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Article ; Online: In vitro susceptibility of eighteen clinical isolates of human monkeypox virus to tecovirimat.

Nunes, Desiree Dos Santos / Higa, Luiza M / Oliveira, Régis Linhares / da Costa, Lendel Correia / Bomfim, Larissa Maciel / Gonçalves, Cássia Cristina Alves / Mariani, Diana / Hruby, Dennis E / Voloch, Carolina Moreira / Castiñeiras, Terezinha Marta Pereira Pinto / Tanuri, Amilcar / Damaso, Clarissa R

Memorias do Instituto Oswaldo Cruz

2023 Volume 118, Page(s) e230056

Abstract: Background: In 2022, an outbreak of mpox that started in European countries spread worldwide through human-to-human transmission. Cases have been mostly mild, but severe clinical presentations have been reported. In these cases, tecovirimat has been the ...

Abstract	Background: In 2022, an outbreak of mpox that started in European countries spread worldwide through human-to-human transmission. Cases have been mostly mild, but severe clinical presentations have been reported. In these cases, tecovirimat has been the drug of choice to treat patients with aggravated disease. Objectives: Here we investigated the tecovirimat susceptibility of 18 clinical isolates of monkeypox virus (MPXV) obtained from different regions of Brazil. Methods: Different concentrations of tecovirimat were added to cell monolayers infected with each MPXV isolate. After 72 hours, cells were fixed and stained for plaque visualization, counting, and measurement. The ortholog of F13L gene from each MPXV isolate was polymerase chain reaction (PCR)-amplified, sequenced, and the predicted protein sequences were analyzed. Findings: The eighteen MPXV isolates generated plaques of different sizes. Although all isolates were highly sensitive to the drug, two showed different response curves and IC50 values. However, the target protein of tecovirimat, F13 (VP37), was 100% conserved in all MPXV isolates and therefore does not explain the difference in sensitivity. Main conclusions: Our results support screening different MPXV isolates for tecovirimat susceptibility as an important tool to better use of the restricted number of tecovirimat doses available in low-income countries to treat patients with mpox.
MeSH term(s)	Humans ; Mpox (monkeypox) ; Monkeypox virus/genetics ; Amino Acid Sequence ; Benzamides
Chemical Substances	Benzamides
Language	English
Publishing date	2023-07-10
Publishing country	Brazil
Document type	Journal Article
ZDB-ID	953293-6
ISSN	1678-8060 ; 0074-0276
ISSN (online)	1678-8060
ISSN	0074-0276
DOI	10.1590/0074-02760230056
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Article ; Online: Impact of the partitioning scheme on divergence times inferred from Mammalian genomic data sets.

Voloch, Carolina M / Schrago, Carlos G

Evolutionary bioinformatics online

2012 Volume 8, Page(s) 207–218

Abstract: Data partitioning has long been regarded as an important parameter for phylogenetic inference. The division of heterogeneous multigene data sets into partitions with similar substitution patterns is known to increase the performance of probabilistic ... ...

Abstract	Data partitioning has long been regarded as an important parameter for phylogenetic inference. The division of heterogeneous multigene data sets into partitions with similar substitution patterns is known to increase the performance of probabilistic phylogenetic methods. However, the effect of the partitioning scheme on divergence time estimates has generally been ignored. To investigate the impact of data partitioning on the estimation of divergence times, we have constructed two genomic data sets. The first one with 15 nuclear genes comprising 50,928 bp were selected from the OrthoMam database; the second set was composed of complete mitochondrial genomes. We studied two partitioning schemes: concatenated supermatrices and partitioned gene analysis. We have also measured the impact of taxonomic sampling on the estimates. After drawing divergence time inferences using the uncorrelated relaxed clock in BEAST, we have compared the age estimates between the partitioning schemes. Our results show that, in general, both schemes resulted in similar chronological estimates, however the concatenated data sets were more efficient than the partitioned ones in attaining suitable effective sample sizes.
Language	English
Publishing date	2012-05-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	2227610-5
ISSN	1176-9343 ; 1176-9343
ISSN (online)	1176-9343
ISSN	1176-9343
DOI	10.4137/EBO.S9627
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Article ; Online: Mpox outbreak in Rio de Janeiro, Brazil: A translational approach.

Lira, Guilherme S / Ota, Victor A / Melo, Mariana Q S / Castiñeiras, Anna C P / Leitão, Isabela C / Silva, Bianca O / Mariani, Diana / Gonçalves, Cássia C A / Ribeiro, Liane J / Halpern, Marcia / Abreu, Thalita F / Carneiro, Fabiana A / Scheid, Helena T / Souza, Leonardo A V / Rodrigues, Débora G M / Cruz, Nádia V G / Cony, Andrea / Carvalho, Silvia / de Lima, Loyze P O /

Viala, Vincent L / Caldas, Lucio A / de Souza, Wanderley / Higa, Luiza M / Voloch, Carolina M / Ferreira, Orlando C / Damaso, Clarissa R / Galliez, Rafael M / Faffe, Débora S / Tanuri, Amilcar / Castiñeiras, Terezinha M P P

Journal of medical virology

2024 Volume 96, Issue 5, Page(s) e29621

Abstract: Mpox is a zoonotic disease historically reported in Africa. Since 2003, limited outbreaks have occurred outside Africa. In 2022, the global spread of cases with sustained interhuman transmission and unusual disease features raised public health concerns. ...

Abstract	Mpox is a zoonotic disease historically reported in Africa. Since 2003, limited outbreaks have occurred outside Africa. In 2022, the global spread of cases with sustained interhuman transmission and unusual disease features raised public health concerns. We explore the mpox outbreak in Rio de Janeiro (RJ) state, Brazil, in an observational study of mpox-suspected cases from June to December 2022. Data collection relied on a public healthcare notification form. Diagnosis was determined by MPXV-PCR. In 46 confirmed cases, anti-OPXV IgG was determined by ELISA, and seven MPXV genomes were sequenced. A total of 3095 cases were included, 816 (26.3%) with positive MPXV-PCR results. Most positive cases were men in their 30 s and MSM. A total of 285 (34.9%) MPXV-PCR+ patients live with HIV. Eight were coinfected with varicella-zoster virus. Anogenital lesions and adenomegaly were associated with the diagnosis of mpox. Females and individuals under 18 represented 9.4% and 5.4% of all confirmed cases, respectively, showing higher PCR cycle threshold (Ct) values and fewer anogenital lesions compared to adult men. Anti-OPXV IgG was detected in 29/46 (63.0%) patients. All analyzed sequences belonged to clade IIb. In RJ state, mpox presented a diverse clinical picture, represented mainly by mild cases with low complication rates and prominent genital involvement. The incidence in females and children was higher than usually reported. The observation of a bimodal distribution of Ct values, with few positive results, may suggest the need to review the diagnostic criteria in these groups.
MeSH term(s)	Humans ; Brazil/epidemiology ; Male ; Female ; Disease Outbreaks ; Adult ; Young Adult ; Adolescent ; Middle Aged ; Animals ; Zoonoses/epidemiology ; Zoonoses/virology ; Herpesvirus 3, Human/genetics ; Herpesvirus 3, Human/isolation & purification ; Child ; HIV Infections/epidemiology ; HIV Infections/virology ; Antibodies, Viral/blood ; Aged ; Immunoglobulin G/blood
Chemical Substances	Antibodies, Viral ; Immunoglobulin G
Language	English
Publishing date	2024-04-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Observational Study
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.29621
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Article ; Online: Comparative evolutionary epidemiology of dengue virus serotypes.

Costa, Raquel L / Voloch, Carolina M / Schrago, Carlos G

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

2012 Volume 12, Issue 2, Page(s) 309–314

Abstract: Evolutionary studies on dengue virus have frequently focused on intra-serotype diversity or on specific epidemics. In this study, we compiled a comprehensive data set of the envelope gene of dengue virus serotypes and conducted an extensive comparative ... ...

Abstract	Evolutionary studies on dengue virus have frequently focused on intra-serotype diversity or on specific epidemics. In this study, we compiled a comprehensive data set of the envelope gene of dengue virus serotypes and conducted an extensive comparative study of evolutionary molecular epidemiology. We found that substitution rates are homogeneous among dengue serotypes, although their population dynamics have differed over the past few years as inferred by Bayesian coalescent methods. On a global scale, DENV-2 is the serotype with the highest effective population size. The genealogies also showed geographical structure within the serotypes. Finally, we also explored the causes of dengue virus serotype diversification by investigating the plausibility that it was driven by adaptive changes. Our results suggest that the envelope gene is under significant purifying selection and the hypothesis that dengue virus serotype diversification was the result of stochastic events cannot be ruled out.
MeSH term(s)	Dengue/epidemiology ; Dengue Virus/classification ; Dengue Virus/genetics ; Evolution, Molecular ; Genetic Variation ; Genetics, Population ; Humans ; Phylogeny ; Phylogeography ; Selection, Genetic ; Serotyping ; Viral Envelope Proteins/genetics
Chemical Substances	Viral Envelope Proteins
Language	English
Publishing date	2012-03
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2037068-4
ISSN	1567-7257 ; 1567-1348
ISSN (online)	1567-7257
ISSN	1567-1348
DOI	10.1016/j.meegid.2011.12.011
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Article ; Online: Analysis of adaptive evolution in Lyssavirus genomes reveals pervasive diversifying selection during species diversification.

Voloch, Carolina M / Capellão, Renata T / Mello, Beatriz / Schrago, Carlos G

Viruses

2014 Volume 6, Issue 11, Page(s) 4465–4478

Abstract: Lyssavirus is a diverse genus of viruses that infect a variety of mammalian hosts, typically causing encephalitis. The evolution of this lineage, particularly the rabies virus, has been a focus of research because of the extensive occurrence of cross- ... ...

Abstract	Lyssavirus is a diverse genus of viruses that infect a variety of mammalian hosts, typically causing encephalitis. The evolution of this lineage, particularly the rabies virus, has been a focus of research because of the extensive occurrence of cross-species transmission, and the distinctive geographical patterns present throughout the diversification of these viruses. Although numerous studies have examined pattern-related questions concerning Lyssavirus evolution, analyses of the evolutionary processes acting on Lyssavirus diversification are scarce. To clarify the relevance of positive natural selection in Lyssavirus diversification, we conducted a comprehensive scan for episodic diversifying selection across all lineages and codon sites of the five coding regions in lyssavirus genomes. Although the genomes of these viruses are generally conserved, the glycoprotein (G), RNA-dependent RNA polymerase (L) and polymerase (P) genes were frequently targets of adaptive evolution during the diversification of the genus. Adaptive evolution is particularly manifest in the glycoprotein gene, which was inferred to have experienced the highest density of positively selected codon sites along branches. Substitutions in the L gene were found to be associated with the early diversification of phylogroups. A comparison between the number of positively selected sites inferred along the branches of RABV population branches and Lyssavirus intespecies branches suggested that the occurrence of positive selection was similar on the five coding regions of the genome in both groups.
MeSH term(s)	Adaptation, Biological ; Cluster Analysis ; Computational Biology ; Evolution, Molecular ; Genetic Variation ; Lyssavirus/genetics ; Phylogeny ; Selection, Genetic ; Sequence Analysis, DNA ; Viral Proteins/genetics
Chemical Substances	Viral Proteins
Language	English
Publishing date	2014-11-19
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v6114465
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Article ; Online: Impact of the Partitioning Scheme on Divergence Times Inferred from Mammalian Genomic Data Sets

Carolina M. Voloch / Carlos G. Schrago

Evolutionary Bioinformatics, Vol 2012, Iss 8, Pp 207-

2012 Volume 218

Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2012-05-01T00:00:00Z
Publisher	SAGE Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil.

Voloch, Carolina M / da Silva Francisco, Ronaldo / de Almeida, Luiz G P / Cardoso, Cynthia C / Brustolini, Otavio J / Gerber, Alexandra L / Guimarães, Ana Paula de C / Mariani, Diana / da Costa, Raissa Mirella / Ferreira, Orlando C / Frauches, Thiago Silva / de Mello, Claudia Maria Braga / Leitão, Isabela de Carvalho / Galliez, Rafael Mello / Faffe, Débora Souza / Castiñeiras, Terezinha M P P / Tanuri, Amilcar / de Vasconcelos, Ana Tereza R

Journal of virology

2021 Volume 95, Issue 10

Abstract: Almost simultaneously, several studies reported the emergence of novel SARS-CoV-2 lineages characterized by their phylogenetic and genetic distinction (1), (2), (3), (4).…. ...

Abstract	Almost simultaneously, several studies reported the emergence of novel SARS-CoV-2 lineages characterized by their phylogenetic and genetic distinction (1), (2), (3), (4).….
Language	English
Publishing date	2021-03-01
Publishing country	United States
Document type	Letter
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.00119-21
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Article ; Online: Epidemic Spread of SARS-CoV-2 Lineage B.1.1.7 in Brazil.

Moreira, Filipe R R / Bonfim, Diego M / Zauli, Danielle A G / Silva, Joice P / Lima, Aline B / Malta, Frederico S V / Ferreira, Alessandro C S / Pardini, Victor C / Magalhães, Wagner C S / Queiroz, Daniel C / Souza, Rafael M / Geddes, Victor E V / Costa, Walyson C / Moreira, Rennan G / Faria, Nuno R / Voloch, Carolina M / Souza, Renan P / Aguiar, Renato S

Viruses

2021 Volume 13, Issue 6

Abstract: The emergence of diverse lineages harboring mutations with functional significance and potentially enhanced transmissibility imposes an increased difficulty on the containment of the SARS-CoV-2 pandemic [ ... ]. ...

Abstract	The emergence of diverse lineages harboring mutations with functional significance and potentially enhanced transmissibility imposes an increased difficulty on the containment of the SARS-CoV-2 pandemic [...].
MeSH term(s)	Brazil/epidemiology ; COVID-19/epidemiology ; COVID-19/transmission ; COVID-19/virology ; Genome, Viral/genetics ; Humans ; Mutation ; Phylogeny ; Phylogeography ; SARS-CoV-2/classification ; SARS-CoV-2/genetics
Language	English
Publishing date	2021-05-26
Publishing country	Switzerland
Document type	Editorial ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13060984
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Article ; Online: Assessing Genetic Diversity after Mangrove Restoration in Brazil

Renan Granado / Luiza C. Pinto Neta / André F. Nunes-Freitas / Carolina M. Voloch / Catarina F. Lira

Diversity, Vol 10, Iss 2, p

Why Is It So Important?

2018 Volume 27

Abstract: Vital for many marine and terrestrial species, and several other environmental services, such as carbon sink areas, the mangrove ecosystem is highly threatened due to the proximity of large urban centers and climate change. The forced fragmentation of ... ...

Abstract	Vital for many marine and terrestrial species, and several other environmental services, such as carbon sink areas, the mangrove ecosystem is highly threatened due to the proximity of large urban centers and climate change. The forced fragmentation of this ecosystem affects the genetic diversity distribution among natural populations. Moreover, while restoration efforts have increased, few studies have analyzed how recently-planted areas impact the original mangrove genetic diversity. We analyzed the genetic diversity of two mangroves species (Laguncularia racemosa and Avicennia schaueriana) in three areas in Brazil, using inter-simple sequence repeat (ISSR) markers. Using the local approach, we identified the genetic diversity pool of a restored area compared to nearby areas, including the remnant plants inside the restored area, one well-conserved population at the shore of Guanabara Bay, and one impacted population in Araçá Bay. The results for L. racemosa showed that the introduced population has lost genetic diversity by drift, but remnant plants with high genetic diversity or incoming propagules could help improve overall genetic diversity. Avicennia schaueriana showed similar genetic diversity, indicating an efficient gene flow. The principal component analysis showing different connections between both species indicate differences in gene flow and dispersal efficiencies, highlighting the needed for further studies. Our results emphasize that genetic diversity knowledge and monitoring associated with restoration actions can help avoid bottlenecks and other pitfalls, especially for the mangrove ecosystem.
Keywords	ISSR ; mangroves ; restoration ; genetic diversity ; conservation ; Biology (General) ; QH301-705.5
Subject code	580 ; 333
Language	English
Publishing date	2018-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Assessing Genetic Diversity after Mangrove Restoration in Brazil: Why Is It So Important?

Granado, Renan / Pinto Neta, Luiza C / Nunes-Freitas, André F / Voloch, Carolina M / Lira, Catarina F

Diversity. 2018 Apr. 26, v. 10, no. 2

2018

Abstract	Vital for many marine and terrestrial species, and several other environmental services, such as carbon sink areas, the mangrove ecosystem is highly threatened due to the proximity of large urban centers and climate change. The forced fragmentation of this ecosystem affects the genetic diversity distribution among natural populations. Moreover, while restoration efforts have increased, few studies have analyzed how recently-planted areas impact the original mangrove genetic diversity. We analyzed the genetic diversity of two mangroves species (Laguncularia racemosa and Avicennia schaueriana) in three areas in Brazil, using inter-simple sequence repeat (ISSR) markers. Using the local approach, we identified the genetic diversity pool of a restored area compared to nearby areas, including the remnant plants inside the restored area, one well-conserved population at the shore of Guanabara Bay, and one impacted population in Araçá Bay. The results for L. racemosa showed that the introduced population has lost genetic diversity by drift, but remnant plants with high genetic diversity or incoming propagules could help improve overall genetic diversity. Avicennia schaueriana showed similar genetic diversity, indicating an efficient gene flow. The principal component analysis showing different connections between both species indicate differences in gene flow and dispersal efficiencies, highlighting the needed for further studies. Our results emphasize that genetic diversity knowledge and monitoring associated with restoration actions can help avoid bottlenecks and other pitfalls, especially for the mangrove ecosystem.
Keywords	Avicennia ; Laguncularia racemosa ; carbon sinks ; climate change ; ecosystem services ; gene flow ; genetic variation ; mangrove ecosystems ; microsatellite repeats ; monitoring ; principal component analysis ; Brazil
Language	English
Dates of publication	2018-0426
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2518137-3
ISSN	1424-2818
ISSN	1424-2818
DOI	10.3390/d10020027
Database	NAL-Catalogue (AGRICOLA)

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