Origin, genetic diversity, adaptive evolution, and transmission dynamics of Getah virus

2021 ◽  
Author(s):  
Ning Shi ◽  
Xiangyu Zhu ◽  
Xiangshu Qiu ◽  
Xinyu Cao ◽  
Zhenyan Jiang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Adaptive Evolution ◽  
Transmission Dynamics ◽  
Getah Virus

Koala retrovirus genetic diversity and transmission dynamics within captive koala populations

2021 ◽  
Vol 118 (38) ◽  
pp. e2024021118
Author(s):  
Briony A. Joyce ◽  
Michaela D. J. Blyton ◽  
Stephen D. Johnston ◽  
Paul R. Young ◽  
Keith J. Chappell
Keyword(s):  
Genetic Diversity ◽  
Antiretroviral Treatment ◽  
Sexual Transmission ◽  
Transmission Dynamics ◽  
Rapid Decline ◽  
Effective Management ◽  
Additional Challenge ◽  
Management Approaches ◽  
Southeast Queensland ◽  
Koala Retrovirus

Koala populations are currently in rapid decline across Australia, with infectious diseases being a contributing cause. The koala retrovirus (KoRV) is a gammaretrovirus present in both captive and wild koala colonies that presents an additional challenge for koala conservation in addition to habitat loss, climate change, and other factors. Currently, nine different subtypes (A to I) have been identified; however, KoRV genetic diversity analyses have been limited. KoRV is thought to be exogenously transmitted between individuals, with KoRV-A also being endogenous and transmitted through the germline. The mechanisms of exogenous KoRV transmission are yet to be extensively investigated. Here, deep sequencing was employed on 109 captive koalas of known pedigree, housed in two institutions from Southeast Queensland, to provide a detailed analysis of KoRV transmission dynamics and genetic diversity. The final dataset included 421 unique KoRV sequences, along with the finding of an additional subtype (KoRV-K). Our analysis suggests that exogenous transmission of KoRV occurs primarily between dam and joey, with evidence provided for multiple subtypes, including nonendogenized KoRV-A. No evidence of sexual transmission was observed, with mating partners found to share a similar number of sequences as unrelated koala pairs. Importantly, both distinct captive colonies showed similar trends. These findings indicate that breeding strategies or antiretroviral treatment of females could be employed as effective management approaches in combating KoRV transmission.

scholarly journals Genomic epidemiology ofMycobacterium bovisinfection in sympatric badger and cattle populations in Northern Ireland

2021 ◽  
Author(s):  
Assel Akhmetova ◽  
Jimena Guerrero ◽  
Paul McAdam ◽  
Liliana C.M. Salvador ◽  
Joseph Crispell ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Spatial Distribution ◽  
Genetic Structure ◽  
Northern Ireland ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Transmission Dynamics ◽  
Data Set ◽  
Hair Samples ◽  
Disease Persistence

AbstractBackgroundBovine tuberculosis (bTB) is a costly epidemiologically complex, multi-host, endemic disease. Lack of understanding of transmission dynamics may undermine eradication efforts. Pathogen whole genome sequencing improves epidemiological inferences, providing a means to determine the relative importance of inter- and intra- species host transmission for disease persistence. We sequenced an exceptional data set of 619Mycobacterium bovisisolates from badgers and cattle in a 100km2bTB ‘hotspot’ in Northern Ireland. Historical molecular subtyping data permitted the targeting of an endemic pathogen lineage, whose long-term persistence provided a unique opportunity to study disease transmission dynamics in unparalleled detail. Additionally, to assess whether badger population genetic structure was associated with the spatial distribution of pathogen genetic diversity, we microsatellite genotyped hair samples from 769 badgers trapped in this area.ResultsGraph transmission tree methods and structured coalescent analyses indicated the majority of bacterial diversity was found in the local cattle population. Results pointed to transmission from cattle to badger being more common than badger to cattle. Furthermore, the presence of significant badger population genetic structure in the landscape was not associated with the spatial distribution ofM. bovisgenetic diversity, suggesting that badger-to-badger transmission may not be a key determinant of disease persistence.SignificanceOur data were consistent with badgers playing a smaller role in the maintenance ofM. bovisinfection in this study site, compared to cattle. Comparison to other areas suggests thatM. bovistransmission dynamics are likely to be context dependent, and the role of wildlife difficult to generalise.

scholarly journals A59 Expansion of genetic diversity and interspecies transmission dynamics of swine influenza viruses in China

2018 ◽  
Vol 4 (suppl_1) ◽  
Author(s):  
Ziying Jin ◽  
Xiaohui Fan ◽  
Malik Peiris ◽  
Yi Guan ◽  
Huachen Zhu
Keyword(s):  
Genetic Diversity ◽  
Swine Influenza ◽  
Influenza Viruses ◽  
Transmission Dynamics ◽  
Interspecies Transmission

scholarly journals Genetic diversity and evolutionary insights of respiratory syncytial virus A ON1 genotype: global and local transmission dynamics

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Venkata R. Duvvuri ◽  
Andrea Granados ◽  
Paul Rosenfeld ◽  
Justin Bahl ◽  
Alireza Eshaghi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Respiratory Syncytial Virus ◽  
Transmission Dynamics ◽  
Syncytial Virus ◽  
Global And Local ◽  
Local Transmission

scholarly journals Genetic diversity and differentiation in natural Plasmodium falciparum populations inferred by molecular typing of the merozoite surface proteins 1 and 2

2002 ◽  
Vol 35 (5) ◽  
pp. 527-530 ◽  
Author(s):  
Fabrício J.T. Pereira ◽  
José A. Cordeiro ◽  
Erika H.E. Hoffmann ◽  
Marcelo U. Ferreira
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Natural Selection ◽  
Population Differentiation ◽  
Molecular Typing ◽  
Allele Frequencies ◽  
Surface Proteins ◽  
Transmission Dynamics ◽  
Polymorphic Genes

Genetic diversity and differentiation, inferred by typing the polymorphic genes coding for the merozoite surface proteins 1 (Msp-1) and 2 (Msp-2), were compared for 345 isolates belonging to seven Plasmodium falciparum populations from three continents. Both loci yielded similar estimates of genetic diversity for each population, but rather different patterns of between-population differentiation, suggesting that natural selection on these loci, rather than the transmission dynamics of P. falciparum, determines the variation in allele frequencies among populations.

scholarly journals Evolution of Plasmodium vivax populations in border areas of the Greater Mekong Subregion during malaria elimination

2020 ◽  
Author(s):  
Yuling Li ◽  
Yubing Hu ◽  
Yan Zhao ◽  
Qinghui Wang ◽  
Huguette Gaelle Ngassa Mbenda ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Vivax ◽  
Malaria Elimination ◽  
Scale Up ◽  
Transmission Dynamics ◽  
Clinical Samples ◽  
Effective Population ◽  
Border Areas ◽  
Greater Mekong Subregion ◽  
International Border

Abstract Background: Countries within the Greater Mekong Subregion (GMS) of Southeast Asia have committed to eliminating malaria by 2030. Although malaria situation has greatly improved, Plasmodium vivax remains at international border regions. Therefore, to gain a better understanding of transmission dynamics, knowledge on the evolution of P. vivax populations after the scale-up of control interventions will guide more effective targeted control efforts. Methods: We investigated genetic diversity and population structures in 206 longitudinally collected P. vivax clinical samples in two international border areas at the China-Myanmar border (CMB, n=50 in 2004 and n=52 in 2016) and western Thailand border (n=50 in 2012 and n=54 in 2015). Parasites were genotyped using 10 microsatellite markers. Results: Despite intensified control efforts, genetic diversity in the four populations remained high (HE = 0.66-0.86). The proportions of polyclonal infections showed substantial decreases to 23.7 and 30.7% in the CMB and western Thailand, respectively, with corresponding decreases in the multiplicity of infection. Consistent with the shrinking map of malaria transmission in the GMS over time, there were also increases in multilocus linkage disequilibrium, suggesting of more fragmented and increasingly inbred parasite populations. There were considerable genetic differentiation and subdivision with the four tested populations. Various degrees of clustering were evident between the older parasite samples collected in 2004 at the CMB with the 2016 CMB and 2012 Thailand populations, suggesting some of these parasites had shared ancestry. In contrast, the 2015 Thailand population was genetically distinctive, which may reflect a process of population replacement. The moderately large effective population sizes and proportions of polyclonal infections highlight the necessity of further coordinated and integrated control efforts on both sides of the borders in the pursuit of malaria elimination. Conclusions: With enhanced control efforts on malaria elimination, P. vivax population in the GMS has fragmented into a limited number of clustered foci, but the presence of large P. vivax reservoirs still sustains genetic diversity and transmission. These findings provide new insights into P. vivax transmission dynamics and population structure in this area.

scholarly journals Unexpected Interfarm Transmission Dynamics during a Highly Pathogenic Avian Influenza Epidemic

2016 ◽  
Vol 90 (14) ◽  
pp. 6401-6411 ◽  
Author(s):  
Alice Fusaro ◽  
Luca Tassoni ◽  
Adelaide Milani ◽  
Joseph Hughes ◽  
Annalisa Salviato ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Avian Influenza ◽  
Cleavage Site ◽  
Highly Pathogenic Avian Influenza ◽  
Index Case ◽  
Genetic Data ◽  
Transmission Dynamics ◽  
Highly Pathogenic ◽  
Pathogenic Avian Influenza ◽  
Naturally Occurring

ABSTRACTNext-generation sequencing technology is now being increasingly applied to study the within- and between-host population dynamics of viruses. However, information on avian influenza virus evolution and transmission during a naturally occurring epidemic is still limited. Here, we use deep-sequencing data obtained from clinical samples collected from five industrial holdings and a backyard farm infected during the 2013 highly pathogenic avian influenza (HPAI) H7N7 epidemic in Italy to unravel (i) the epidemic virus population diversity, (ii) the evolution of virus pathogenicity, and (iii) the pathways of viral transmission between different holdings and sheds. We show a high level of genetic diversity of the HPAI H7N7 viruses within a single farm as a consequence of separate bottlenecks and founder effects. In particular, we identified the cocirculation in the index case of two viral strains showing a different insertion at the hemagglutinin cleavage site, as well as nine nucleotide differences at the consensus level and 92 minority variants. To assess interfarm transmission, we combined epidemiological and genetic data and identified the index case as the major source of the virus, suggesting the spread of different viral haplotypes from the index farm to the other industrial holdings, probably at different time points. Our results revealed interfarm transmission dynamics that the epidemiological data alone could not unravel and demonstrated that delay in the disease detection and stamping out was the major cause of the emergence and the spread of the HPAI strain.IMPORTANCEThe within- and between-host evolutionary dynamics of a highly pathogenic avian influenza (HPAI) strain during a naturally occurring epidemic is currently poorly understood. Here, we perform for the first time an in-depth sequence analysis of all the samples collected during a HPAI epidemic and demonstrate the importance to complement outbreak investigations with genetic data to reconstruct the transmission dynamics of the viruses and to evaluate the within- and between-farm genetic diversity of the viral population. We show that the evolutionary transition from the low pathogenic form to the highly pathogenic form occurred within the first infected flock, where we identified haplotypes with hemagglutinin cleavage site of different lengths. We also identify the index case as the major source of virus, indicating that prompt application of depopulation measures is essential to limit virus spread to other farms.

scholarly journals Evolution of Plasmodium vivax populations in border areas of the Greater Mekong Subregion during malaria elimination

2019 ◽  
Author(s):  
Yuling Li ◽  
Yubing Hu ◽  
Yan Zhao ◽  
Qinghui Wang ◽  
Huguette Gaelle Ngassa Mbenda ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Vivax ◽  
Malaria Elimination ◽  
Scale Up ◽  
Transmission Dynamics ◽  
Clinical Samples ◽  
Effective Population ◽  
Border Areas ◽  
Greater Mekong Subregion ◽  
International Border

Abstract BackgroundCountries within the Greater Mekong Subregion (GMS) of Southeast Asia have committed to eliminating malaria by 2030. Although malaria situation has greatly improved, Plasmodium vivax remains at international border regions. Therefore, to gain a better understanding of transmission dynamics, knowledge on the evolution of P. vivax populations after the scale-up of control interventions will guide more effective targeted control efforts. MethodsWe investigated genetic diversity and population structures in 206 longitudinally collected P. vivax clinical samples in two international border areas at the China-Myanmar border (CMB, n=50 in 2004 and n=52 in 2016) and western Thailand border (n=50 in 2012 and n=54 in 2015). Parasites were genotyped using 10 microsatellite markers. ResultsDespite intensified control efforts, genetic diversity in the four populations remained high (HE = 0.66-0.86). The proportions of polyclonal infections showed substantial decreases to 23.7 and 30.7% in the CMB and western Thailand, respectively, with corresponding decreases in the multiplicity of infection. Consistent with the shrinking map of malaria transmission in the GMS over time, there were also increases in multilocus linkage disequilibrium, suggesting of more fragmented and increasingly inbred parasite populations. There were considerable genetic differentiation and subdivision with the four tested populations. Various degrees of clustering were evident between the older parasite samples collected in 2004 at the CMB with the 2016 CMB and 2012 Thailand populations, suggesting some of these parasites had shared ancestry. In contrast, the 2015 Thailand population was genetically distinctive, which may reflect a process of population replacement. The moderately large effective population sizes and proportions of polyclonal infections highlight the necessity of further coordinated and integrated control efforts on both sides of the borders in the pursuit of malaria elimination. ConclusionsWith enhanced control efforts on malaria elimination, P. vivax population in the GMS has fragmented into a limited number of clustered foci, but the presence of large P. vivax reservoirs still sustains genetic diversity and transmission. These findings provide new insights into P. vivax transmission dynamics and population structure in this area.

scholarly journals Genetic diversity, transmission dynamics, and drug resistance of Mycobacterium tuberculosis in Luanda, Angola

2016 ◽  
Vol 5 ◽  
pp. S38-S39
Author(s):  
João Perdigão ◽  
Sofia Clemente ◽  
Jorge Ramos ◽  
Pedro Masakidi ◽  
Diana Machado ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Drug Resistance ◽  
Mycobacterium Tuberculosis ◽  
Transmission Dynamics ◽  
Diversity Transmission

scholarly journals Phylogeny of North American Powassan virus

2001 ◽  
Vol 82 (7) ◽  
pp. 1657-1665 ◽  
Author(s):  
Gregory D. Ebel ◽  
Andrew Spielman ◽  
Sam R. Telford
Keyword(s):  
Genetic Diversity ◽  
New York ◽  
Amino Acid ◽  
North America ◽  
Adaptive Evolution ◽  
Envelope Protein ◽  
Amino Acid Sequences ◽  
Ixodid Ticks ◽  
Genetic Lineages ◽  
Powassan Virus

To determine whether Powassan virus (POW) and deer tick virus (DTV) constitute distinct flaviviral populations transmitted by ixodid ticks in North America, we analysed diverse nucleotide sequences from 16 strains of these viruses. Two distinct genetic lineages are evident, which may be defined by geographical and host associations. The nucleotide and amino acid sequences of lineage one (comprising New York and Canadian POW isolates) are highly conserved across time and space, but those of lineage two (comprising isolates from deer ticks and a fox) are more variable. The divergence between lineages is much greater than the variation within either lineage, and lineage two appears to be more diverse genetically than is lineage one. Application of McDonald–Kreitman tests to the sequences of these strains indicates that adaptive evolution of the envelope protein separates lineage one from lineage two. The two POW lineages circulating in North America possess a pattern of genetic diversity suggesting that they comprise distinct subtypes that may perpetuate in separate enzootic cycles.

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