scholarly journals Predicting mammalian hosts in which novel coronaviruses can be generated

2020 ◽  
Author(s):  
Maya Wardeh ◽  
Matthew Baylis ◽  
Marcus S.C. Blagrove
Keyword(s):  
High Risk ◽  
Homologous Recombination ◽  
Host Cell ◽  
Host Species ◽  
Genetic Material ◽  
Domesticated Animals ◽  
Host Interactions ◽  
Livestock Markets ◽  
Single Host ◽  
Novel Coronavirus

ABSTRACTNovel pathogenic coronaviruses – including SARS-CoV and SARS-CoV-2 – arise by homologous recombination in a host cell1,2. This process requires a single host to be infected with more than one type of coronavirus, which recombine to form novel strains of virus with unique combinations of genetic material. Identifying possible sources of novel coronaviruses requires identifying hosts (termed recombination hosts) of more than one coronavirus type, in which recombination might occur. However, the majority of coronavirus-host interactions remain unknown, and therefore the vast majority of recombination hosts for coronaviruses cannot be identified. Here we show that there are 11.5-fold more coronavirus-host associations, and over 30-fold more potential SARS-CoV-2 recombination hosts, than have been observed to date. We show there are over 40-fold more host species with four or more different subgenera of coronaviruses. This underestimation of both number and novel coronavirus generation in wild and domesticated animals. Our results list specific high-risk hosts in which our model predicts homologous recombination could occur, our model identifies both wild and domesticated mammals including known important and understudied species. We recommend these species for coronavirus surveillance, as well as enforced separation in livestock markets and agriculture.

scholarly journals Predicting mammalian hosts in which novel coronaviruses can be generated

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Maya Wardeh ◽  
Matthew Baylis ◽  
Marcus S. C. Blagrove
Keyword(s):  
High Risk ◽  
Homologous Recombination ◽  
Single Cell ◽  
Host Species ◽  
Domesticated Animals ◽  
Host Interactions ◽  
Potential Scale ◽  
Novel Coronavirus ◽  
Host Associations

AbstractNovel pathogenic coronaviruses – such as SARS-CoV and probably SARS-CoV-2 – arise by homologous recombination between co-infecting viruses in a single cell. Identifying possible sources of novel coronaviruses therefore requires identifying hosts of multiple coronaviruses; however, most coronavirus-host interactions remain unknown. Here, by deploying a meta-ensemble of similarity learners from three complementary perspectives (viral, mammalian and network), we predict which mammals are hosts of multiple coronaviruses. We predict that there are 11.5-fold more coronavirus-host associations, over 30-fold more potential SARS-CoV-2 recombination hosts, and over 40-fold more host species with four or more different subgenera of coronaviruses than have been observed to date at >0.5 mean probability cut-off (2.4-, 4.25- and 9-fold, respectively, at >0.9821). Our results demonstrate the large underappreciation of the potential scale of novel coronavirus generation in wild and domesticated animals. We identify high-risk species for coronavirus surveillance.

scholarly journals Ability of a bacterial chromosome segment to invert is dictated by included material rather than flanking sequence.

Genetics ◽  
1991 ◽  
Vol 129 (4) ◽  
pp. 1021-1032 ◽  
Author(s):  
M J Mahan ◽  
J R Roth
Keyword(s):  
Homologous Recombination ◽  
Parent Strain ◽  
Genetic Material ◽  
Chromosomal Inversion ◽  
Chromosome Segment ◽  
Bacterial Chromosome ◽  
Flanking Sequence ◽  
Flanking Sequences ◽  
Almost All

Abstract Homologous recombination between sequences present in inverse order within the same chromosome can result in inversion formation. We have previously shown that inverse order sequences at some sites (permissive) recombine to generate the expected inversion; no inversions are found when the same inverse order sequences flank other (nonpermissive) regions of the chromosome. In hopes of defining how permissive and nonpermissive intervals are determined, we have constructed a strain that carries a large chromosomal inversion. Using this inversion mutant as the parent strain, we have determined the "permissivity" of a series of chromosomal sites for secondary inversions. For the set of intervals tested, permissivity seems to be dictated by the nature of the genetic material present within the chromosomal interval being tested rather than the flanking sequences or orientation of this material in the chromosome. Almost all permissive intervals include the origin or terminus of replication. We suggest that the rules for recovery of inversions reflect mechanistic restrictions on the occurrence of inversions rather than lethal consequences of the completed rearrangement.

scholarly journals Role of Structural and Non-Structural Proteins and Therapeutic Targets of SARS-CoV-2 for COVID-19

Cells ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 821
Author(s):  
Rohitash Yadav ◽  
Jitendra Kumar Chaudhary ◽  
Neeraj Jain ◽  
Pankaj Kumar Chaudhary ◽  
Supriya Khanra ◽  
...  
Keyword(s):  
Host Cell ◽  
Protein S ◽  
Structural Similarity ◽  
Cell Receptor ◽  
Molecular Assembly ◽  
The Body ◽  
Spike Protein ◽  
Structural Proteins ◽  
Structural Protein ◽  
Novel Coronavirus

Coronavirus belongs to the family of Coronaviridae, comprising single-stranded, positive-sense RNA genome (+ ssRNA) of around 26 to 32 kilobases, and has been known to cause infection to a myriad of mammalian hosts, such as humans, cats, bats, civets, dogs, and camels with varied consequences in terms of death and debilitation. Strikingly, novel coronavirus (2019-nCoV), later renamed as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), and found to be the causative agent of coronavirus disease-19 (COVID-19), shows 88% of sequence identity with bat-SL-CoVZC45 and bat-SL-CoVZXC21, 79% with SARS-CoV and 50% with MERS-CoV, respectively. Despite key amino acid residual variability, there is an incredible structural similarity between the receptor binding domain (RBD) of spike protein (S) of SARS-CoV-2 and SARS-CoV. During infection, spike protein of SARS-CoV-2 compared to SARS-CoV displays 10–20 times greater affinity for its cognate host cell receptor, angiotensin-converting enzyme 2 (ACE2), leading proteolytic cleavage of S protein by transmembrane protease serine 2 (TMPRSS2). Following cellular entry, the ORF-1a and ORF-1ab, located downstream to 5′ end of + ssRNA genome, undergo translation, thereby forming two large polyproteins, pp1a and pp1ab. These polyproteins, following protease-induced cleavage and molecular assembly, form functional viral RNA polymerase, also referred to as replicase. Thereafter, uninterrupted orchestrated replication-transcription molecular events lead to the synthesis of multiple nested sets of subgenomic mRNAs (sgRNAs), which are finally translated to several structural and accessory proteins participating in structure formation and various molecular functions of virus, respectively. These multiple structural proteins assemble and encapsulate genomic RNA (gRNA), resulting in numerous viral progenies, which eventually exit the host cell, and spread infection to rest of the body. In this review, we primarily focus on genomic organization, structural and non-structural protein components, and potential prospective molecular targets for development of therapeutic drugs, convalescent plasm therapy, and a myriad of potential vaccines to tackle SARS-CoV-2 infection.

scholarly journals Do parasites adopt different strategies in different intermediate hosts? Host size, not host species, influences Coitocaecum parvum (Trematoda) life history strategy, size and egg production

Parasitology ◽  
2012 ◽  
Vol 140 (2) ◽  
pp. 275-283 ◽  
Author(s):  
R. RUIZ DANIELS ◽  
S. BELTRAN ◽  
R. POULIN ◽  
C. LAGRUE
Keyword(s):  
Host Species ◽  
Egg Production ◽  
Life History Strategy ◽  
Host Size ◽  
Life Strategy ◽  
Amphipod Species ◽  
Intermediate Hosts ◽  
Host Interactions ◽  
Resource Limitations ◽  
Coitocaecum Parvum

SUMMARYHost exploitation induces host defence responses and competition between parasites, resulting in individual parasites facing highly variable environments. Alternative life strategies may thus be expressed in context-dependent ways, depending on which host species is used and intra-host competition between parasites. Coitocaecum parvum (Trematode) can use facultative progenesis in amphipod intermediate hosts, Paracalliope fluviatilis, to abbreviate its life cycle in response to such environmental factors. Coitocaecum parvum also uses another amphipod host, Paracorophium excavatum, a species widely different in size and ecology from P. fluviatilis. In this study, parasite infection levels and strategies in the two amphipod species were compared to determine whether the adoption of progenesis by C. parvum varied between these two hosts. Potential differences in size and/or egg production between C. parvum individuals according to amphipod host species were also investigated. Results show that C. parvum life strategy was not influenced by host species. In contrast, host size significantly affected C. parvum strategy, size and egg production. Since intra-host interactions between co-infecting parasites also influenced C. parvum strategy, size and fecundity, it is highly likely that within-host resource limitations affect C. parvum life strategy and overall fitness regardless of host species.

scholarly journals Emergence of SARS-CoV-2 through recombination and strong purifying selection

2020 ◽  
Vol 6 (27) ◽  
pp. eabb9153 ◽  
Author(s):  
Xiaojun Li ◽  
Elena E. Giorgi ◽  
Manukumar Honnayakanahalli Marichannegowda ◽  
Brian Foley ◽  
Chuan Xiao ◽  
...  
Keyword(s):  
Host Species ◽  
Purifying Selection ◽  
New Drugs ◽  
Evolutionary Constraints ◽  
Binding Motif ◽  
The Novel ◽  
Global Pandemic ◽  
Show Evidence ◽  
Human Coronaviruses ◽  
Novel Coronavirus

COVID-19 has become a global pandemic caused by the novel coronavirus SARS-CoV-2. Understanding the origins of SARS-CoV-2 is critical for deterring future zoonosis, discovering new drugs, and developing a vaccine. We show evidence of strong purifying selection around the receptor binding motif (RBM) in the spike and other genes among bat, pangolin, and human coronaviruses, suggesting similar evolutionary constraints in different host species. We also demonstrate that SARS-CoV-2’s entire RBM was introduced through recombination with coronaviruses from pangolins, possibly a critical step in the evolution of SARS-CoV-2’s ability to infect humans. Similar purifying selection in different host species, together with frequent recombination among coronaviruses, suggests a common evolutionary mechanism that could lead to new emerging human coronaviruses.

scholarly journals Quantifying relative virulence: when μ max fails and AUC alone just is not enough

2020 ◽  
Author(s):  
Ruben Michael Ceballos ◽  
Carson Len Stacy
Keyword(s):  
Specific Growth ◽  
Area Under The Curve ◽  
Maximum Specific Growth Rate ◽  
Curve Analysis ◽  
Growth Curve Analysis ◽  
Virus Infections ◽  
Susceptible Host ◽  
Host Interactions ◽  
Biological Phenomena ◽  
Single Host

A challenge in virology is quantifying relative virulence (V R) between two (or more) viruses that exhibit different replication dynamics in a given susceptible host. Host growth curve analysis is often used to mathematically characterize virus–host interactions and to quantify the magnitude of detriment to host due to viral infection. Quantifying V R using canonical parameters, like maximum specific growth rate (μ max), can fail to provide reliable information regarding virulence. Although area-under-the-curve (AUC) calculations are more robust, they are sensitive to limit selection. Using empirical data from Sulfolobus Spindle-shaped Virus (SSV) infections, we introduce a novel, simple metric that has proven to be more robust than existing methods for assessing V R. This metric (I SC) accurately aligns biological phenomena with quantified metrics to determine V R. It also addresses a gap in virology by permitting comparisons between different non-lytic virus infections or non-lytic versus lytic virus infections on a given host in single-virus/single-host infections.

scholarly journals Hantavirus host/virus interactions within Southeast Europe

2004 ◽  
Vol 4 (4) ◽  
pp. 13-18 ◽  
Author(s):  
Jerrold J. Scharninghausen ◽  
Michael Faulde ◽  
Semra Cavaljuga
Keyword(s):  
Phylogenetic Analysis ◽  
Cytochrome B ◽  
Geographic Area ◽  
Southeast Europe ◽  
Host Interactions ◽  
Single Host ◽  
Actual Environment ◽  
Genetic Sequences ◽  
Host Virus Interactions ◽  
The Impact

Viral studies have historically approached their phylogenetic analysis without consideration of the impact of the role the host plays in evolution. Our study examines host/viral interactions through analysis of the phylogenetic relationship between hantavirus genetic sequences and host cytochrome B sequences. Phylogenetic analysis of known Hantavirus genetic sequences were performed using PAUP 3.1.1 (vers. 4.0.0d64). Only sequences available through GENBANK were analyzed. Phylogenetic analysis of hantavirus sequences revealed distinct patterns based upon geographic area. These patterns coincided with the known ranges of reservoir hosts. Multiple hosts for individual viruses and multiple viruses in a single host species for hantaviruses have been described. This may be due to accidental exposure, host-switching, co-speciation, or broad co-accommodation. Since the host is the actual environment that the virus survives in, changes in the host over time could potentially directly influence changes in the virus. Multiple viruses and hosts collide in Southeastern Europe increasing the prospect of finding distinct viral/host relationships. Rodent Cytochrome B is very well conserved and can be used to tract host lineage. By tracking the relationship of infected hosts, we theorize that patterns in host DNA will emerge that will mirror patterns in viral sequences. This analysis of the host DNA could provide an understanding into the causes of variation in hantaviral sequences, pathogenicity, transmissibility, infectivity, viral range and expand our knowledge of viral/host interactions. Surveillance for viruses in the field should include analysis of the host DNA in combination with the viral analysis.

scholarly journals The Spread of COVID-19 in Nigeria: The Influence of Transportation and Economic Zones

2021 ◽  
pp. 27-35
Author(s):  
Nathaniel O. Ajayi ◽  
Richard O. Awonusika ◽  
Adeniyi S. Ale ◽  
Ayooluwade Ebiwonjumi
Keyword(s):  
High Risk ◽  
Large Scale ◽  
National Policy ◽  
Human Movement ◽  
Health Crisis ◽  
Spatial Spread ◽  
The Status ◽  
The Government ◽  
Novel Coronavirus ◽  
Economic Zones

The novel coronavirus (2019-nCoV) now known as Covid-19 was first detected in the city of Wuhan, China in December 2019. The disease rapidly spread to other cities in China and to other parts of the world. The aim of this study is to investigate the contribution which the economic zones and movement of people into the country and from city to city and State to State within the country have on the spread of the disease in Nigeria. Data of the daily update of Covid-19 occurrence in Nigeria as given by the NCDC Covid-19 Situation report were assembled. The data of the first index in each State between February 27 and March 28, 2020 with the status of whether they were from foreign travel or from within the community was compiled. The results show that economic zones and human movement contribute to the early spread of the disease. The initial spatial spread in Nigeria was observed to follow closely behind the test laboratory distribution pattern. This may suggest that samples from the locations far from the laboratories were not obtained, hence the suggestion for early aggressive country-wide-large scale testing to cover almost everyone should be started very early before the spread is everywhere. The test labs should cover the whole country with the tests made free and mandatory to encourage and force people to come out for it and the restriction protocols should strictly be adhered to. The boarders of the country should be closed early to stop further import of the disease from the high risk countries. When the airports are later re-opened, they should not be to the high-risk countries of the disease. There is also a need for a national policy on responding to and managing any future public health crisis such as Covid-19 pandemic before its occurrence. This policy will help the government to know what to start doing quickly when there is any occurrence. Government should also look inward to mobilize the scientists inside the country by providing research grants purposely to combat the pandemic. Such grants will enable our scientists to make their contribution in addition to the ones made by the scientists outside the country.

Genetic variation in the mitochondrial cytochrome c oxidase subunit 1 within Progamotaenia festiva (Cestoda: Anoplocephalidae) from macropodid marsupials

Parasitology ◽  
2007 ◽  
Vol 134 (10) ◽  
pp. 1465-1476 ◽  
Author(s):  
I. BEVERIDGE ◽  
S. SHAMSI ◽  
M. HU ◽  
N. B. CHILTON ◽  
R. B. GASSER
Keyword(s):  
Genetic Variation ◽  
Host Species ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Enzyme Electrophoresis ◽  
Single Strand Conformational Polymorphism ◽  
Oxidase Subunit ◽  
Single Host ◽  
Distinct Sequence ◽  
Sequence Types

SUMMARYGenetic variation was examined in the anoplocephalid cestode Progamotaenia festiva, from Australian marsupials, in order to test the hypothesis that P. festiva, is a complex of sibling species and to assess the extent of host switching reported previously based on multilocus enzyme electrophoresis (MEE). Polymerase chain reaction (PCR)-based single-strand conformational polymorphism (SSCP) was used for the analysis of sequence variation in the cytochrome c oxidase subunit 1 (cox1) gene among 179 specimens of P. festiva (identified based on morphology and predilection site in the host) from 13 different host species, followed by selective DNA sequencing. Fifty-three distinct sequence types (haplotypes) representing all specimens were defined. Phylogenetic analyses of these sequence data (utilizing maximum parsimony and neighbour-joining methods) revealed 12 distinct clades. Other heterologous species, P. ewersi and P. macropodis, were used as outgroups and the remaining bile-duct inhabiting species, P. diaphana and P. effigia, were included in the analysis for comparative purposes. The latter 2 species were nested within the clades representing P. festiva. Most clades of P. festiva identified were restricted to a single host species; one clade primarily in Macropus robustus was also found in the related host species M. antilopinus in an area of host sympatry; another clade occurring primarily in M. robustus occurred also in additional kangaroo species, M. rufus and M. dorsalis. High levels of genetic divergence, the existence of distinct clades and their occurrence in sympatry provide support for the hypothesis that P. festiva represents a complex of numerous species, most of which, but not all, are host specific. Three distinct clades of cestodes were found within a single host, M. robustus, but there was no evidence of within-host speciation.

The effects of seasonality on host–bat fly ecological networks in a temperate mountain cave

Parasitology ◽  
2016 ◽  
Vol 144 (5) ◽  
pp. 692-697 ◽  
Author(s):  
KARINA D. RIVERA-GARCÍA ◽  
CÉSAR A. SANDOVAL-RUIZ ◽  
ROMEO A. SALDAÑA-VÁZQUEZ ◽  
JORGE E. SCHONDUBE
Keyword(s):  
Species Composition ◽  
Host Species ◽  
Rainy Season ◽  
Ecological Networks ◽  
Host Interactions ◽  
Bat Flies ◽  
Bat Fly ◽  
Low Prevalence ◽  
Host Parasite

SUMMARYChanges in the specialization of parasite–host interactions will be influenced by variations in host species composition. We evaluated this hypothesis by comparing the composition of bats and bat flies within a roost cave over one annual. Five bat and five bat fly species occupied the cave over the course of the study. Bat species composition was 40% different in the rainy season compared with the dry–cold and dry–warm seasons. Despite the incorporation of three new bat species into the cave during the rainy season, bat fly species composition was not affected by seasonality, since the bats that arrived in the rainy season only contributed one new bat fly species at a low prevalence. Bat–bat fly ecological networks were less specialized in the rainy season compared with the dry–cold and dry–warm seasons because of the increase of host overlap among bat fly species during this season. This study suggests that seasonality promote: (1) differences in host species composition, and (2) a reduction in the specialization of host–parasite ecological networks.

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