scholarly journals Variable routes to genomic and host adaptation among coronaviruses

2021 ◽  
Author(s):  
Vincent Montoya ◽  
Angela McLaughlin ◽  
Gideon J. Mordecai ◽  
Rachel L. Miller ◽  
Jeffrey B. Joy
Keyword(s):  
Host Adaptation

scholarly journals Recent Progress in Torovirus Molecular Biology

Viruses ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 435
Author(s):  
Makoto Ujike ◽  
Fumihiro Taguchi
Keyword(s):  
Molecular Biology ◽  
Recent Progress ◽  
Reverse Genetics ◽  
Cultured Cells ◽  
Host Adaptation ◽  
Economic Losses ◽  
New Family ◽  
Enteric Diseases ◽  
Long Time ◽  
Medical Importance

Torovirus (ToV) has recently been classified into the new family Tobaniviridae, although it belonged to the Coronavirus (CoV) family historically. ToVs are associated with enteric diseases in animals and humans. In contrast to CoVs, which are recognised as pathogens of veterinary and medical importance, little attention has been paid to ToVs because their infections are usually asymptomatic or not severe; for a long time, only one equine ToV could be propagated in cultured cells. However, bovine ToVs, which predominantly cause diarrhoea in calves, have been detected worldwide, leading to economic losses. Porcine ToVs have also spread globally; although they have not caused serious economic losses, coinfections with other pathogens can exacerbate their symptoms. In addition, frequent inter- or intra-recombination among ToVs can increase pathogenesis or unpredicted host adaptation. These findings have highlighted the importance of ToVs as pathogens and the need for basic ToV research. Here, we review recent progress in the study of ToV molecular biology including reverse genetics, focusing on the similarities and differences between ToVs and CoVs.

scholarly journals Within-Host Adaptation Mediated by Intergenic Evolution in Pseudomonas aeruginosa

2019 ◽  
Vol 11 (5) ◽  
pp. 1385-1397 ◽  
Author(s):  
S M Hossein Khademi ◽  
Pavelas Sazinas ◽  
Lars Jelsbak
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Host Adaptation

scholarly journals Guapiaçu virus, a new insect-specific flavivirus isolated from two species of Aedes mosquitoes from Brazil

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Geovani de Oliveira Ribeiro ◽  
Antonio Charlys da Costa ◽  
Danielle Elise Gill ◽  
Edcelha Soares D’Athaide Ribeiro ◽  
Marlisson Octavio da S. Rego ◽  
...  
Keyword(s):  
Codon Usage ◽  
Mammalian Cells ◽  
Plasma Sample ◽  
Genetic Characterization ◽  
Secondary Structures ◽  
Host Adaptation ◽  
Major Group ◽  
Aedes Mosquitoes ◽  
Evolutionary Relatedness

AbstractClassical insect-flaviviruses (cISFVs) and dual host-related insect-specific flavivirus (dISFV) are within the major group of insect-specific flavivirus. Remarkably dISFV are evolutionarily related to some of the pathogenic flavivirus, such as Zika and dengue viruses. The Evolutionary relatedness of dISFV to flavivirus allowed us to investigate the evolutionary principle of host adaptation. Additionally, dISFV can be used for the development of flavivirus vaccines and to explore underlying principles of mammalian pathogenicity. Here we describe the genetic characterization of a novel putative dISFV, termed Guapiaçu virus (GUAPV). Distinct strains of GUAPV were isolated from pools of Aedes terrens and Aedes scapularis mosquitoes. Additionally, we also detected viral GUAPV RNA in a plasma sample of an individual febrile from the Amazon region (North of Brazil). Although GUAPV did not replicate in tested mammalian cells, 3′UTR secondary structures duplication and codon usage index were similar to pathogenic flavivirus.

scholarly journals Prisoners of war — host adaptation and its constraints on virus evolution

2018 ◽  
Vol 17 (5) ◽  
pp. 321-328 ◽  
Author(s):  
Peter Simmonds ◽  
Pakorn Aiewsakun ◽  
Aris Katzourakis
Keyword(s):  
Virus Evolution ◽  
Host Adaptation ◽  
Prisoners Of War

scholarly journals Comparative genomics of Lactobacillus salivarius strains focusing on their host adaptation

2017 ◽  
Vol 205 ◽  
pp. 48-58 ◽  
Author(s):  
Jun-Yeong Lee ◽  
Geon Goo Han ◽  
Eun Bae Kim ◽  
Yun-Jaie Choi
Keyword(s):  
Comparative Genomics ◽  
Host Adaptation ◽  
Lactobacillus Salivarius

The nuclear import machinery is a determinant of influenza virus host adaptation

BioEssays ◽  
2012 ◽  
Vol 35 (1) ◽  
pp. 23-27 ◽  
Author(s):  
Patricia Resa-Infante ◽  
Gülsah Gabriel
Keyword(s):  
Influenza Virus ◽  
Nuclear Import ◽  
Host Adaptation

scholarly journals Host-Adaptation of Francisella tularensis Alters the Bacterium's Surface-Carbohydrates to Hinder Effectors of Innate and Adaptive Immunity

PLoS ONE ◽  
2011 ◽  
Vol 6 (7) ◽  
pp. e22335 ◽  
Author(s):  
Tiffany M. Zarrella ◽  
Anju Singh ◽  
Constantine Bitsaktsis ◽  
Tabassum Rahman ◽  
Bikash Sahay ◽  
...  
Keyword(s):  
Adaptive Immunity ◽  
Francisella Tularensis ◽  
Host Adaptation ◽  
Innate And Adaptive Immunity ◽  
Surface Carbohydrates

scholarly journals Brucella Genomics: Macro and Micro Evolution

2020 ◽  
Vol 21 (20) ◽  
pp. 7749
Author(s):  
Marcela Suárez-Esquivel ◽  
Esteban Chaves-Olarte ◽  
Edgardo Moreno ◽  
Caterina Guzmán-Verri
Keyword(s):  
Tandem Repeats ◽  
Host Adaptation ◽  
Genomic Diversity ◽  
Brucella Species ◽  
Host Preferences ◽  
Genome Variability ◽  
Zoonotic Risk ◽  
Genome Level ◽  
Single Nucleotide Polymorphism Variation ◽  
The Relationship

Brucella organisms are responsible for one of the most widespread bacterial zoonoses, named brucellosis. The disease affects several species of animals, including humans. One of the most intriguing aspects of the brucellae is that the various species show a ~97% similarity at the genome level. Still, the distinct Brucella species display different host preferences, zoonotic risk, and virulence. After 133 years of research, there are many aspects of the Brucella biology that remain poorly understood, such as host adaptation and virulence mechanisms. A strategy to understand these characteristics focuses on the relationship between the genomic diversity and host preference of the various Brucella species. Pseudogenization, genome reduction, single nucleotide polymorphism variation, number of tandem repeats, and mobile genetic elements are unveiled markers for host adaptation and virulence. Understanding the mechanisms of genome variability in the Brucella genus is relevant to comprehend the emergence of pathogens.

scholarly journals Within-Host Adaptation of Staphylococcus aureus in a Bovine Mastitis Infection Is Associated with Increased Cytotoxicity

2021 ◽  
Vol 22 (16) ◽  
pp. 8840
Author(s):  
Katharina Mayer ◽  
Martin Kucklick ◽  
Helene Marbach ◽  
Monika Ehling-Schulz ◽  
Susanne Engelmann ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Bovine Mastitis ◽  
Adaptive Strategy ◽  
Subclinical Mastitis ◽  
Growth Conditions ◽  
Typical Feature ◽  
Host Adaptation ◽  
Bovine Mammary Epithelial Cells ◽  
Strain Pair

Within-host adaptation is a typical feature of chronic, persistent Staphylococcus aureus infections. Research projects addressing adaptive changes due to bacterial in-host evolution increase our understanding of the pathogen’s strategies to survive and persist for a long time in various hosts such as human and bovine. In this study, we investigated the adaptive processes of S. aureus during chronic, persistent bovine mastitis using a previously isolated isogenic strain pair from a dairy cow with chronic, subclinical mastitis, in which the last variant (host-adapted, Sigma factor SigB-deficient) quickly replaced the initial, dominant variant. The strain pair was cultivated under specific in vitro infection-relevant growth-limiting conditions (iron-depleted RPMI under oxygen limitation). We used a combinatory approach of surfaceomics, molecular spectroscopic fingerprinting and in vitro phenotypic assays. Cellular cytotoxicity assays using red blood cells and bovine mammary epithelial cells (MAC-T) revealed changes towards a more cytotoxic phenotype in the host-adapted isolate with an increased alpha-hemolysin (α-toxin) secretion, suggesting an improved capacity to penetrate and disseminate the udder tissue. Our results foster the hypothesis that within-host evolved SigB-deficiency favours extracellular persistence in S. aureus infections. Here, we provide new insights into one possible adaptive strategy employed by S. aureus during chronic, bovine mastitis, and we emphasise the need to analyse genotype–phenotype associations under different infection-relevant growth conditions.

Host Adaptation of Codon Usage in SARS-CoV-2 From Mammals Indicate Natural Selection

2021 ◽  
Author(s):  
Yanan Fu ◽  
Yanping Huang ◽  
Jingjing Rao ◽  
Feng Zeng ◽  
Ruiping Yang ◽  
...  
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Binding Affinity ◽  
Codon Bias ◽  
Synonymous Codon ◽  
Host Adaptation ◽  
Synonymous Codon Usage ◽  
Mutation Pressure ◽  
Usage Analysis ◽  
Human Receptor

Abstract The outbreak of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, spread across hosts from humans to animals, transmitting particularly effectively in mink. How SARS-CoV-2 selects and evolves in the host, and the differences in the evolution of different animals are still unclear. To analysis the mutation and codon usage bias of SARS-CoV-2 in infected humans and animals. The SARS-CoV-2 sequence in mink (Mink-SARS2) and binding energy with receptor were calculated compared with human. The relative synonymous codon usage of viral encoded gene was analyzed to characterize the differences and the evolutionary characteristics. A synonymous codon usage analysis showed that SARS-CoV-2 is optimized to adapt in the animals in which it is currently reported, and all of the animals showed decreased adaptability relative to that of humans, except for mink. The neutrality plot showed that the effect of natural selection on different SARS-CoV-2 sequences is stronger than mutation pressure. A binding affinity analysis indicated that the spike protein of the SARS-CoV-2 variant in mink showed a greater preference for binding with the mink receptor ACE2 than with the human receptor, especially as the mutation Y453F and N501T in Mink-SARS2 lead to improvement of binding affinity for mink receptor. In summary, mutations Y453F and N501T in Mink-SARS2 lead to improvement of binding affinity with mink receptor, indicating possible natural selection and current host adaptation. Monitoring the variation and codon bias of SARS-CoV-2 provides a theoretical basis for tracing the epidemic, evolution and cross-species spread of SARS-CoV-2.

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