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Cardoso BTM, de Deus DR, Sousa EC, Pinheiro KDC, da Costa JN, Maués MAC, Mesquita MJDF, Teixeira DM, Siqueira JAM, Resque HR, Gabbay YB, da Silva LD. Molecular analysis of canine circovirus in dogs from animal shelters in Belém, Pará, northern Brazil: first detection at the amazon region. BRAZILIAN JOURNAL OF VETERINARY MEDICINE 2023; 45:e000723. [PMID: 37859867 PMCID: PMC10583600 DOI: 10.29374/2527-2179.bjvm000723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 08/03/2023] [Indexed: 10/21/2023] Open
Abstract
The canine circovirus (CanCV) is a single-stranded DNA virus that has become an important emerging virus associated with gastroenteritis in dogs worldwide. In the present study, the CanCV was detected by PCR in 15% (22/147) of dogs from animal shelters in Belém, between 2019 and 2020. We observed an association between the CanCV infection and the presence of diarrhea in animals younger than one year of age (p > 0.01). The Brazilian strains were grouped in Chinese genotypes, with 99.54 to 100% nucleotilde homology. The GMRF Bayesian Skyride used the molecular clock model, which was the best suited technique to plot the dataset. The most recent common ancestor (TMRCA) was estimated in 2017, with the evolution rate of 1.6 x 10-3 s/s/y. The viral family diversity was also investigated, with emphasis on the families of the enteric pathogenic viruses Parvoviridae, Picornaviridae and Astroviridae, which were detected in the CanCV positive pooled samples. This study highlights the importance of the CanCV as an emergent virus that causes diarrhea in Brazilian dogs. The results found herein contribute to the understanding of the role of CanCV in enteric diseases and in the evolutionary molecular characterization of the circulating genotypes. Furthermore, we increased the understanding of the fecal virome in dogs with diarrhea, providing data for the monitoring and prevention viral gastroenteric diseases in domestic animals.
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Affiliation(s)
- Bruna Trindade Moreira Cardoso
- Biomedical Scientist, Programa de Pós-graduação em Biologia Parasitária da Amazônia (PPGBPA), Centro de Ciências Biológicas e da Saúde (CCBS), Universidade do Estado do Pará, Belém, PA, Brazil.
| | - Danielle Rodrigues de Deus
- Biologist, MSc., Programa de Pós-graduação em Virologia, Instituto Evandro Chagas, Ananindeua, PA, Brazil.
| | - Edivaldo Costa Sousa
- Biomedical Scientist, DSc., Seção de Parasitologia, Instituto Evandro Chagas, Ananindeua, PA, Brazil.
| | - Kenny da Costa Pinheiro
- Biomedical Scientist, DSc., Seção de Virologia, Instituto Evandro Chagas, Ananindeua, PA, Brazil.
| | - Jonaia Novaes da Costa
- Biomedical Scientist, Programa de Pós-graduação em Biologia Parasitária da Amazônia (PPGBPA), Centro de Ciências Biológicas e da Saúde (CCBS), Universidade do Estado do Pará, Belém, PA, Brazil.
| | | | | | - Dielle Monteiro Teixeira
- Biomedical Scientist, DSc., Seção de Virologia, Instituto Evandro Chagas, Ananindeua, PA, Brazil.
| | | | - Hugo Reis Resque
- Biomedical Scientist, DSc., Seção de Virologia, Instituto Evandro Chagas, Ananindeua, PA, Brazil.
| | - Yvone Benchimol Gabbay
- Biomedical Scientist, DSc., Seção de Virologia, Instituto Evandro Chagas, Ananindeua, PA, Brazil.
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Wang Y, Zhao Z, Miao X, Wang Y, Qian X, Chen L, Wang C, Li S. eSMC: a statistical model to infer admixture events from individual genomics data. BMC Genomics 2022; 23:827. [PMCID: PMC9748406 DOI: 10.1186/s12864-022-09033-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
Abstract
Background
Inferring historical population admixture events yield essential insights in understanding a species demographic history. Methods are available to infer admixture events in demographic history with extant genetic data from multiple sources. Due to the deficiency in ancient population genetic data, there lacks a method for admixture inference from a single source. Pairwise Sequentially Markovian Coalescent (PSMC) estimates the historical effective population size from lineage genomes of a single individual, based on the distribution of the most recent common ancestor between the diploid’s alleles. However, PSMC does not infer the admixture event.
Results
Here, we proposed eSMC, an extended PSMC model for admixture inference from a single source. We evaluated our model’s performance on both in silico data and real data. We simulated population admixture events at an admixture time range from 5 kya to 100 kya (5 years/generation) with population admix ratio at 1:1, 2:1, 3:1, and 4:1, respectively. The root means the square error is $$\pm 7.61$$
±
7.61
kya for all experiments. Then we implemented our method to infer the historical admixture events in human, donkey and goat populations. The estimated admixture time for both Han and Tibetan individuals range from 60 kya to 80 kya (25 years/generation), while the estimated admixture time for the domesticated donkeys and the goats ranged from 40 kya to 60 kya (8 years/generation) and 40 kya to 100 kya (6 years/generation), respectively. The estimated admixture times were concordance to the time that domestication occurred in human history.
Conclusion
Our eSMC effectively infers the time of the most recent admixture event in history from a single individual’s genomics data. The source code of eSMC is hosted at https://github.com/zachary-zzc/eSMC.
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Diversity, Transmission, and Cophylogeny of Ledanteviruses ( Rhabdoviridae: Ledantevirus) and Nycteribiid Bat Flies Parasitizing Angolan Soft-Furred Fruit Bats in Bundibugyo District, Uganda. Microorganisms 2020; 8:microorganisms8050750. [PMID: 32429498 PMCID: PMC7285350 DOI: 10.3390/microorganisms8050750] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 01/01/2023] Open
Abstract
Obligate hematophagous ectoparasitic flies of the superfamily Hippoboscoidea are distributed worldwide, but their role as vectors and reservoirs of viruses remains understudied. We examined hippoboscoid bat flies (family Nycteribiidae) parasitizing Angolan soft-furred fruit bats (Lissonycteris angolensis ruwenzorii) from Bundibugyo District, Uganda. Using metagenomic methods, we detected 21 variants of the rhabdovirid genus Ledantevirus, which contains medically important "bat-associated" viruses. These 21 viruses, representing at least two divergent viral lineages, infected 26 bat flies from 8 bats in a single roost. Cophylogenetic analyses of viruses and bat flies resulted in strong evidence of virus-host codivergence, indicating vertical transmission of bat fly ledanteviruses. Examination of oral swabs from bats revealed ledantevirus RNA in the saliva of 1 out of 11 bats, with no evidence of insect genetic material in the mouth of this bat. These data demonstrate that bat flies can harbor diverse ledanteviruses even in a single roost and that the predominant mode of transmission is likely vertical (among bat flies), but that bats can become infected and shed viruses orally. In conclusion, bat flies may serve as ectoparasitic reservoirs of "bat-associated" viruses that only transiently or sporadically infect bats.
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Mather N, Traves SM, Ho SYW. A practical introduction to sequentially Markovian coalescent methods for estimating demographic history from genomic data. Ecol Evol 2020; 10:579-589. [PMID: 31988743 PMCID: PMC6972798 DOI: 10.1002/ece3.5888] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 10/11/2019] [Accepted: 11/12/2019] [Indexed: 12/31/2022] Open
Abstract
A common goal of population genomics and molecular ecology is to reconstruct the demographic history of a species of interest. A pair of powerful tools based on the sequentially Markovian coalescent have been developed to infer past population sizes using genome sequences. These methods are most useful when sequences are available for only a limited number of genomes and when the aim is to study ancient demographic events. The results of these analyses can be difficult to interpret accurately, because doing so requires some understanding of their theoretical basis and of their sensitivity to confounding factors. In this practical review, we explain some of the key concepts underpinning the pairwise and multiple sequentially Markovian coalescent methods (PSMC and MSMC, respectively). We relate these concepts to the use and interpretation of these methods, and we explain how the choice of different parameter values by the user can affect the accuracy and precision of the inferences. Based on our survey of 100 PSMC studies and 30 MSMC studies, we describe how the two methods are used in practice. Readers of this article will become familiar with the principles, practice, and interpretation of the sequentially Markovian coalescent for inferring demographic history.
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Affiliation(s)
- Niklas Mather
- School of Life and Environmental SciencesUniversity of SydneySydneyNSWAustralia
| | - Samuel M. Traves
- School of Life and Environmental SciencesUniversity of SydneySydneyNSWAustralia
| | - Simon Y. W. Ho
- School of Life and Environmental SciencesUniversity of SydneySydneyNSWAustralia
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Tunstall T, Kock R, Vahala J, Diekhans M, Fiddes I, Armstrong J, Paten B, Ryder OA, Steiner CC. Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells. Genome Res 2018; 28:780-788. [PMID: 29798851 PMCID: PMC5991516 DOI: 10.1101/gr.227603.117] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 04/26/2018] [Indexed: 01/04/2023]
Abstract
The critically endangered northern white rhinoceros is believed to be extinct in the wild, with the recent death of the last male leaving only two remaining individuals in captivity. Its extinction would appear inevitable, but the development of advanced cell and reproductive technologies such as cloning by nuclear transfer and the artificial production of gametes via stem cells differentiation offer a second chance for its survival. In this work, we analyzed genome-wide levels of genetic diversity, inbreeding, population history, and demography of the white rhinoceros sequenced from cryopreserved somatic cells, with the goal of informing how genetically valuable individuals could be used in future efforts toward the genetic rescue of the northern white rhinoceros. We present the first sequenced genomes of the northern white rhinoceros, which show relatively high levels of heterozygosity and an average genetic divergence of 0.1% compared with the southern subspecies. The two white rhinoceros subspecies appear to be closely related, with low genetic admixture and a divergent time <80,000 yr ago. Inbreeding, as measured by runs of homozygosity, appears slightly higher in the southern than the northern white rhinoceros. This work demonstrates the value of the northern white rhinoceros cryopreserved genetic material as a potential gene pool for saving this subspecies from extinction.
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Affiliation(s)
- Tate Tunstall
- San Diego Zoo Institute for Conservation Research, Escondido, California 92027, USA
| | - Richard Kock
- Royal Veterinary College, University of London, London NW1 0TU, United Kingdom
| | - Jiri Vahala
- Dvur Krlov Zoo, Dvr Krlov nad Labem 544 01, Czech Republic
| | - Mark Diekhans
- Jack Baskin School of Engineering, University California Santa Cruz, Santa Cruz, California 95064, USA
| | - Ian Fiddes
- Jack Baskin School of Engineering, University California Santa Cruz, Santa Cruz, California 95064, USA
| | - Joel Armstrong
- Jack Baskin School of Engineering, University California Santa Cruz, Santa Cruz, California 95064, USA
| | - Benedict Paten
- Jack Baskin School of Engineering, University California Santa Cruz, Santa Cruz, California 95064, USA
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, California 92027, USA
| | - Cynthia C Steiner
- San Diego Zoo Institute for Conservation Research, Escondido, California 92027, USA
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