benefits

Reassortment is an important source of genetic diversity in segmented viruses and is the main source of novel pathogenic influenza viruses. Despite this, studying the reassortment process has been constrained by the lack of a coherent, model-based inference framework. Here, we introduce a coalescent-based model that allows us to explicitly model the joint coalescent and reassortment process. In order to perform inference under this model, we present an efficient Markov chain Monte Carlo algorithm to sample rooted networks and the embedding of phylogenetic trees within networks. This algorithm provides the means to jointly infer coalescent and reassortment rates with the reassortment network and the embedding of segments in that network from full-genome sequence data. Studying reassortment patterns of different human influenza datasets, we find large differences in reassortment rates across different human influenza viruses. Additionally, we find that reassortment events predominantly occur on selectively fitter parts of reassortment networks showing that on a population level, reassortment positively contributes to the fitness of human influenza viruses.

scholarly journals Global transmission of influenza viruses from humans to swine

2012 ◽  
Vol 93 (10) ◽  
pp. 2195-2203 ◽  
Author(s):  
Martha I. Nelson ◽  
Marie R. Gramer ◽  
Amy L. Vincent ◽  
Edward C. Holmes
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Influenza Virus ◽  
Large Scale ◽  
Sequence Data ◽  
Virus Genome ◽  
Influenza Viruses ◽  
Substantial Contribution ◽  
Human Influenza ◽  
Swine Workers

To determine the extent to which influenza viruses jump between human and swine hosts, we undertook a large-scale phylogenetic analysis of pandemic A/H1N1/09 (H1N1pdm09) influenza virus genome sequence data. From this, we identified at least 49 human-to-swine transmission events that occurred globally during 2009–2011, thereby highlighting the ability of the H1N1pdm09 virus to transmit repeatedly from humans to swine, even following adaptive evolution in humans. Similarly, we identified at least 23 separate introductions of human seasonal (non-pandemic) H1 and H3 influenza viruses into swine globally since 1990. Overall, these results reveal the frequency with which swine are exposed to human influenza viruses, indicate that humans make a substantial contribution to the genetic diversity of influenza viruses in swine, and emphasize the need to improve biosecurity measures at the human–swine interface, including influenza vaccination of swine workers.

scholarly journals Limited Genetic Diversity Detected in Middle East Respiratory Syndrome-Related Coronavirus Variants Circulating in Dromedary Camels in Jordan

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 592
Author(s):  
Stephanie N. Seifert ◽  
Jonathan E. Schulz ◽  
Stacy Ricklefs ◽  
Michael Letko ◽  
Elangeni Yabba ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Middle East ◽  
United Arab Emirates ◽  
Sequence Data ◽  
Case Fatality ◽  
High Sensitivity ◽  
Middle East Respiratory Syndrome ◽  
Full Genome Sequence ◽  
Genome Sequences ◽  
Dromedary Camels

Middle East respiratory syndrome-related coronavirus (MERS-CoV) is a persistent zoonotic pathogen with frequent spillover from dromedary camels to humans in the Arabian Peninsula, resulting in limited outbreaks of MERS with a high case-fatality rate. Full genome sequence data from camel-derived MERS-CoV variants show diverse lineages circulating in domestic camels with frequent recombination. More than 90% of the available full MERS-CoV genome sequences derived from camels are from just two countries, the Kingdom of Saudi Arabia (KSA) and United Arab Emirates (UAE). In this study, we employ a novel method to amplify and sequence the partial MERS-CoV genome with high sensitivity from nasal swabs of infected camels. We recovered more than 99% of the MERS-CoV genome from field-collected samples with greater than 500 TCID50 equivalent per nasal swab from camel herds sampled in Jordan in May 2016. Our subsequent analyses of 14 camel-derived MERS-CoV genomes show a striking lack of genetic diversity circulating in Jordan camels relative to MERS-CoV genome sequences derived from large camel markets in KSA and UAE. The low genetic diversity detected in Jordan camels during our study is consistent with a lack of endemic circulation in these camel herds and reflective of data from MERS outbreaks in humans dominated by nosocomial transmission following a single introduction as reported during the 2015 MERS outbreak in South Korea. Our data suggest transmission of MERS-CoV among two camel herds in Jordan in 2016 following a single introduction event.

scholarly journals Genetic evolution of the neuraminidase of influenza A (H3N2) viruses from 1968 to 2009 and its correspondence to haemagglutinin evolution

2012 ◽  
Vol 93 (9) ◽  
pp. 1996-2007 ◽  
Author(s):  
Kim B. Westgeest ◽  
Miranda de Graaf ◽  
Mathieu Fourment ◽  
Theo M. Bestebroer ◽  
Ruud van Beek ◽  
...  
Keyword(s):  
Humoral Immunity ◽  
Influenza A ◽  
Phylogenetic Trees ◽  
Influenza Viruses ◽  
Genetic Maps ◽  
Genetic Evolution ◽  
Human Influenza ◽  
Nucleotide Level ◽  
Antigenic Evolution ◽  
Positively Selected Sites

Each year, influenza viruses cause epidemics by evading pre-existing humoral immunity through mutations in the major glycoproteins: the haemagglutinin (HA) and the neuraminidase (NA). In 2004, the antigenic evolution of HA of human influenza A (H3N2) viruses was mapped (Smith et al., Science 305, 371–376, 2004) from its introduction in humans in 1968 until 2003. The current study focused on the genetic evolution of NA and compared it with HA using the dataset of Smith and colleagues, updated to the epidemic of the 2009/2010 season. Phylogenetic trees and genetic maps were constructed to visualize the genetic evolution of NA and HA. The results revealed multiple reassortment events over the years. Overall rates of evolutionary change were lower for NA than for HA1 at the nucleotide level. Selection pressures were estimated, revealing an abundance of negatively selected sites and sparse positively selected sites. The differences found between the evolution of NA and HA1 warrant further analysis of the evolution of NA at the phenotypic level, as has been done previously for HA.

scholarly journals Origin of the European avian-like swine influenza viruses

2014 ◽  
Vol 95 (11) ◽  
pp. 2372-2376 ◽  
Author(s):  
Andi Krumbholz ◽  
Jeannette Lange ◽  
Andreas Sauerbrei ◽  
Marco Groth ◽  
Matthias Platzer ◽  
...  
Keyword(s):  
Avian Influenza ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Swine Influenza ◽  
H1n1 Influenza ◽  
Molecular Data ◽  
Influenza Viruses ◽  
Time Resolved ◽  
Genotype Constellation ◽  
Tree Inference

The avian-like swine influenza viruses emerged in 1979 in Belgium and Germany. Thereafter, they spread through many European swine-producing countries, replaced the circulating classical swine H1N1 influenza viruses, and became endemic. Serological and subsequent molecular data indicated an avian source, but details remained obscure due to a lack of relevant avian influenza virus sequence data. Here, the origin of the European avian-like swine influenza viruses was analysed using a collection of 16 European swine H1N1 influenza viruses sampled in 1979–1981 in Germany, the Netherlands, Belgium, Italy and France, as well as several contemporaneous avian influenza viruses of various serotypes. The phylogenetic trees suggested a triple reassortant with a unique genotype constellation. Time-resolved maximum clade credibility trees indicated times to the most recent common ancestors of 34–46 years (before 2008) depending on the RNA segment and the method of tree inference.

scholarly journals Improving pandemic influenza risk assessment

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Colin A Russell ◽  
Peter M Kasson ◽  
Ruben O Donis ◽  
Steven Riley ◽  
John Dunbar ◽  
...  
Keyword(s):  
Risk Assessment ◽  
Pandemic Influenza ◽  
Influenza A ◽  
Sequence Data ◽  
Virus Genome ◽  
Influenza Viruses ◽  
Influenza Surveillance ◽  
Human Influenza ◽  
Influenza A Viruses ◽  
Virus Genotype

Assessing the pandemic risk posed by specific non-human influenza A viruses is an important goal in public health research. As influenza virus genome sequencing becomes cheaper, faster, and more readily available, the ability to predict pandemic potential from sequence data could transform pandemic influenza risk assessment capabilities. However, the complexities of the relationships between virus genotype and phenotype make such predictions extremely difficult. The integration of experimental work, computational tool development, and analysis of evolutionary pathways, together with refinements to influenza surveillance, has the potential to transform our ability to assess the risks posed to humans by non-human influenza viruses and lead to improved pandemic preparedness and response.

scholarly journals Complete Genome Sequence of Psittacine Adenovirus 1, Identified from Poicephalus senegalus in Italy

2018 ◽  
Vol 7 (11) ◽  
Author(s):  
Adelaide Milani ◽  
Gianpiero Zamperin ◽  
Alice Fusaro ◽  
Annalisa Salviato ◽  
Luca Bano ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Full Genome Sequence ◽  
Full Genome ◽  
High Genetic Diversity ◽  
Content Type ◽  
First Time

Using a metagenomics approach, we were able to determine for the first time the full-genome sequence of a psittacine adenovirus 1 isolate that was recovered from the liver of a dead Senegal parrot (Poicephalus senegalus) in Italy. The results of the phylogenetic investigations revealed the existence of high genetic diversity among adenoviruses circulating in psittacine birds.

Intra- and interspecific genetic diversity of New Zealand hairworms (Nematomorpha)

Parasitology ◽  
2017 ◽  
Vol 144 (8) ◽  
pp. 1026-1040 ◽  
Author(s):  
ZACHARY J. C. TOBIAS ◽  
ARUN K. YADAV ◽  
ANDREAS SCHMIDT-RHAESA ◽  
ROBERT POULIN
Keyword(s):  
Genetic Diversity ◽  
New Zealand ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Population Level ◽  
Morphological Classification ◽  
Widespread Species ◽  
Sampling Locations ◽  
Host Parasite ◽  
Eggs And Larvae

SUMMARYHairworms (Nematomorpha) are a little-known group of parasites, and despite having been represented in the taxonomic literature for over a century, the implementation of molecular genetics in studies of hairworm ecology and evolution lags behind that of other parasitic taxa. In this study, we characterize the genetic diversity of the New Zealand nematomorph fauna and test for genetic structure within the most widespread species found. We provide new mitochondrial and nuclear ribosomal sequence data for three previously described species from New Zealand:Gordius paranensis, Parachordodes diblastusandEuchordodes nigromaculatus. We also present genetic data on a previously reported but undescribedGordiussp., as well as data from specimens of a newGordionussp., a genus new for New Zealand. Phylogenetic analyses of CO1 and nuclear rDNA regions correspond with morphological classification based on scanning electron microscopy, and demonstrate paraphyly of the genusGordionusand the potential for cryptic species withinG. paranensis. Population-level analyses ofE. nigromaculatusshowed no genetic differentiation among sampling locations across the study area, in contrast to previously observed patterns in known and likely definitive hosts. Taken together, this raises the possibility that factors such as definitive host specificity, intermediate host movement, and passive dispersal of eggs and larvae may influence host–parasite population co-structure in hairworms.

scholarly journals An Attenuated LC16m8 Smallpox Vaccine: Analysis of Full-Genome Sequence and Induction of Immune Protection

2005 ◽  
Vol 79 (18) ◽  
pp. 11873-11891 ◽  
Author(s):  
Shigeru Morikawa ◽  
Tokuki Sakiyama ◽  
Hideki Hasegawa ◽  
Masayuki Saijo ◽  
Akihiko Maeda ◽  
...  
Keyword(s):  
Vaccinia Virus ◽  
Sequence Data ◽  
Open Reading Frames ◽  
World Health ◽  
Full Genome Sequence ◽  
Pcr Analysis ◽  
Envelope Gene ◽  
Immune Protection ◽  
Full Genome ◽  
Potential Threat

ABSTRACT The potential threat of smallpox bioterrorism has made urgent the development of lower-virulence vaccinia virus vaccines. An attenuated LC16m8 (m8) vaccine was developed in 1975 from the Lister strain used in the World Health Organization smallpox eradication program but was not used against endemic smallpox. Today, no vaccines can be tested with variola virus for efficacy in humans, and the mechanisms of immune protection against the major intracellular mature virion (IMV) and minor extracellular enveloped virion (EEV) populations of poxviruses are poorly understood. Here, we determined the full-genome sequences of the m8, parental LC16mO (mO), and grandparental Lister (LO) strains and analyzed their evolutionary relationships. Sequence data and PCR analysis indicated that m8 was a progeny of LO and that m8 preserved almost all of the open reading frames of vaccinia virus except for the disrupted EEV envelope gene B5R. In accordance with this genomic background, m8 induced 100% protection against a highly pathogenic vaccinia WR virus in mice by a single vaccination, despite the lack of anti-B5R and anti-EEV antibodies. The immunogenicity and priming efficacy with the m8 vaccine consisting mainly of IMV were as high as those with the intact-EEV parental mO and grandparental LO vaccines. Thus, mice vaccinated with 107 PFU of m8 produced low levels of anti-B5R antibodies after WR challenge, probably because of quick clearance of B5R-expressing WR EEV by strong immunity induced by the vaccination. These results suggest that priming with m8 IMV provides efficient protection despite undetectable levels of immunity against EEV.

scholarly journals ‘Seq & Destroy’: the full genome sequencing of archived wild type and vaccine rinderpest virus isolates prior to their destruction

2020 ◽  
Vol 2 (7A) ◽  
Author(s):  
Simon King ◽  
Paulina Rajko-Nenow ◽  
Honorata Ropiak ◽  
Paolo Ribeca ◽  
Carrie Batten ◽  
...  
Keyword(s):  
Fusion Protein ◽  
Sequence Data ◽  
Illumina Miseq ◽  
Start Codon ◽  
Full Genome Sequence ◽  
Full Genome ◽  
Rinderpest Virus ◽  
Full Genome Sequencing ◽  
Historical Epidemiology ◽  
In The Wild

Rinderpest, a once much feared livestock disease, was declared eradicated in 2011, however virus-containing material is still held in laboratories worldwide. Prior to the destruction of our institute’s stocks, we determined the full genome sequence of the distinct samples of rinderpest virus (RPV) in our repository. This data would decipher the historical epidemiology of RPV and allow for recovery of the virus should the need arise. For each sample (n=123), sequencing libraries were prepared using either transposon-based fragmentation of cDNA (Nextera XT DNA Library Prep kit) or single primer isothermal amplification (Trio RNA-Seq kit) and sequenced on the Illumina MiSeq. Regions of low or no coverage were re-sequenced using a Sanger sequencing approach. Examination of the sequences of RPV isolates has shown that the African isolates form a single disparate clade, rather than two separate clades as was previously believed. We have also identified two groups of goat-passaged viruses which have acquired an extra 6 bases in the long untranslated region between the matrix and fusion protein coding sequences, and a group of African isolates where translation of the fusion protein begins from a non-standard start codon (AUA). In addition, the viruses that were force-passaged through alternate hosts such as rabbits or goats, appear to diverge from the clades that represent viruses which were maintained in the wild. Our unique set of sequence data will be invaluable for forensic epidemiology investigations in the event of an unforeseen outbreak and aid in the understanding of the evolution of related morbilliviruses.

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