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Article ; Online: Assessment of the Risk of Exotic Zika Virus Strain Transmission by

Gaye, Alioune / Fall, Cheikh / Faye, Oumar / Dupont-Rouzeyrol, Myrielle / Ndiaye, El Hadji / Diallo, Diawo / de Andrade Zanotto, Paolo Marinho / Dia, Ibrahima / Weaver, Scott C / Diallo, Mawlouth

Tropical medicine and infectious disease

2023 Volume 8, Issue 2

Abstract: Zika virus (ZIKV) shows an enigmatic epidemiological profile in Africa. Despite its frequent detection in mosquitoes, few human cases have been reported. This could be due to the low infectious potential or low virulence of African ZIKV lineages. This ... ...

Abstract	Zika virus (ZIKV) shows an enigmatic epidemiological profile in Africa. Despite its frequent detection in mosquitoes, few human cases have been reported. This could be due to the low infectious potential or low virulence of African ZIKV lineages. This study sought to assess the susceptibility of
Language	English
Publishing date	2023-02-20
Publishing country	Switzerland
Document type	Journal Article
ISSN	2414-6366
ISSN (online)	2414-6366
DOI	10.3390/tropicalmed8020130
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Article: Co-circulation of

de França Cirilo, Marcus Vinicius / Pour, Shahab Zaki / de Fatima Benedetti, Viviane / Farias, Jéssica Pires / Fogaça, Mayanna Moreira Costa / da Conceição Simões, Rafael / Vidal, Paloma Oliveira / Birbrair, Alexander / de Andrade Zanotto, Paolo Marinho / Luiz, Wilson Barros / Amorim, Jaime Henrique

Frontiers in microbiology

2023 Volume 14, Page(s) 1240860

Abstract: Chikungunya, mayaro, dengue, zika, and yellow fever are mosquito-borne viral diseases caused, respectively, ... ...

Abstract	Chikungunya, mayaro, dengue, zika, and yellow fever are mosquito-borne viral diseases caused, respectively, by
Language	English
Publishing date	2023-08-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2023.1240860
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Article: Evaluation of patients treated by telemedicine in the beginning of the COVID-19 pandemic in São Paulo, Brazil: A non-randomized clinical trial preliminary study.

Chechter, Michelle / Dutra da Silva, Gustavo Maximiliano / E Costa, Rute Alves Pereira / Miklos, Thomas Gabriel / Antonio da Silva, Nilzio / Lorber, Gabriel / Vasconcellos Mota, Natacha Rivero / Dos Santos Cortada, Aline Pinheiro / de Nazare Lima da Cruz, Luciana / de Melo, Paulo Macio Porto / de Souza, Bruno Campello / Emmerich, Francisco G / de Andrade Zanotto, Paolo Marinho / Aaron Scheinberg, Morton

Heliyon

2023 Volume 9, Issue 4, Page(s) e15337

Abstract: We performed a pilot open-label, non-randomized controlled clinical trial in a clinic in São Paulo, Brazil in the beginning of the COVID-19 pandemic. "This medical pilot project was carried out during the pandemic of a new and unknown agent. It was ... ...

Abstract	We performed a pilot open-label, non-randomized controlled clinical trial in a clinic in São Paulo, Brazil in the beginning of the COVID-19 pandemic. "This medical pilot project was carried out during the pandemic of a new and unknown agent. It was necessary to find a new and safe therapeutic approach for pathogens with high potential for severity and contamination. The repositioning of safe and accessible pre-existing and approved medications and the telemedicine approach improved treated covid patients' symptoms and reduced the risk of disease transmission. The emergency application of a new medical technology was the major limitation of the study. This innovative care model is a low-cost safe strategy, and we understand that applicability can be expanded to other regions in emergency situations." The 187 patients of the study (mean age of 37.6 ± 15,6 years) were divided into four groups: (1) asymptomatic, (2) mild symptoms, (3) moderate symptoms and (4) severe symptoms and were followed up for five days. A drug intervention was performed in group 3 and the patients of Group 4 were oriented to seek hospital care. Of all the patients, 23.0% were asymptomatic, 29.4% reported mild symptoms, 43.9% moderate symptoms and 3.7% severe symptoms. Three patients were hospitalized and discharged after recovery. Our results indicate that the use of telemedicine with diagnosis and drug treatment is a safe and effective strategy to reduce overload of health services and the exposure of healthcare providers and the population. The patients that initiated the treatment in the early stages of the disease presented satisfactory clinical response, reducing the need of face-to-face consultations and hospitalizations. The patients who followed the protocol treatment for COVID-19 with hydroxychloroquine and azithromycin for five days presented statistically significant improvement of clinical symptoms when compared to moderate patients who opted for not following the protocol (p < 0.05) and to all no treatment patients (p < 0.001).
Language	English
Publishing date	2023-04-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2023.e15337
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Article ; Online: Codon adaptation biases among sylvatic and urban genotypes of Dengue virus type 2.

Dos Passos Cunha, Marielton / Ortiz-Baez, Ayda Susana / de Melo Freire, Caio César / de Andrade Zanotto, Paolo Marinho

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

2018 Volume 64, Page(s) 207–211

Abstract: Dengue virus (DENV) emerged from the sylvatic environment and colonized urban settings, being sustained in a human-Aedes-human transmission chain, mainly by the bites of females of the anthropophilic species Aedes aegypti. Herein, we sought evidence for ... ...

Abstract	Dengue virus (DENV) emerged from the sylvatic environment and colonized urban settings, being sustained in a human-Aedes-human transmission chain, mainly by the bites of females of the anthropophilic species Aedes aegypti. Herein, we sought evidence for fine-tuning in viral codon usage, possibly due to viral adaptation to human transmission. We compared the codon adaptation of DENV serotype 2 (DENV-2) genotypes from urban and sylvatic habitats and tried to correlate the findings with key evolutionary determinants. We found that DENV-2 codons of urban and sylvatic genotypes had a higher CAI to humans than to Ae. aegypti. Remarkably, we found no significant differences in codon adaptation to human between urban American/Asian and sylvatic DENV-2 genotypes. Moreover, CAI values were significantly different, when comparing all genotypes to Ae. aegypti codon preferences, with lower values for sylvatic than urban genotypes. In summary, our findings suggest the presence of a molecular signature among the genotypes that circulate in sylvatic and urban environments, and may help explain the trafficking of DENV-2 strains to an urban cycle.
MeSH term(s)	Adaptation, Biological ; Aedes/virology ; Animals ; Codon ; Dengue/virology ; Dengue Virus/classification ; Dengue Virus/genetics ; Genotype ; Humans ; Mosquito Vectors/virology ; Open Reading Frames ; Phylogeny
Chemical Substances	Codon
Keywords	covid19
Language	English
Publishing date	2018-05-21
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.2018.05.017
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Article: Codon adaptation biases among sylvatic and urban genotypes of Dengue virus type 2

dos Passos Cunha, Marielton / Ortiz-Baez, Ayda Susana / de Melo Freire, Caio César / de Andrade Zanotto, Paolo Marinho

Infection, genetics, and evolution. 2018 Oct., v. 64

2018

Abstract	Dengue virus (DENV) emerged from the sylvatic environment and colonized urban settings, being sustained in a human-Aedes-human transmission chain, mainly by the bites of females of the anthropophilic species Aedes aegypti. Herein, we sought evidence for fine-tuning in viral codon usage, possibly due to viral adaptation to human transmission. We compared the codon adaptation of DENV serotype 2 (DENV-2) genotypes from urban and sylvatic habitats and tried to correlate the findings with key evolutionary determinants. We found that DENV-2 codons of urban and sylvatic genotypes had a higher CAI to humans than to Ae. aegypti. Remarkably, we found no significant differences in codon adaptation to human between urban American/Asian and sylvatic DENV-2 genotypes. Moreover, CAI values were significantly different, when comparing all genotypes to Ae. aegypti codon preferences, with lower values for sylvatic than urban genotypes. In summary, our findings suggest the presence of a molecular signature among the genotypes that circulate in sylvatic and urban environments, and may help explain the trafficking of DENV-2 strains to an urban cycle.
Keywords	Aedes aegypti ; Dengue virus ; codons ; females ; genotype ; habitats ; humans ; serotypes ; urban areas ; covid19
Language	English
Dates of publication	2018-10
Size	p. 207-211.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2037068-4
ISSN	1567-1348
ISSN	1567-1348
DOI	10.1016/j.meegid.2018.05.017
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Article: Genomic mosaicism in two strains of dengue virus type 3

Villabona-Arenas, Christian Julián / de Brito, Anderson Fernandes / de Andrade Zanotto, Paolo Marinho

Infection, genetics, and evolution. 2013 Aug., v. 18

2013

Abstract: Recombination is a significant factor driving genomic evolution, but it is not well understood in Dengue virus. We used phylogenetic methods to search for recombination in 636 Dengue virus type 3 (DENV-3) genomes and unveiled complex recombination ... ...

Abstract	Recombination is a significant factor driving genomic evolution, but it is not well understood in Dengue virus. We used phylogenetic methods to search for recombination in 636 Dengue virus type 3 (DENV-3) genomes and unveiled complex recombination patterns in two strains, which appear to be the outcome of recombination between genotype II and genotype I parental DENV-3 lineages. Our findings of genomic mosaic structures suggest that strand switching during RNA synthesis may be involved in the generation of genetic diversity in dengue viruses.
Keywords	Dengue virus ; RNA ; dengue ; genetic variation ; genome ; genotype ; phylogeny ; viruses
Language	English
Dates of publication	2013-08
Size	p. 202-212.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2037068-4
ISSN	1567-1348
ISSN	1567-1348
DOI	10.1016/j.meegid.2013.05.012
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Article ; Online: Influence of the HIV GWG variant in the HIV infection progression in mono and HCV coinfected patients.

Hebeler-Barbosa, Flavia / Massolini, Viviam Milanez / Watanabe, Thais / Silva, Giovanni Faria / Barbosa, Alexandre Naime / Simões, Rafael Plana / Ferrasi, Adriana Camargo / de Andrade Zanotto, Paolo Marinho / de Moura Campos Pardini, Maria Inês / Grotto, Rejane Maria Tommasini

Medicine

2019 Volume 98, Issue 29, Page(s) e16376

Abstract: The HIV subtype B is the most frequent in Brazil. The HIV subtype B' codes the amino acids glicine-tryptophan-glicine (GWG) instead of glicine-proline-glicine on the tip of gp120 V3 loop. This variant was associated to a slower HIV progression in mono- ... ...

Abstract	The HIV subtype B is the most frequent in Brazil. The HIV subtype B' codes the amino acids glicine-tryptophan-glicine (GWG) instead of glicine-proline-glicine on the tip of gp120 V3 loop. This variant was associated to a slower HIV progression in mono-infected patients; however, there is no information in coinfected patients. This study evaluated the infection progression of HIV variant B' on the hepatitis C virus presence. RNA isolated from plasma of the 601 infected patients were used to human immunodeficiency virus (HIV) subtyping and to classify the virus according their syncytium-inducing ability. The HIV infection progression was evaluated by clinical and laboratorial data. The results showed a significant association between HIV B' variant and CD4 count and time of AIDS in HIV mono-infected patients. Notwithstanding the fact that we did not find a direct association between GWG variant and AIDS and in HIV coinfected patients no mitigating effect due to GWG presence was found. We did observe that the association between GWG variant and CD4 counts is lost in coinfected patients. This is first work showing influence of the HIV GWG variant in coinfected patients. Nevertheless, the presence of the GWG variant can indicate a better prognostic in the mono-infected patients.
MeSH term(s)	Adult ; Brazil/epidemiology ; CD4 Lymphocyte Count/methods ; Coinfection/epidemiology ; Coinfection/virology ; Disease Progression ; Female ; HIV Envelope Protein gp120/genetics ; HIV Infections/epidemiology ; HIV Infections/immunology ; HIV Infections/virology ; HIV-1/genetics ; Hepacivirus/isolation & purification ; Hepatitis C/epidemiology ; Hepatitis C/virology ; Humans ; Male ; Prognosis ; RNA, Viral/analysis
Chemical Substances	HIV Envelope Protein gp120 ; RNA, Viral
Language	English
Publishing date	2019-08-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	80184-7
ISSN	1536-5964 ; 0025-7974
ISSN (online)	1536-5964
ISSN	0025-7974
DOI	10.1097/MD.0000000000016376
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Article ; Online: Complete genome viral phylogenies suggests the concerted evolution of regulatory cores and accessory satellites.

de Andrade Zanotto, Paolo Marinho / Krakauer, David C

PloS one

2008 Volume 3, Issue 10, Page(s) e3500

Abstract: We consider the concerted evolution of viral genomes in four families of DNA viruses. Given the high rate of horizontal gene transfer among viruses and their hosts, it is an open question as to how representative particular genes are of the evolutionary ... ...

Abstract	We consider the concerted evolution of viral genomes in four families of DNA viruses. Given the high rate of horizontal gene transfer among viruses and their hosts, it is an open question as to how representative particular genes are of the evolutionary history of the complete genome. To address the concerted evolution of viral genes, we compared genomic evolution across four distinct, extant viral families. For all four viral families we constructed DNA-dependent DNA polymerase-based (DdDp) phylogenies and in addition, whole genome sequence, as quantitative descriptions of inter-genome relationships. We found that the history of the polymerase gene was highly predictive of the history of the genome as a whole, which we explain in terms of repeated, co-divergence events of the core DdDp gene accompanied by a number of satellite, accessory genetic loci. We also found that the rate of gene gain in baculovirus and poxviruses proceeds significantly more quickly than the rate of gene loss and that there is convergent acquisition of satellite functions promoting contextual adaptation when distinct viral families infect related hosts. The congruence of the genome and polymerase trees suggests that a large set of viral genes, including polymerase, derive from a phylogenetically conserved core of genes of host origin, secondarily reinforced by gene acquisition from common hosts or co-infecting viruses within the host. A single viral genome can be thought of as a mutualistic network, with the core genes acting as an effective host and the satellite genes as effective symbionts. Larger virus genomes show a greater departure from linkage equilibrium between core and satellites functions.
MeSH term(s)	Biological Evolution ; DNA Viruses/genetics ; DNA, Satellite ; DNA-Directed DNA Polymerase/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Viral ; Kinetics ; Linkage Disequilibrium ; Phylogeny
Chemical Substances	DNA, Satellite ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
Keywords	covid19
Language	English
Publishing date	2008
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0003500
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Article ; Online: Genomic mosaicism in two strains of Dengue virus type 3.

Villabona-Arenas, Christian Julián / de Brito, Anderson Fernandes / de Andrade Zanotto, Paolo Marinho

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

2013 Volume 18, Page(s) 202–212

Abstract	Recombination is a significant factor driving genomic evolution, but it is not well understood in Dengue virus. We used phylogenetic methods to search for recombination in 636 Dengue virus type 3 (DENV-3) genomes and unveiled complex recombination patterns in two strains, which appear to be the outcome of recombination between genotype II and genotype I parental DENV-3 lineages. Our findings of genomic mosaic structures suggest that strand switching during RNA synthesis may be involved in the generation of genetic diversity in dengue viruses.
MeSH term(s)	Bayes Theorem ; Dengue Virus/classification ; Dengue Virus/genetics ; Evolution, Molecular ; Genome, Viral ; Phylogeny ; Recombination, Genetic
Language	English
Publishing date	2013-08
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.2013.05.012
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Article ; Online: Modularity and evolutionary constraints in a baculovirus gene regulatory network.

Oliveira, Juliana Velasco / de Brito, Anderson Fernandes / Braconi, Carla Torres / de Melo Freire, Caio César / Iamarino, Atila / de Andrade Zanotto, Paolo Marinho

BMC systems biology

2013 Volume 7, Page(s) 87

Abstract: Background: The structure of regulatory networks remains an open question in our understanding of complex biological systems. Interactions during complete viral life cycles present unique opportunities to understand how host-parasite network take shape ... ...

Abstract	Background: The structure of regulatory networks remains an open question in our understanding of complex biological systems. Interactions during complete viral life cycles present unique opportunities to understand how host-parasite network take shape and behave. The Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is a large double-stranded DNA virus, whose genome may encode for 152 open reading frames (ORFs). Here we present the analysis of the ordered cascade of the AgMNPV gene expression. Results: We observed an earlier onset of the expression than previously reported for other baculoviruses, especially for genes involved in DNA replication. Most ORFs were expressed at higher levels in a more permissive host cell line. Genes with more than one copy in the genome had distinct expression profiles, which could indicate the acquisition of new functionalities. The transcription gene regulatory network (GRN) for 149 ORFs had a modular topology comprising five communities of highly interconnected nodes that separated key genes that are functionally related on different communities, possibly maximizing redundancy and GRN robustness by compartmentalization of important functions. Core conserved functions showed expression synchronicity, distinct GRN features and significantly less genetic diversity, consistent with evolutionary constraints imposed in key elements of biological systems. This reduced genetic diversity also had a positive correlation with the importance of the gene in our estimated GRN, supporting a relationship between phylogenetic data of baculovirus genes and network features inferred from expression data. We also observed that gene arrangement in overlapping transcripts was conserved among related baculoviruses, suggesting a principle of genome organization. Conclusions: Albeit with a reduced number of nodes (149), the AgMNPV GRN had a topology and key characteristics similar to those observed in complex cellular organisms, which indicates that modularity may be a general feature of biological gene regulatory networks.
MeSH term(s)	Animals ; Baculoviridae/genetics ; Baculoviridae/physiology ; Cell Line ; Conserved Sequence ; Evolution, Molecular ; Gene Regulatory Networks ; Genes, Viral/genetics ; Genomics ; Kinetics ; Lepidoptera/virology ; Promoter Regions, Genetic/genetics ; Transcription, Genetic ; Transcriptome
Language	English
Publishing date	2013-09-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2265490-2
ISSN	1752-0509 ; 1752-0509
ISSN (online)	1752-0509
ISSN	1752-0509
DOI	10.1186/1752-0509-7-87
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