1
|
Couto RDS, Abreu WU, Rodrigues LRR, Marinho LF, Morais VDS, Villanova F, Pandey RP, Deng X, Delwart E, da Costa AC, Leal E. Genomoviruses in Liver Samples of Molossus molossus Bats. Microorganisms 2024; 12:688. [PMID: 38674632 PMCID: PMC11052389 DOI: 10.3390/microorganisms12040688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 03/15/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
CRESS-DNA encompasses a broad spectrum of viruses documented across diverse organisms such as animals, plants, diatoms, fungi, and marine invertebrates. Despite this prevalence, the full extent of these viruses' impact on the environment and their respective hosts remains incompletely understood. Furthermore, an increasing number of viruses within this category lack detailed characterization. This investigation focuses on unveiling and characterizing viruses affiliated with the Genomoviridae family identified in liver samples from the bat Molossus molossus. Leveraging viral metagenomics, we identified seven sequences (MmGmV-PA) featuring a circular DNA genome housing two ORFs encoding replication-associated protein (Rep) and capsid protein (Cap). Predictions based on conserved domains typical of the Genomoviridae family were established. Phylogenetic analysis revealed the segregation of these sequences into two clades aligning with the genera Gemycirculavirus (MmGmV-06-PA and MmGmV-07-PA) and Gemykibivirus (MmGmV-01-PA, MmGmV-02-PA, MmGmV-03-PA, MmGmV-05-PA, and MmGmV-09-PA). At the species level, pairwise comparisons based on complete nucleotide sequences indicated the potential existence of three novel species. In summary, our study significantly contributes to an enhanced understanding of the diversity of Genomoviridae within bat samples, shedding light on previously undiscovered viral entities and their potential ecological implications.
Collapse
Affiliation(s)
- Roseane da Silva Couto
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (F.V.)
| | - Wandercleyson Uchôa Abreu
- Programa de Pos-Graduação REDE Bionorte, Polo Pará, Universidade Federal do Oeste do Pará, Santarém 68040-255, PA, Brazil;
| | - Luís Reginaldo Ribeiro Rodrigues
- Laboratory of Genetics & Biodiversity, Institute of Educational Sciences, Universidade Federal do Oeste do Pará, Santarém 68040-255, PA, Brazil;
| | | | - Vanessa dos Santos Morais
- Laboratory of Virology (LIM 52), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (V.d.S.M.); (A.C.d.C.)
| | - Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (F.V.)
| | - Ramendra Pati Pandey
- School of Health Sciences & Technology, UPES University, Dehradun 248007, Uttarakhand, India;
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA 94143, USA;
| | - Eric Delwart
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA;
| | - Antonio Charlys da Costa
- Laboratory of Virology (LIM 52), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (V.d.S.M.); (A.C.d.C.)
| | - Elcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (F.V.)
| |
Collapse
|
2
|
Honorato L, Ferreira NE, Domingues RB, Senne C, Leite FBVDM, Santos MVD, Fernandes GBP, Paião HGO, Vilas Boas LS, da Costa AC, Tozetto-Mendoza TR, Witkin SS, Mendes-Correa MC. Evaluation of enterovirus concentration, species identification, and cerebrospinal fluid parameters in patients of different ages with aseptic meningitis in São Paulo, Brazil. J Med Virol 2024; 96:e29471. [PMID: 38353496 DOI: 10.1002/jmv.29471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/10/2024] [Accepted: 02/05/2024] [Indexed: 02/16/2024]
Abstract
Human enteroviruses (EV) are the most common cause of aseptic meningitis worldwide. Data on EV viral load in cerebrospinal fluid (CSF) and related epidemiological studies are scarce in Brazil. This study investigated the influence of EV viral load on CSF parameters, as well as identifying the involved species. CSF samples were collected in 2018-2019 from 140 individuals at The Hospital das Clínicas, São Paulo. The EV viral load was determined using real-time quantitative polymerase chain reaction, while EV species were identified by 5'UTR region sequencing. Median viral load was 5.72 log10 copies/mL and did not differ by subjects' age and EV species. Pleocytosis was observed in 94.3% of cases, with the highest white blood cell (WBC) counts in younger individuals. Viral load and WBC count were correlated in children (p = 0.0172). Elevated lactate levels were observed in 60% of cases and correlated with the viral load in preteen-teenagers (p = 0.0120) and adults (p = 0.0184). Most individuals had normal total protein levels (70.7%), with higher in preteen-teenagers and adults (p < 0.0001). By sequencing, 8.2% were identified as EV species A and 91.8% as species B. Age-specific variations in CSF characteristics suggest distinct inflammatory responses in each group.
Collapse
Affiliation(s)
- Layla Honorato
- Laboratory of Virology (LIM 52), Department of Infectious Diseases, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Noely Evangelista Ferreira
- Laboratory of Virology (LIM 52), Department of Infectious Diseases, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | | | | | - Heuder Gustavo Oliveira Paião
- Laboratory of Virology (LIM 52), Department of Infectious Diseases, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Lucy Santos Vilas Boas
- Laboratory of Virology (LIM 52), Department of Infectious Diseases, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Antonio Charlys da Costa
- Laboratory of Virology (LIM 52), Department of Infectious Diseases, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Tânia Regina Tozetto-Mendoza
- Laboratory of Virology (LIM 52), Department of Infectious Diseases, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Steven S Witkin
- Laboratory of Virology (LIM 52), Department of Infectious Diseases, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Obstetrics and Gynecology, Weill Cornel Medicine, New York, New York, USA
| | - Maria Cássia Mendes-Correa
- Laboratory of Virology (LIM 52), Department of Infectious Diseases, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| |
Collapse
|
3
|
Couto RDS, Ramos EDSF, Abreu WU, Rodrigues LRR, Marinho LF, Morais VDS, Villanova F, Pandey RP, Deng X, Delwart E, da Costa AC, Leal E. Metagenomic of Liver Tissue Identified at Least Two Genera of Totivirus-like Viruses in Molossus molossus Bats. Microorganisms 2024; 12:206. [PMID: 38276191 PMCID: PMC10819564 DOI: 10.3390/microorganisms12010206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
The Totiviridae family of viruses has a unique genome consisting of double-stranded RNA with two open reading frames that encode the capsid protein (Cap) and the RNA-dependent RNA polymerase (RdRpol). Most virions in this family are isometric in shape, approximately 40 nm in diameter, and lack an envelope. There are five genera within this family, including Totivirus, Victorivirus, Giardiavirus, Leishmaniavirus, and Trichomonasvirus. While Totivirus and Victorivirus primarily infect fungi, Giardiavirus, Leishmaniavirus, and Trichomonasvirus infect diverse hosts, including protists, insects, and vertebrates. Recently, new totivirus-like species have been discovered in fish and plant hosts, and through metagenomic analysis, a novel totivirus-like virus (named Tianjin totivirus) has been isolated from bat guano. Interestingly, Tianjin totivirus causes cytopathic effects in insect cells but cannot grow in mammalian cells, suggesting that it infects insects consumed by insectivorous bats. In this study, we used next-generation sequencing and identified totivirus-like viruses in liver tissue from Molossus molossus bats in the Amazon region of Brazil. Comparative phylogenetic analysis based on the RNA-dependent RNA polymerase region revealed that the viruses identified in Molossus bats belong to two distinct phylogenetic clades, possibly comprising different genera within the Totiviridae family. Notably, the mean similarity between the Tianjin totivirus and the totiviruses identified in Molossus bats is less than 18%. These findings suggest that the diversity of totiviruses in bats is more extensive than previously recognized and highlight the potential for bats to serve as reservoirs for novel toti-like viruses.
Collapse
Affiliation(s)
- Roseane da Silva Couto
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (E.d.S.F.R.); (F.V.)
| | - Endrya do Socorro Foro Ramos
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (E.d.S.F.R.); (F.V.)
| | - Wandercleyson Uchôa Abreu
- Programa de Pos-Graduação REDE Bionorte, Polo Pará, Universidade Federal do Oeste do Pará, Santarém 68040-255, PA, Brazil;
| | - Luis Reginaldo Ribeiro Rodrigues
- Laboratory of Genetics & Biodiversity, Institute of Educational Sciences, Universidade Federal do Oeste do Pará, Santarém 68040-255, PA, Brazil;
| | | | - Vanessa dos Santos Morais
- Laboratory of Virology (LIM 52), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (V.d.S.M.); (A.C.d.C.)
| | - Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (E.d.S.F.R.); (F.V.)
| | - Ramendra Pati Pandey
- School of Health Sciences and Technology (SoHST), UPES, Dehradun 248007, Uttarakhand, India;
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA 94143, USA;
| | - Eric Delwart
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA;
| | - Antonio Charlys da Costa
- Laboratory of Virology (LIM 52), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (V.d.S.M.); (A.C.d.C.)
| | - Elcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (E.d.S.F.R.); (F.V.)
| |
Collapse
|
4
|
Carmona RDCC, Cilli A, da Costa AC, Reis FC, Leal É, dos Santos FCP, Machado BC, Lopes CS, Afonso AMS, Timenetsky MDCST. Pegivirus Detection in Cerebrospinal Fluid from Patients with Central Nervous System Infections of Unknown Etiology in Brazil by Viral Metagenomics. Microorganisms 2023; 12:19. [PMID: 38257846 PMCID: PMC10818654 DOI: 10.3390/microorganisms12010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 01/24/2024] Open
Abstract
Metagenomic next-generation sequencing (mNGS) methodology serves as an excellent supplement in cases where diagnosis is challenging to establish through conventional laboratory tests, and its usage is increasingly prevalent. Examining the causes of infectious diseases in the central nervous system (CNS) is vital for understanding their spread, managing outbreaks, and effective patient care. In a study conducted in the state of São Paulo, Brazil, cerebrospinal fluid (CSF) samples from 500 patients with CNS diseases of indeterminate etiology, collected between 2017 and 2021, were analyzed. Employing a mNGS approach, we obtained the complete coding sequence of Pegivirus hominis (HPgV) genotype 2 in a sample from a patient with encephalitis (named IAL-425/BRA/SP/2019); no other pathogen was detected. Subsequently, to determine the extent of this virus's presence, both polymerase chain reaction (PCR) and/or real-time PCR assays were utilized on the entire collection. The presence of the virus was identified in 4.0% of the samples analyzed. This research constitutes the first report of HPgV detection in CSF samples in South America. Analysis of the IAL-425 genome (9107 nt) revealed a 90% nucleotide identity with HPgV strains from various countries. Evolutionary analyses suggest that HPgV is both endemic and extensively distributed. The direct involvement of HPgV in CNS infections in these patients remains uncertain.
Collapse
Affiliation(s)
| | - Audrey Cilli
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo 01246-900, Brazil; (A.C.); (F.C.R.); (B.C.M.)
| | | | - Fabricio Caldeira Reis
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo 01246-900, Brazil; (A.C.); (F.C.R.); (B.C.M.)
| | - Élcio Leal
- Institute of Biological Sciences, Federal University of Pará, Belem 66075-000, Brazil;
| | | | - Bráulio Caetano Machado
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo 01246-900, Brazil; (A.C.); (F.C.R.); (B.C.M.)
| | - Cristina Santiago Lopes
- Respiratory Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo 01246-900, Brazil; (F.C.P.d.S.); (C.S.L.); (A.M.S.A.)
| | - Ana Maria Sardinha Afonso
- Respiratory Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo 01246-900, Brazil; (F.C.P.d.S.); (C.S.L.); (A.M.S.A.)
| | | |
Collapse
|
5
|
Morais VDS, Reis Santana LM, Bezerra JF, Cruz FE, Rocha de Souza T, Tahmasebi R, Alves Raposo RA, Marcatti R, Garcia Barbosa EM, Hefford PM, Buccheri R, Cerdeira Sabino E, Charlys da Costa A. Detection of coinfection with Primate Erythroparvovirus 1 and arboviruses (DENV, CHIKV and ZIKV) in individuals with acute febrile illness in the state of Rio Grande do Norte in 2016. PLoS Negl Trop Dis 2023; 17:e0011701. [PMID: 37917659 PMCID: PMC10645361 DOI: 10.1371/journal.pntd.0011701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 11/14/2023] [Accepted: 10/05/2023] [Indexed: 11/04/2023] Open
Abstract
BACKGROUND Arthropod-borne viruses, known as arboviruses, pose substantial risks to global public health. Dengue (DENV), Chikungunya (CHIKV) and Zika (ZIKV) viruses stand out as significant concerns in Brazil and worldwide. Their overlapping clinical manifestations make accurate diagnosis a challenge, underscoring the need for reliable laboratory support. This study employs a comprehensive molecular diagnostic approach to track viral infections in individuals with acute febrile illness, a period marked by widespread outbreaks of DENV, CHIKV and ZIKV. METHODS Between January and August 2016, we received a total of 713 serum samples obtained from individuals with acute febrile illness, previously tested for DENV, CHIKV or ZIKV, with initial negative results, from LACEN-NATAL. Of the total 713 samples, 667 were from females (354 of them pregnant) and 46 from males. Molecular diagnosis was conducted using the Multiplex RT-qPCR technique for simultaneous detection of DENV, CHIKV and ZIKV. Additionally, we performed differential diagnosis by RT-qPCR for other viruses of the Flavivirus, Alphavirus Enterovirus genera and qPCR for Primate Erythroparvovirus 1 (B19V) species, in accordance with Ministry of Health guidelines. RESULTS Among the 713 cases, 78.2% tested positive for viral infections, including 48% with CHIKV viremia, 0.6% with DENV and 0.1% with ZIKV. Arboviral coinfections totaled 2.4%, including DENV-CHIKV (1.7%) and CHIKV-ZIKV (0.7%). Moreover, 8% exhibited B19V viremia. Simultaneous infections were identified in 17.5%, encompassing B19V-CHIKV (17.1%), B19V-DENV (0.1%), and B19V-ZIKV (0.3%) Triple infections were observed in 1.3% of cases with B19V-DENV-CHIKV (1%) and B19V-CHIKV-ZIKV (0.3%). CONCLUSION Molecular testing demonstrated high efficacy in diagnosing prevalent arboviruses and detecting multiple coinfections. This approach helps to elucidate etiologies for symptomatic cases, especially during arbovirus outbreaks, and aids comprehensive surveillance. Our findings underscore the importance of monitoring co-circulating pathogens, such as B19V, with implications for clinical management, particularly in pregnant individuals. This study enhances our understanding of arbovirus epidemiology and reinforces the critical role of molecular diagnosis in disease surveillance and control.
Collapse
Affiliation(s)
| | - Lídia Maria Reis Santana
- Sao Paulo Health Department/Epidemiological Surveillance Center “Prof. Alexandre Vranjac”, Sao Paulo, Brazil
- Federal University of São Paulo, Sao Paulo, Brazil
| | | | | | | | - Roozbeh Tahmasebi
- University of Sao Paulo/Department of Infectious and Parasitic Diseases, Sao Paulo, Brazil
| | | | - Roberta Marcatti
- University of Sao Paulo/Department of Infectious and Parasitic Diseases, Sao Paulo, Brazil
| | | | | | - Renata Buccheri
- Vitalant Research Institute, Department of Epidemiology, San Francisco, California, United States of America
| | - Ester Cerdeira Sabino
- University of Sao Paulo/Department of Infectious and Parasitic Diseases, Sao Paulo, Brazil
| | | |
Collapse
|
6
|
Charlys da Costa A, Mendes-Correa MC, Tozetto-Mendoza TR, Villas-Boas LS, de Paula AV, Paiao HGO, Leal FE, Ferreira NE, Honorato L, Leal E, Grandi G, dos Santos Morais V, Manuli ER, Sabino EC, Witkin SS. Detailed characterization of Redondovirus in saliva of SARS-CoV-2-infected individuals in Sao Paulo, Brazil. PLoS One 2023; 18:e0291027. [PMID: 37651462 PMCID: PMC10470920 DOI: 10.1371/journal.pone.0291027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/20/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND Redondovirus (ReDoV) is a DNA virus present in the respiratory tract of many healthy individuals. Since SARS-CoV-2, the virus responsible for COVID-19, also primarily infects the same site, we evaluated whether ReDoV was present at increased frequency in patients with COVID-19 and influenced infection parameters. METHODS Saliva samples were collected weekly from 59 individuals with COVID-19 and from 132 controls. ReDoV was detected by polymerase chain reaction and the genotypes were identified by metagenomics. Torque Teno Virus (TTV) in these samples were previously reported. RESULTS ReDoV was detected in saliva more frequently from COVID-19 patients (72.9%) than from controls (50.0%) (p = 0.0015). There were no associations between ReDoV detection and either continuous or intermittent SARS-CoV-2 shedding, the duration of SARS-CoV-2 detection in saliva, patients' sex or if infection was by the B1 or Gamma strain. The two ReDoV strains, Brisavirus and Vientovirus, were present in equivalent frequencies in ReDoV-positive COVID-19 patients and controls. Phylogenetic analysis suggested that the two ReDoV strains in Brazil were similar to strains previously detected on other continents. CONCLUSION ReDoV expression in saliva is increased in males and females in Brazil with mild COVID-19 but its presence does not appear to influence properties of the SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Antonio Charlys da Costa
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Maria C. Mendes-Correa
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Tania Regina Tozetto-Mendoza
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Faculdade de Medicina da Universidade Municipal de Sao Caetano do Sul, São Paulo, Brazil
| | - Lucy S. Villas-Boas
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Faculdade de Medicina da Universidade Municipal de Sao Caetano do Sul, São Paulo, Brazil
| | - Anderson Vicente de Paula
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Heuder Gustavo Oliveira Paiao
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Fabio E. Leal
- Faculdade de Medicina da Universidade Municipal de Sao Caetano do Sul, São Paulo, Brazil
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Noely E. Ferreira
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Layla Honorato
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Elcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Pará, Brazil
| | | | - Vanessa dos Santos Morais
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Erika R. Manuli
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Faculdade de Medicina da Universidade Municipal de Sao Caetano do Sul, São Paulo, Brazil
| | - Ester C. Sabino
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Faculdade de Medicina da Universidade Municipal de Sao Caetano do Sul, São Paulo, Brazil
| | - Steven S. Witkin
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, United States of America
| |
Collapse
|
7
|
de Souza LM, de Oliveira ID, Sales FCS, da Costa AC, Campos KR, Abbud A, Guerra JM, Dos Santos Cirqueira Borges C, Takahashi CPFJ, de Araújo LJT. Technical comparison of MinIon and Illumina technologies for genotyping Chikungunya virus in clinical samples. J Genet Eng Biotechnol 2023; 21:88. [PMID: 37642827 PMCID: PMC10465416 DOI: 10.1186/s43141-023-00536-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 07/27/2023] [Indexed: 08/31/2023]
Abstract
New-generation sequencing (NGS) techniques have brought the opportunity for genomic monitoring of several microorganisms potentially relevant to public health. The establishment of different methods with different mechanisms provides a wide choice, taking into account several aspects. With that in mind, the present aim of the study was to compare basic genomic sequencing metrics that could potentially impact genotyping by nanopores from Oxford Nanopore Technologies and by synthesis from Illumina in clinical samples positive for Chikungunya (CHIKV). Among the metrics studied, running time, read production, and Q score were better represented in Illumina sequencing, while the MinIOn platform showed better response time and greater diversity of generated files. That said, it was possible to establish differences between the studied metrics in addition to verifying that the distinctions in the methods did not impact the identification of the CHIKV virus genotype.
Collapse
Affiliation(s)
- Leandro Menezes de Souza
- Centro de Patologia, Instituto Adolfo Lutz, Sao Paulo, Brazil
- Programa de Pós Graduação em Ciências da Saúde do Instituto de Assistência Médica ao Servidor Público Estadual - IAMSPE, Sao Paulo, Brazil
| | - Isabelle Dias de Oliveira
- Centro de Patologia, Instituto Adolfo Lutz, Sao Paulo, Brazil
- Programa de Pós Graduação em Ciências da Saúde do Instituto de Assistência Médica ao Servidor Público Estadual - IAMSPE, Sao Paulo, Brazil
| | - Flávia Cristina Silva Sales
- Departamento de Moléstias Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, Brazil
| | - Antonio Charlys da Costa
- Departamento de Moléstias Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, Brazil
| | | | - Adriano Abbud
- Centro de Respostas Rápidas, Instituto Adolfo Lutz, Sao Paulo, Brazil
| | | | | | | | - Leonardo José Tadeu de Araújo
- Centro de Patologia, Instituto Adolfo Lutz, Sao Paulo, Brazil.
- Programa de Pós Graduação em Ciências da Saúde do Instituto de Assistência Médica ao Servidor Público Estadual - IAMSPE, Sao Paulo, Brazil.
- Departamento de Moléstias Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Sao Paulo, Brazil.
| |
Collapse
|
8
|
Himanshu, Mukherjee R, Vidic J, Leal E, da Costa AC, Prudencio CR, Raj VS, Chang CM, Pandey RP. Nanobiotics and the One Health Approach: Boosting the Fight against Antimicrobial Resistance at the Nanoscale. Biomolecules 2023; 13:1182. [PMID: 37627247 PMCID: PMC10452580 DOI: 10.3390/biom13081182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/22/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Antimicrobial resistance (AMR) is a growing public health concern worldwide, and it poses a significant threat to human, animal, and environmental health. The overuse and misuse of antibiotics have contributed significantly and others factors including gene mutation, bacteria living in biofilms, and enzymatic degradation/hydrolyses help in the emergence and spread of AMR, which may lead to significant economic consequences such as reduced productivity and increased health care costs. Nanotechnology offers a promising platform for addressing this challenge. Nanoparticles have unique properties that make them highly effective in combating bacterial infections by inhibiting the growth and survival of multi-drug-resistant bacteria in three areas of health: human, animal, and environmental. To conduct an economic evaluation of surveillance in this context, it is crucial to obtain an understanding of the connections to be addressed by several nations by implementing national action policies based on the One Health strategy. This review provides an overview of the progress made thus far and presents potential future directions to optimize the impact of nanobiotics on AMR.
Collapse
Affiliation(s)
- Himanshu
- Graduate Institute of Biomedical Sciences, Chang Gung University, No. 259, Wenhua 1st Road, Guishan Dist., Taoyuan City 33302, Taiwan; (H.); (R.M.)
- Master & Ph.D. Program in Biotechnology Industry, Chang Gung University, No. 259, Wenhua 1st Road, Guishan Dist., Taoyuan City 33302, Taiwan
| | - Riya Mukherjee
- Graduate Institute of Biomedical Sciences, Chang Gung University, No. 259, Wenhua 1st Road, Guishan Dist., Taoyuan City 33302, Taiwan; (H.); (R.M.)
- Master & Ph.D. Program in Biotechnology Industry, Chang Gung University, No. 259, Wenhua 1st Road, Guishan Dist., Taoyuan City 33302, Taiwan
| | - Jasmina Vidic
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France;
| | - Elcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil
| | | | - Carlos Roberto Prudencio
- Laboratório de Imunobiotecnologia, Centro de Imunologia, Instituto Adolfo Lutz, 351, São Paulo 01246-902, SP, Brazil
| | - V. Samuel Raj
- Centre for Drug Design Discovery and Development (C4D), Department of Biotechnology & Microbiology, SRM University, Sonepat 131 029, Haryana, India
| | - Chung-Ming Chang
- Master & Ph.D. Program in Biotechnology Industry, Chang Gung University, No. 259, Wenhua 1st Road, Guishan Dist., Taoyuan City 33302, Taiwan
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, No. 259, Wenhua 1st Road, Guishan Dist., Taoyuan City 33302, Taiwan
- Laboratory Animal Center, Chang Gung University, No. 259, Wenhua 1st Road, Guishan Dist., Taoyuan City 33302, Taiwan
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), Department of Biotechnology & Microbiology, SRM University, Sonepat 131 029, Haryana, India
| |
Collapse
|
9
|
Tozetto-Mendoza TR, Mendes-Correa MC, Linhares IM, de Cássia Raymundi V, de Oliveira Paião HG, Barbosa EMG, Luna-Muschi A, Honorato L, Correa GF, da Costa AC, Costa SF, Witkin SS. Association between development of severe COVID-19 and a polymorphism in the CIAS1 gene that codes for an inflammasome component. Sci Rep 2023; 13:11252. [PMID: 37438453 DOI: 10.1038/s41598-023-38095-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 07/03/2023] [Indexed: 07/14/2023] Open
Abstract
An elevated pro-inflammatory cytokine response is associated with severe life-threatening symptoms in individuals with Coronavirus Disease-2019 (COVID). The inflammasome is an intracellular structure responsible for generation of interleukin (IL)-1β and IL-18. NALP3, a product of the CIAS1 gene, is the rate-limiting component for inflammasome activity. We evaluated if a CIAS1 42 base pair length polymorphism (rs74163773) was associated with severe COVID. DNA from 93 individuals with severe COVID, 38 with mild COVID, and 98 controls were analyzed for this polymorphism. The 12 unit repeat allele is associated with the highest inflammasome activity. Five alleles, corresponding to 6, 7, 9, 12 or 13 repeat units, divided into 12 genotypes were identified. The frequency of the 12 unit repeat allele was 45.3% in those with severe disease as opposed to 30.0% in those with mild disease and 26.0% in controls (p < 0.0001, severe vs. controls). In contrast, the 7 unit repeat allele frequency was 30.1% in controls as opposed to 14.0% and 12.5% in those with severe or mild disease, respectively (p ≤ 0.0017). We conclude that individuals positive for the CIAS1 12 allele may be at elevated risk for development of severe COVID due to an increased level of induced pro-inflammatory cytokine production.
Collapse
Affiliation(s)
- Tania R Tozetto-Mendoza
- Laboratório de Virologia LIM 52, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.
| | - Maria Cassia Mendes-Correa
- Laboratório de Virologia LIM 52, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Iara Moreno Linhares
- Departamento de Ginecologia e Obstetricia, Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Vanessa de Cássia Raymundi
- Laboratório de Virologia LIM 52, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Heuder Gustavo de Oliveira Paião
- Laboratório de Virologia LIM 52, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Erick Matheus Garcia Barbosa
- Laboratório de Virologia LIM 52, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Alessandra Luna-Muschi
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Layla Honorato
- Laboratório de Virologia LIM 52, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Giovanna Francisco Correa
- Laboratório de Virologia LIM 52, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Antonio Charlys da Costa
- Laboratório de Virologia LIM 52, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Silvia Figueiredo Costa
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Steven S Witkin
- Laboratório de Virologia LIM 52, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
- Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, USA
| |
Collapse
|
10
|
Azevedo LS, Costa FF, Ghani MBA, Viana E, França Y, Medeiros RS, Guiducci R, Morillo SG, Primo D, Lopes RD, Gomes-Gouvêa MS, da Costa AC, Luchs A. Full genotype characterization of Brazilian canine G3P[3] strains during a 10-year survey (2012-2021) of rotavirus infection in domestic dogs and cats. Arch Virol 2023; 168:176. [PMID: 37306860 DOI: 10.1007/s00705-023-05807-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 04/25/2023] [Indexed: 06/13/2023]
Abstract
There is a dearth of information on the molecular epidemiology of rotaviruses in pets in Brazil. The aim of this study was to monitor rotavirus infections in household dogs and cats, determine full-genotype constellations, and obtain data on evolutionary relationships. Between 2012 and 2021, 600 fecal samples from dogs and cats (516 and 84, respectively) were collected at small animal clinics in São Paulo state, Brazil. Rotavirus screening was conducted using ELISA, PAGE, RT-PCR, sequencing, and phylogenetic analysis. Rotavirus type A (RVA) was detected in 0.5% (3/600) of the animals. No non-RVA types were detected. The three canine RVA strains were found to have a novel genetic constellation, G3-P[3] -I2-R3-C2-M3-A9-N2-T3-E3-H6, which has never been reported in dogs. As expected, all of the viral genes, except those encoding NSP2 and VP7, were closely related to the corresponding genes from canine, feline, and canine-like-human RVA strains. A novel N2 (NSP2) lineage was identified, grouping together Brazilian canine, human, rat and bovine strains, suggesting that genetic reassortment had occurred. Uruguayan G3 strains obtained from sewage contained VP7 genes that were phylogenetically close to those of the Brazilian canine strains, which suggests that these strains are widely distributed in pet populations in South American countries. For the NSP2 (I2), NSP3 (T3), NSP4 (E3), NSP5 (H6), VP1 (R3), VP3 (M3), and VP6 (I2) segments, phylogenetic analysis revealed possibly new lineages. The epidemiological and genetic data presented here point out the necessity for collaborative efforts to implement the One Health strategy in the field of RVA research and to provide an updated understanding of RVA strains circulating canines in Brazil.
Collapse
Affiliation(s)
- Lais Sampaio Azevedo
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | | | | | - Ellen Viana
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | - Yasmin França
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | | | - Raquel Guiducci
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | | | - Dieli Primo
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | | | - Michele Soares Gomes-Gouvêa
- Laboratorio de Gastroenterologia e Hepatologia Tropical-LIM07, Departamento de Gastroenterologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Antonio Charlys da Costa
- Laboratorio de Parasitologia Médica-LIM46, Departamento de Doenças Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Adriana Luchs
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil.
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil.
| |
Collapse
|
11
|
Mendes-Correa MC, Salomão MC, Ghilardi F, Tozetto-Mendoza TR, Santos Villas-Boas L, de Paula AV, Paiao HGO, da Costa AC, Leal FE, Ferraz ADBC, Sales FCS, Claro IM, Ferreira NE, Pereira GM, da Silva AR, Freire W, Espinoza EPS, Manuli ER, Romano CM, de Jesus JG, Sabino EC, Witkin SS. SARS-CoV-2 Detection and Culture in Different Biological Specimens from Immunocompetent and Immunosuppressed COVID-19 Patients Infected with Two Different Viral Strains. Viruses 2023; 15:1270. [PMID: 37376568 DOI: 10.3390/v15061270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 06/29/2023] Open
Abstract
Introduction-The dynamics of SARS-CoV-2 shedding and replication in humans remain incompletely understood. Methods-We analyzed SARS-CoV-2 shedding from multiple sites in individuals with an acute COVID-19 infection by weekly sampling for five weeks in 98 immunocompetent and 25 immunosuppressed individuals. Samples and culture supernatants were tested via RT-PCR for SARS-CoV-2 to determine viral clearance rates and in vitro replication. Results-A total of 2447 clinical specimens were evaluated, including 557 nasopharyngeal swabs, 527 saliva samples, 464 urine specimens, 437 anal swabs and 462 blood samples. The SARS-CoV-2 genome sequences at each site were classified as belonging to the B.1.128 (ancestral strain) or Gamma lineage. SARS-CoV-2 detection was highest in nasopharyngeal swabs regardless of the virus strain involved or the immune status of infected individuals. The duration of viral shedding varied between clinical specimens and individual patients. Prolonged shedding of potentially infectious virus varied from 10 days up to 191 days, and primarily occurred in immunosuppressed individuals. Virus was isolated in culture from 18 nasal swab or saliva samples collected 10 or more days after onset of disease. Conclusions-Our findings indicate that persistent SARS-CoV-2 shedding may occur in both competent or immunosuppressed individuals, at multiple clinical sites and in a minority of subjects is capable of in vitro replication.
Collapse
Affiliation(s)
- Maria Cássia Mendes-Correa
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, São Paulo 05403-010, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Matias Chiarastelli Salomão
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, São Paulo 05403-010, Brazil
- Rua Peixoto Gomide, 645, Sao Paulo 01409-002, Brazil
| | - Fábio Ghilardi
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Tania Regina Tozetto-Mendoza
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Lucy Santos Villas-Boas
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Anderson Vicente de Paula
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Heuder Gustavo Oliveira Paiao
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Antonio Charlys da Costa
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Fábio E Leal
- Faculdade de Medicina da, Universidade Municipal de Sao Caetano do Sul, São Paulo 09521-160, Brazil
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro 20230-130, Brazil
| | | | - Flavia C S Sales
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Ingra M Claro
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Noely E Ferreira
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Geovana M Pereira
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Almir Ribeiro da Silva
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Wilton Freire
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Evelyn Patricia Sánchez Espinoza
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Erika R Manuli
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
- Faculdade de Medicina da, Universidade Municipal de Sao Caetano do Sul, São Paulo 09521-160, Brazil
| | - Camila M Romano
- Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, São Paulo 05403-010, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Jaqueline G de Jesus
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Ester C Sabino
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
- Faculdade de Medicina da, Universidade Municipal de Sao Caetano do Sul, São Paulo 09521-160, Brazil
| | - Steven S Witkin
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY 10065, USA
| |
Collapse
|
12
|
do Socorro Fôro Ramos E, Bahia SL, de Oliveira Ribeiro G, Villanova F, de Pádua Milagres FA, Brustulin R, Pandey RP, Deng X, Delwart E, da Costa AC, Leal É. Characterization of Phietavirus Henu 2 in the virome of individuals with acute gastroenteritis. Virus Genes 2023; 59:464-472. [PMID: 37004601 DOI: 10.1007/s11262-023-01990-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/15/2023] [Indexed: 04/04/2023]
Abstract
There is a growing interest in phages as potential biotechnological tools in human health owing to the antibacterial activity of these viruses. In this study, we characterized a new member (named PhiV_005_BRA/2016) of the recently identified phage species Phietavirus Henu 2. PhiV_005_BRA/2016 was detected through metagenomic analysis of stool samples of individuals with acute gastroenteritis. PhiV_005_BRA/2016 contains double-stranded linear DNA (dsDNA), it has a genome of 43,513 base pairs (bp), with a high identity score (99%) with phage of the genus Phietavirus, species of Phietavirus Henu 2. Life style prediction indicated that PhiV_005_BRA/2016 is a lysogenic phage whose the main host is methicillin-resistant Staphylococcus aureus (MRSA). Indeed, we found PhiV_005_BRA/2016 partially integrated in the genome of distinct MRSA strains. Our findings highlights the importance of large-scale screening of bacteriophages to better understand the emergence of multi-drug resistant bacterial.
Collapse
Affiliation(s)
- Endrya do Socorro Fôro Ramos
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicais, Universidade Federal do Pará, Belém, Pará, 66075-000, Brazil
| | - Santana Lobato Bahia
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicais, Universidade Federal do Pará, Belém, Pará, 66075-000, Brazil
| | - Geovani de Oliveira Ribeiro
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicais, Universidade Federal do Pará, Belém, Pará, 66075-000, Brazil
| | - Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicais, Universidade Federal do Pará, Belém, Pará, 66075-000, Brazil
| | - Flávio Augusto de Pádua Milagres
- Secretaria de Saúde do Tocantins, Palmas, Tocantins, 77453-000, Brazil
- Laboratório Central de Saúde Pública do Tocantins (LACEN/TO), Palmas, Tocantins, 77016-330, Brazil
| | - Rafael Brustulin
- Secretaria de Saúde do Tocantins, Palmas, Tocantins, 77453-000, Brazil
- Laboratório Central de Saúde Pública do Tocantins (LACEN/TO), Palmas, Tocantins, 77016-330, Brazil
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University Delhi-NCR, Rajiv Gandhi Education City, Sonepat, Haryana, 131029, India
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, 94118-4417, USA
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, 94118-4417, USA
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | | | - Élcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicais, Universidade Federal do Pará, Belém, Pará, 66075-000, Brazil.
| |
Collapse
|
13
|
Azevedo LSD, França Y, Viana E, Medeiros RS, Morillo SG, Guiducci R, Ribeiro CD, Vieira HR, Barrio-Nuevo KM, Cunha MS, Guerra JM, Silva DDMCE, Filho VBD, Araújo ELL, Ferreira SRS, Batista CF, Silva GCDD, Nogueira ML, Ahagon CM, Moreira RC, Cunha L, Morais VS, da Costa AC, Luchs A. Lack of molecular evidence of fecal-borne viruses in capybaras from São Paulo state, Brazil, 2018-2020: a minor public health issue. Braz J Microbiol 2023; 54:543-551. [PMID: 36342660 PMCID: PMC9640885 DOI: 10.1007/s42770-022-00859-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022] Open
Abstract
Capybara (Hydrochoerus hydrochaeris) is the world's largest rodent species distributed throughout South America. These animals are incredibly tolerant to anthropogenic environments and are occupying large urban centers. Capybaras are known to carry potentially zoonotic agents, including R. rickettsia, Leishmania spp., Leptospira spp., Trypanosoma spp., Salmonella spp., Toxoplasma gondii, and rabies virus. Focusing on the importance of monitoring potential sources of emerging zoonotic viruses and new viral reservoirs, the aim of the present study was to assess the presence of fecal-borne viruses in the feces of capybaras living in urban parks in São Paulo state, Brazil. A total of 337 fecal samples were collected between 2018 and 2020 and screened for the following: (i) Rotavirus group A (RVA) by ELISA; (ii) non-RVA species and Picobirnavirus (PBV) using PAGE; (iii) Human Bocaparvovirus (HBoV), Bufavirus (BuV), Tusavirus (TuV), and Cutavirus (CuV) qPCR; (iv) Human Enterovirus (EV), Norovirus GII (NoV), and Hantavirus by in houses RT-qPCR; (v) SARS-CoV-2 via commercial RT-qPCR kit assay; and (vi) Astrovirus (AstV) and Adenovirus (AdV) using conventional nested (RT)-PCRs. All fecal samples tested were negative for fecal-borne viruses. This study adds further evidence that the fecal-borne viruses is a minor public health issue in Brazilian capybaras, at least during the surveillance period and surveyed areas. Continuous monitoring of sylvatic animals is essential to prevent and control the emergence or re-emergence of newly discovered virus as well as viruses with known zoonotic potential.
Collapse
Affiliation(s)
| | - Yasmin França
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | - Ellen Viana
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | | | | | - Raquel Guiducci
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | - Cibele Daniel Ribeiro
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | - Heloisa Rosa Vieira
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | | | - Mariana Sequetin Cunha
- Vector Borne Diseases Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | - Juliana Mariotti Guerra
- Quantitative Pathology Laboratory, Pathology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | | | | | - Emerson Luiz Lima Araújo
- General Coordination of Public Health, Laboratories of the Strategic Articulation, Department of the Health, Surveillance Secretariat, Ministry of Health (CGLAB/DAEVS/SVS-MS), Brasília, Brazil
| | | | | | | | | | - Cintia Mayumi Ahagon
- Blood and Sexual Diseases - Retrovirus Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | | | - Lia Cunha
- Hepatitis Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | - Vanessa Santos Morais
- Medical Parasitology Laboratory (LIM/46), Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Antonio Charlys da Costa
- Medical Parasitology Laboratory (LIM/46), Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Adriana Luchs
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil.
- Centro de Virologia, Núcleo de Doenças Entéricas, Instituto Adolfo Lutz, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brasil.
| |
Collapse
|
14
|
Leal É, Ribeiro ESD'A, Monteiro FJC, Marques JP, Dos Santos Mendes D, Morais VS, Araújo ELL, Pandey RP, Chang CM, Deng X, Delwart E, da Costa AC, Lima K. Aedes aegypti Totivirus identified in mosquitoes in the Brazilian Amazon region. Virus Genes 2023; 59:167-172. [PMID: 36394716 DOI: 10.1007/s11262-022-01955-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/31/2022] [Indexed: 11/19/2022]
Abstract
The totiviridae family contains viruses with double-stranded RNA genomes of 4.6-7.0 kpb, which encode a capsid protein (CP) and RNA-dependent RNA polymerase (RdRp), and they are approximately 40 nm in diameter with icosahedral symmetry. Totiviruses were first isolated from mosquitoes collected in Shaanxi Province (China). Here, we report a new Aedes aegypti Totivirus (AaTV) identified in mosquitoes from the Amazon rainforest. Mosquitoes (Diptera: Culicidae) were collected from a forest reserve belonging to the Amazon forest in the city of Macapá, Amapá state, Northern Brazil. A viral sequence with a 5748 nucleotide length that was nearly identical to Aedes aegypti Totivirus (AaTV), here named Aedes aegypti Totivirus BR59AP, was detected. A detailed molecular analysis was performed and shows that AaTV-BR59AP is highly related to the AaTV strain from the Caribbean region. We emphasize the importance of the characterization of new viruses in mosquitoes to deepen our understanding of viral diversity in insects and their potential role in disease.
Collapse
Affiliation(s)
- Élcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal Do Pará, Belem, Pará, 66075-000, Brazil
| | | | - Fred Julio Costa Monteiro
- Public Health Laboratory of Amapa-LACEN/AP, Health Surveillance Superintendence of Amapa, Macapa, 68905-230, Brazil
| | - Julia Pantoja Marques
- Public Health Laboratory of Amapa-LACEN/AP, Health Surveillance Superintendence of Amapa, Macapa, 68905-230, Brazil
| | - Diuliana Dos Santos Mendes
- Public Health Laboratory of Amapa-LACEN/AP, Health Surveillance Superintendence of Amapa, Macapa, 68905-230, Brazil
| | - Vanessa S Morais
- Faculdade de Medicina, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, 05403-000, Brazil
| | - Emerson Luiz Lima Araújo
- General Coordination of Public Health Laboratories of the Strategic Articulation, Department of the Health Surveillance, Secretariat of the Ministry of Health (CGLAB/DAEVS/SVS-MS), Brasília, 70719-040, Brazil
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat, Haryana, 131029, India
| | - Chung-Ming Chang
- Master & Ph.D. Program in Biotechnology Industry, Chang Gung University, No.259, Wenhua 1St Rd., Guishan Dist, Taoyuan, 33302, Taiwan, ROC
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, 94118-4417, USA.,Department Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, 94118-4417, USA.,Department Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Antonio Charlys da Costa
- Faculdade de Medicina, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, 05403-000, Brazil
| | - Kledoaldo Lima
- Hospital das Clínicas, Federal University of Pernambuco, Recife, PE, 50670-901, Brazil. .,European Virus Bioinformatics Center, Leutragraben 1, 07743, Jena, Germany. .,Faculdade Pernambucana de Saúde, Recife, PE, 51150-000, Brazil.
| |
Collapse
|
15
|
Kumar S, Dhiman R, Prudencio CR, da Costa AC, Vibhuti A, Leal E, Chang CM, Raj VS, Pandey RP. Chitosan: Applications in Drug Delivery System. Mini Rev Med Chem 2023; 23:187-191. [PMID: 35692143 DOI: 10.2174/1389557522666220609102010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/01/2022] [Accepted: 01/27/2022] [Indexed: 11/22/2022]
Abstract
Chitin and chitosan have unique structures with significant functional groups carrying useful chemical capabilities. Chitin and chitosan are acknowledged as novel biomaterials with advantageous biocompatibility and biodegradability. Chitosan is a polysaccharide that is made from chitin. There have been several attempts to employ this biopolymer in the biomedical area. This material's application in the production of artificial skin, drug targeting, and other areas is explored. The most prevalent strategies for recovering chitin from sea organisms are described and various pharmacological and biological uses are discussed. This review article targets drug delivery with the help of chitosan derived nanomaterial. The drug delivery system applications through nonmaterial have encountered a considerable role in the pharmaceutical, medical, biological, and other sectors in recent years. Nanomaterials have advanced applications as novel drug delivery systems in many fields, especially in industry, biology, and medicine. In the biomedical and pharmaceutical arena, the natural polymer-based nanoparticulate method has now been widely studied as particulate vehicles. By mixing alginate with other biopolymers, by immobilizing specific molecules such as sugar molecules and peptides by chemical or physical cross-linking, different properties and structures such as biodegradability, gelling properties, mechanical strength, and cell affinity can be obtained. Owing to their inherent ability to deliver both hydrophilic and hydrophobic drug molecules, increase stability, decrease toxicity, and enhance commonly formulated medications, these particles are now widely used in imaging and molecular diagnostics, cosmetics, household chemicals, sunscreens, radiation safety, and novel drug delivery.
Collapse
Affiliation(s)
- Suresh Kumar
- National Institute of Biologicals, Ministry of Health & Family Welfare, Govt. of India, India
| | - Ruby Dhiman
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi, Haryana, India
| | | | | | - Arpana Vibhuti
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi, Haryana, India
| | - Elcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem, Pará, Brazil, 66075-000, Brazil
| | - Chung-Ming Chang
- Biotechnology Industry, Chang Gung University, No.259, Wenhua, Taoyuan City 33302, Taiwan (R.O.C.)
| | - Vethakkani Samuel Raj
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi, Haryana, India
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi, Haryana, India
| |
Collapse
|
16
|
Villanova F, Milagres FADP, Brustulin R, Araújo ELL, Pandey RP, Raj VS, Deng X, Delwart E, Luchs A, da Costa AC, Leal É. A New Circular Single-Stranded DNA Virus Related with Howler Monkey Associated Porprismacovirus 1 Detected in Children with Acute Gastroenteritis. Viruses 2022; 14:v14071472. [PMID: 35891454 PMCID: PMC9319269 DOI: 10.3390/v14071472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/17/2022] [Accepted: 06/30/2022] [Indexed: 12/04/2022] Open
Abstract
Putative replication-associated protein (REP) and capsid-like (CAP) proteins are encoded by circular single-stranded DNA viruses (CRESS DNA), which have been found in samples from most eukaryotic groups. However, the details of these viruses’ life cycles and their significance in diseases have yet to be established. We presented and analyzed two full-length CRESS DNA genomes acquired from two children diagnosed with acute gastroenteritis (GI) in the northeast state of Tocantins, Brazil, using next-generation sequencing and a virus-like filtration approach. Both sequences (named SmaCV3BR08 and SmaCV3BR291) are closely similar to a prior CRESS DNA sequence discovered in the feces of a new world monkey (Alouatta caraya) from the United States in 2009 and termed Howler monkey-associated porprismacovirus 1 (Genbank ID: NC 026317). According to our comparative study, these porprismacovirus genomes deviate by 10% at the nucleotide level. For comparative reasons, the divergence between our sequences (SmaCV3BR08 and SmaCV3BR291) and a porprismacovirus recently identified in a human fecal sample from Peru is 37%. These data suggest that there is a great diversity of porprismacoviruses in South America, perhaps more than two species. In addition, the finding of closely related sequences of porprismacoviruses in humans and native monkeys highlights the zoonotic potential of these viruses.
Collapse
Affiliation(s)
- Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Pará, Brazil;
| | - Flávio Augusto de Padua Milagres
- Secretary of Health of Tocantins, Palmas 77453-000, Tocantins, Brazil; (F.A.d.P.M.); (R.B.)
- Public Health Laboratory of Tocantins State (LACEN/TO), Palmas 77016-330, Tocantins, Brazil
| | - Rafael Brustulin
- Secretary of Health of Tocantins, Palmas 77453-000, Tocantins, Brazil; (F.A.d.P.M.); (R.B.)
| | - Emerson Luiz Lima Araújo
- General Coordination of Public Health Laboratories of the Strategic Articulation Department of the Health Surveillance Secretariat of the Ministry of Health (CGLAB/DAEVS/SVS-MS), Brasília 70719-040, Distrito Federal, Brazil;
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India; (R.P.P.); (V.S.R.)
| | - V. Samuel Raj
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India; (R.P.P.); (V.S.R.)
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94118, USA; (X.D.); (E.D.)
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94118, USA; (X.D.); (E.D.)
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Adriana Luchs
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo 01246-000, São Paulo, Brazil;
| | - Antonio Charlys da Costa
- Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, São Paulo, Brazil;
| | - Élcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Pará, Brazil;
- Correspondence:
| |
Collapse
|
17
|
de Oliveira Ribeiro G, Gill DE, do Socorro Foro Ramos E, Villanova F, Soares D’Athaide Ribeiro E, Monteiro FJC, Morais VS, Rego MODS, Araújo ELL, Pandey RP, Raj VS, Deng X, Delwart E, da Costa AC, Leal É. Chikungunya Virus Asian Lineage Infection in the Amazon Region Is Maintained by Asiatic and Caribbean-Introduced Variants. Viruses 2022; 14:v14071445. [PMID: 35891427 PMCID: PMC9319912 DOI: 10.3390/v14071445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/22/2022] [Accepted: 06/25/2022] [Indexed: 02/04/2023] Open
Abstract
The simultaneous transmission of two lineages of the chikungunya virus (CHIKV) was discovered after the pathogen’s initial arrival in Brazil. In Oiapoque (Amapá state, north Brazil), the Asian lineage (CHIKV-Asian) was discovered, while in Bahia state, the East-Central-South-African lineage (CHIKV-ECSA) was discovered (northeast Brazil). Since then, the CHIKV-Asian lineage has been restricted to the Amazon region (mostly in the state of Amapá), whereas the ECSA lineage has expanded across the country. Despite the fact that the Asian lineage was already present in the Amazon region, the ECSA lineage brought from the northeast caused a large outbreak in the Amazonian state of Roraima (north Brazil) in 2017. Here, CHIKV spread in the Amazon region was studied by a Zika–Dengue–Chikungunya PCR assay in 824 serum samples collected between 2013 and 2016 from individuals with symptoms of viral infection in the Amapá state. We found 11 samples positive for CHIKV-Asian, and, from these samples, we were able to retrieve 10 full-length viral genomes. A comprehensive phylogenetic study revealed that nine CHIKV sequences came from a local transmission cluster related to Caribbean strains, whereas one sequence was related to sequences from the Philippines. These findings imply that CHIKV spread in different ways in Roraima and Amapá, despite the fact that both states had similar climatic circumstances and mosquito vector frequencies.
Collapse
Affiliation(s)
- Geovani de Oliveira Ribeiro
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Brazil; (G.d.O.R.); (E.d.S.F.R.); (F.V.)
| | - Danielle Elise Gill
- Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil; (D.E.G.); (V.S.M.); (A.C.d.C.)
| | - Endrya do Socorro Foro Ramos
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Brazil; (G.d.O.R.); (E.d.S.F.R.); (F.V.)
| | - Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Brazil; (G.d.O.R.); (E.d.S.F.R.); (F.V.)
| | - Edcelha Soares D’Athaide Ribeiro
- Public Health Laboratory of Amapa-LACEN/AP, Health Surveillance Superintendence of Amapa, Macapa 68905-230, Brazil; (E.S.D.R.); (F.J.C.M.); (M.O.d.S.R.)
| | - Fred Julio Costa Monteiro
- Public Health Laboratory of Amapa-LACEN/AP, Health Surveillance Superintendence of Amapa, Macapa 68905-230, Brazil; (E.S.D.R.); (F.J.C.M.); (M.O.d.S.R.)
| | - Vanessa S. Morais
- Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil; (D.E.G.); (V.S.M.); (A.C.d.C.)
| | - Marlisson Octavio da S. Rego
- Public Health Laboratory of Amapa-LACEN/AP, Health Surveillance Superintendence of Amapa, Macapa 68905-230, Brazil; (E.S.D.R.); (F.J.C.M.); (M.O.d.S.R.)
| | - Emerson Luiz Lima Araújo
- General Coordination of Public Health, Laboratories of the Strategic Articulation, Department of the Health Surveillance Secretariat of the Ministry of Health (CGLAB/DAEVS/SVS-MS), Brasília 70719-040, Brazil;
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India; (R.P.P.); (V.S.R.); (E.D.)
| | - V. Samuel Raj
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India; (R.P.P.); (V.S.R.); (E.D.)
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94118, USA;
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118, USA
| | - Eric Delwart
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India; (R.P.P.); (V.S.R.); (E.D.)
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94118, USA;
| | - Antonio Charlys da Costa
- Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil; (D.E.G.); (V.S.M.); (A.C.d.C.)
| | - Élcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Brazil; (G.d.O.R.); (E.d.S.F.R.); (F.V.)
- Correspondence:
| |
Collapse
|
18
|
Mirahmadizadeh A, Semati A, Heiran A, Ebrahimi M, Hemmati A, Karimi M, Basir S, Zare M, Charlys da Costa A, Zeinali M, Sargolzaee M, Eilami O. Efficacy of single-dose and double-dose ivermectin early treatment in preventing progression to hospitalization in mild COVID-19: A multi-arm, parallel-group randomized, double-blind, placebo-controlled trial. Respirology 2022; 27:758-766. [PMID: 35738778 PMCID: PMC9350312 DOI: 10.1111/resp.14318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/13/2022] [Indexed: 12/02/2022]
Abstract
Background and objective Ivermectin is a known anti‐parasitic agent that has been investigated as an antiviral agent against coronavirus disease 2019 (COVID‐19). This study aimed to evaluate the efficacy of ivermectin in mild COVID‐19 patients. Methods In this multi‐arm randomized clinical trial conducted between 9 April 2021 and 20 May 2021, a total of 393 patients with reverse transcription‐PCR‐confirmed COVID‐19 infection and mild symptoms were enrolled. Subjects were randomized in a 1:1:1 ratio to receive single‐dose ivermectin (12 mg), double‐dose ivermectin (24 mg) or placebo. The primary outcome was need for hospitalization. Results There was no significant difference in the proportion of subjects who required hospitalization between the placebo and single‐dose ivermectin groups (absolute difference in the proportions: −2.3 [95% CI = −8.5, 4.1]) and between the placebo and double‐dose ivermectin groups (absolute difference in the proportions: −3.9 [95% CI = −9.8, 2.2]). The odds of differences in mean change in severity score between single‐dose ivermectin and placebo groups (ORdifference = 1.005 [95% CI: 0.972, 1.040]; p = 0.762) and double‐dose ivermectin and placebo groups (ORdifference = 1.010 [95% CI: 0.974, 1.046]; p = 0.598) were not statistically significant. None of the six adverse events (including mild dermatitis, tachycardia and hypertension) were serious and required extra action. Conclusion Single‐dose and double‐dose ivermectin early treatment were not superior to the placebo in preventing progression to hospitalization and improving clinical course in mild COVID‐19. We conducted a double‐blinded randomized placebo‐controlled trial including 393 patients with mild coronavirus disease 2019 (COVID‐19) and found that ivermectin, an anti‐parasitic medication with known antiviral properties, was non‐superior to the placebo. Neither a single nor a double dose was better in preventing progression to hospitalization and worsening of the clinical course of COVID‐19 infection.
Collapse
Affiliation(s)
- Alireza Mirahmadizadeh
- Non-communicable Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Semati
- Non-communicable Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Alireza Heiran
- Non-communicable Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mostafa Ebrahimi
- Communicable Diseases Control Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abdolrasool Hemmati
- Department of Health Affairs, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammadreza Karimi
- Department of Health Affairs, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Souzan Basir
- Shiraz University of Medical Sciences, Shiraz, Iran
| | - Marjan Zare
- Non-communicable Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Mohammad Zeinali
- National Zoonoses Control Department, Ministry of Health and Medical Education, Tehran, Iran
| | - Maryam Sargolzaee
- Communicable Diseases Control Center, Ministry of Health and Medical Education, Tehran, Iran
| | - Owrang Eilami
- Department of Family Medicine and Infectious Diseases, Shiraz University of Medical Sciences, Shiraz, Iran
| |
Collapse
|
19
|
Barbosa MRF, Garcia SC, Bruni ADC, Machado FS, de Oliveira RX, Dropa M, da Costa AC, Leal E, Brandão CJ, da Silva RLO, Iko BY, Kondo VKM, de Araújo RS, da Silveira VB, de Andrade TM, Nunes DR, Janini LMR, Braconi CT, Maricato JT, Sato MIZ. One-year surveillance of SARS-CoV-2 in wastewater from vulnerable urban communities in metropolitan São Paulo, Brazil. J Water Health 2022; 20:471-490. [PMID: 36366999 DOI: 10.2166/wh.2022.210] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The current COVID-19 pandemic has emphasized the vulnerability of communities living in the urban outskirts and informal settlements. The lack of reliable COVID-19 case data highlights the importance and application of wastewater-based epidemiology. This study aimed to monitor the COVID-19 trends in four vulnerable urban communities (slums and low-income neighborhoods) in metropolitan São Paulo by assessing the SARS-CoV-2 RNA viral load in wastewater. We analyzed 160 samples from May 2020 to June 2021 with weekly or fortnightly samplings. The samples were ultracentrifuged with glycine elution and quantified by N1/N2 SARS-CoV-2 RT-qPCR. The results of positivity were 100% (Paraisópolis, Heliópolis and Cidade Tiradentes) and 76.9% (Vila Brasilândia). The new case numbers of COVID-19, counted from the onset of symptoms, positively correlated with SARS-CoV-2 N1 viral loads from the two largest communities (p<0.001). SARS-CoV-2 infectivity was tested in Vero E6 cells after concentration with the two techniques, ultrafiltration (Centricon® Plus-70 10 kDa) and sucrose cushion ultracentrifugation, but none of the evaluated samples presented positive results. Next-generation sequencing (NGS) analysis from samples collected in March and August 2021 revealed the presence of the clade 20 J (lineage P.1) belonging to the most prevalent circulating variant in the country. Our results showed that wastewater surveillance data can be used as complementary indicators to monitor the dynamics and temporal trends of COVID-19. The infectivity test results strengthened the evidence of low risk of infection associated with SARS-CoV-2 in wastewater.
Collapse
Affiliation(s)
- Mikaela Renata Funada Barbosa
- Department of Environmental Analysis, Division of Microbiology and Parasitology, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo, CEP 05459-900, Brazil E-mail:
| | - Suzi Cristina Garcia
- Department of Environmental Analysis, Division of Microbiology and Parasitology, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo, CEP 05459-900, Brazil E-mail:
| | - Antonio de Castro Bruni
- Department of Environmental Analysis, Division of Microbiology and Parasitology, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo, CEP 05459-900, Brazil E-mail:
| | | | - Roberto Xavier de Oliveira
- Department of Environmental Analysis, Division of Microbiology and Parasitology, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo, CEP 05459-900, Brazil E-mail:
| | - Milena Dropa
- School of Public Health, Universidade de São Paulo (USP), São Paulo, Brazil
| | | | - Elcio Leal
- Institute of Biological Sciences, Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Carlos Jesus Brandão
- Department of Environmental Analysis, Division of Microbiology and Parasitology, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo, CEP 05459-900, Brazil E-mail:
| | - Renan Lourenço Oliveira da Silva
- Department of Environmental Analysis, Division of Microbiology and Parasitology, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo, CEP 05459-900, Brazil E-mail:
| | - Beatriz Yukie Iko
- Department of Environmental Analysis, Division of Microbiology and Parasitology, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo, CEP 05459-900, Brazil E-mail:
| | - Victor Kenji Matsuoka Kondo
- Department of Environmental Analysis, Division of Microbiology and Parasitology, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo, CEP 05459-900, Brazil E-mail:
| | - Ronalda Silva de Araújo
- Department of Environmental Analysis, Division of Microbiology and Parasitology, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo, CEP 05459-900, Brazil E-mail:
| | - Vanessa Barbosa da Silveira
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, (UNIFESP), São Paulo, Brazil
| | - Tatiane Montes de Andrade
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, (UNIFESP), São Paulo, Brazil
| | - Danilo Rosa Nunes
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, (UNIFESP), São Paulo, Brazil
| | - Luiz Mário Ramos Janini
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, (UNIFESP), São Paulo, Brazil
| | - Carla Torres Braconi
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, (UNIFESP), São Paulo, Brazil
| | - Juliana Terzi Maricato
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, (UNIFESP), São Paulo, Brazil
| | - Maria Inês Zanoli Sato
- Department of Environmental Analysis, Division of Microbiology and Parasitology, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo, CEP 05459-900, Brazil E-mail:
| |
Collapse
|
20
|
Luchs A, Azevedo LSD, Souza EVD, Medeiros RS, Souza YFVPD, Teixeira DLF, Carneiro TFDO, Alencar GMFD, Morais FLDSL, Pinto DDFA, Okay TS, Yamamoto L, Morais VDS, Araújo ELL, Leal E, Costa ACD. Coxsackievirus A6 strains causing an outbreak of hand-foot-and-mouth disease in Northeastern Brazil in 2018. Rev Inst Med Trop Sao Paulo 2022; 64:e16. [PMID: 35195198 PMCID: PMC8862545 DOI: 10.1590/s1678-9946202264016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/24/2022] [Indexed: 12/13/2022] Open
Abstract
Hand-foot-and-mouth disease (HFMD) is a highly contagious viral disease commonly
associated to Enteroviruses (EV). During 2018, Brazil faced massive HFMD
outbreaks spread across the country. This study aimed to characterize the EV
responsible for the HFMD outbreak that occurred in Paraiba State, Brazilian
Northeastern region, in 2018, followed by a phylogenetic analysis to detail
information on its genetic diversity. A total of 49 serum samples (one from each
patient) collected from children ≤ 15 years old, clinically diagnosed with HFMD
were tested for EV using conventional RT-PCR and RT-qPCR. EV infection was
confirmed in 71.4% (35/49) of samples. The mean and median ages were 1.83 years
and one year old, respectively. Twenty-two EV-positive samples were successfully
sequenced and classified as EV-A species; 13 samples were also identified with
the CV-A6 genotype. The phylogenetic analysis (VP1 region) of three samples
revealed that the detected CV-A6 strains belonged to sub-lineage D3. The CV-A6
strains detected here clustered with strains from South America, Europe and West
Asia strains that were also involved in HFMD cases during the 2017-2018 seasons,
in addition to the previously detected Brazilian CV-A6 strains from 2012 to
2017, suggesting a global co-circulation of a set of different CV-A6 strains
introduced in the country at different times. The growing circulation of the
emerging CV-A6 associated with HFMD, together with the detection of more severe
cases worldwide, suggests the need for a more intense surveillance system of
HFMD in Brazil. In addition, this investigation was performed exclusively on
serum samples, and the analysis of whole blood samples should be considered and
could have shown advantages when employed in the diagnosis of enteroviral HFMD
outbreaks.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Thelma Suely Okay
- Universidade de São Paulo, Brazil; Universidade de São Paulo, Brazil
| | | | | | | | | | | |
Collapse
|
21
|
Carvalho Reis AP, Valério Silva Moreira D, Barbaro Del Negro GM, Charlys da Costa A, Benard G, Teixeira Sousa MG, Veasey JV. A case of cutaneous phaeohyphomycosis caused by Biatriospora mackinnonii. Med Mycol Case Rep 2021; 34:32-34. [PMID: 34745853 PMCID: PMC8556491 DOI: 10.1016/j.mmcr.2021.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/27/2021] [Accepted: 10/11/2021] [Indexed: 11/07/2022] Open
Abstract
Phaeohyphomycosis is a fungal infection common in immunocompromised patients such as those with hematologic malignancies, transplant recipients or under prolonged corticosteroid use. Here we describe a rare case of phaeohyphomycosis due to Biatriospora mackinnonii in a kidney transplant patient. We confirmed B. mackinnonii identity by sequencing of the internal transcribed spaces (ITS) region of ribosomal DNA (rDNA) and achieved a satisfactory therapeutic response with itraconazole administration.
Collapse
Affiliation(s)
- Ana Paula Carvalho Reis
- Universidade de São Paulo, Instituto de Medicina Tropical, Laboratório de Micologia Médica, São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Divisão de Clínica Dermatológica, Laboratório de Investigação Médica LIM 53, São Paulo, São Paulo, Brazil
| | - Daniel Valério Silva Moreira
- Universidade de São Paulo, Instituto de Medicina Tropical, Laboratório de Micologia Médica, São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Divisão de Clínica Dermatológica, Laboratório de Investigação Médica LIM 53, São Paulo, São Paulo, Brazil
| | - Gilda Maria Barbaro Del Negro
- Universidade de São Paulo, Instituto de Medicina Tropical, Laboratório de Micologia Médica, São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Divisão de Clínica Dermatológica, Laboratório de Investigação Médica LIM 53, São Paulo, São Paulo, Brazil
| | - Antonio Charlys da Costa
- Universidade de São Paulo, Instituto de Medicina Tropical, Laboratório de Micologia Médica, São Paulo, São Paulo, Brazil
| | - Gil Benard
- Universidade de São Paulo, Instituto de Medicina Tropical, Laboratório de Micologia Médica, São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Divisão de Clínica Dermatológica, Laboratório de Investigação Médica LIM 53, São Paulo, São Paulo, Brazil
| | - Maria Gloria Teixeira Sousa
- Universidade de São Paulo, Instituto de Medicina Tropical, Laboratório de Micologia Médica, São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Divisão de Clínica Dermatológica, Laboratório de Investigação Médica LIM 53, São Paulo, São Paulo, Brazil
| | | |
Collapse
|
22
|
Luchs A, Tardy K, Tahmasebi R, Morillo SG, Milagres FADP, Morais VDS, Brustulin R, Teles MDAR, de Azevedo LS, de Souza EV, Medeiros RS, de Souza YFVP, Araújo ELL, Witkin SS, Deng X, Delwart E, Sabino EC, Leal E, da Costa AC. Human astrovirus types 1, 4 and 5 circulating among children with acute gastroenteritis in a rural Brazilian state, 2010-2016. Arch Virol 2021; 166:3165-3172. [PMID: 34417874 DOI: 10.1007/s00705-021-05206-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/22/2021] [Indexed: 11/30/2022]
Abstract
This study combined conventional epidemiology of human astroviruses. From 2010 to 2016, 232 stool samples from children under 5 years of age were screened using NGS and conventional RT-PCR followed by genetic analysis in order to investigate the genotypic diversity of classical human astrovirus (HAstV) circulating in Tocantins State, Brazil. HAstV was detected in 16 cases (6.9%). Seven specimens (43.7%; 7/16) were positive according RT-PCR and next-generation sequencing (NGS) to investigate the molecular to both NGS and RT-PCR. NGS and RT-PCR individually revealed six (37.5%; 6/16) and three (18.8%; 3/16) additional positive samples, respectively. Sequencing of the HAstV-positive samples revealed HAstV-1a (9/16), HAstV-4c (3/16), and HAstV-5c (4/16) lineages.
Collapse
Affiliation(s)
- Adriana Luchs
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil.
| | - Kaelan Tardy
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil
| | - Roozbeh Tahmasebi
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil
| | - Simone Guadagnucci Morillo
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil
| | - Flavio Augusto de Pádua Milagres
- Universidade Federal do Tocantins, Tocantins, Brazil.,Laboratório Central de Saúde Pública do Tocantins (Lacen-TO), Tocantins, Brazil
| | - Vanessa Dos Santos Morais
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil
| | - Rafael Brustulin
- Universidade Federal do Tocantins, Tocantins, Brazil.,Laboratório Central de Saúde Pública do Tocantins (Lacen-TO), Tocantins, Brazil
| | | | - Lais Sampaio de Azevedo
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil
| | - Ellen Viana de Souza
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil
| | - Roberta Salzone Medeiros
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil
| | | | - Emerson Luiz Lima Araújo
- Coordenação Geral de Laboratórios de Saúde Pública, Departamento de Articulação Estratégica de Vigilância em Saúde da Secretaria de Vigilância em Saúde do Ministério da Saúde do Brasil (CGLAB/DAEVS/SVS-MS), Brasília, Brazil
| | - Steven S Witkin
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil.,Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, USA
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, USA.,Department Laboratory Medicine, University of California San Francisco, San Francisco, USA
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, USA.,Department Laboratory Medicine, University of California San Francisco, San Francisco, USA
| | - Ester Cerdeira Sabino
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil
| | - Elcio Leal
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Pará, Brazil
| | - Antonio Charlys da Costa
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil.
| |
Collapse
|
23
|
Villanova F, Marcatti R, Bertanhe M, Morais VDS, Milagres FADP, Brustulin R, Araújo ELL, Tahmasebi R, Witkin SS, Deng X, Delwart E, Sabino EC, Abreu-Junior CH, Leal É, da Costa AC. New Variants of Squash Mosaic Viruses Detected in Human Fecal Samples. Microorganisms 2021; 9:microorganisms9071349. [PMID: 34206387 PMCID: PMC8307838 DOI: 10.3390/microorganisms9071349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/02/2021] [Accepted: 06/06/2021] [Indexed: 11/16/2022] Open
Abstract
Squash mosaic virus (SqMV) is a phytovirus that infects great diversity of plants worldwide. In Brazil, the SqMV has been identified in the states of Ceará, Maranhão, Piauí, Rio Grande do Norte, and Tocantins. The presence of non-pathogenic viruses in animals, such as phytoviruses, may not be completely risk-free. Similarities in gene repertories between these viruses and viruses that affect animal species have been reported. The present study describes the fully sequenced genomes of SqMV found in human feces, collected in Tocantins, and analyzes the viral profile by metagenomics in the context of diarrhea symptomatology. The complete SqMV genome was obtained in 39 of 253 analyzed samples (15.5%); 97.4% of them belonged to children under 5 years old. There was no evidence that the observed symptoms were related to the presence of SqMV. Of the different virus species detected in these fecal samples, at least 4 (rotavirus, sapovirus, norovirus, parechovirus) are widely known to cause gastrointestinal symptoms. The presence of SqMV nucleic acid in fecal samples is likely due to recent dietary consumption and it is not evidence of viral replication in the human intestinal cells. Identifying the presence of SqMV in human feces and characterization of its genome is a relevant precursor to determining whether and how plant viruses interact with host cells or microorganisms in the human gastrointestinal tract.
Collapse
Affiliation(s)
- Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil;
| | - Roberta Marcatti
- Departamento de Moléstias Infecciosas e Parasitárias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (R.M.); (M.B.); (V.d.S.M.); (R.T.); (S.S.W.); (E.C.S.); (A.C.d.C.)
| | - Mayara Bertanhe
- Departamento de Moléstias Infecciosas e Parasitárias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (R.M.); (M.B.); (V.d.S.M.); (R.T.); (S.S.W.); (E.C.S.); (A.C.d.C.)
- School of Veterinary Medicine and Animal Science, University of Sao Paulo, São Paulo 05508-270, SP, Brazil
| | - Vanessa dos Santos Morais
- Departamento de Moléstias Infecciosas e Parasitárias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (R.M.); (M.B.); (V.d.S.M.); (R.T.); (S.S.W.); (E.C.S.); (A.C.d.C.)
| | - Flavio Augusto de Padua Milagres
- Instituto de Ciências Biológicas, Universidade Federal do Tocantins, Palmas 77001-090, TO, Brazil; (F.A.d.P.M.); (R.B.)
- Public Health Laboratory of Tocantins State (LACEN/TO), Palmas 77016-330, TO, Brazil
| | - Rafael Brustulin
- Instituto de Ciências Biológicas, Universidade Federal do Tocantins, Palmas 77001-090, TO, Brazil; (F.A.d.P.M.); (R.B.)
- Public Health Laboratory of Tocantins State (LACEN/TO), Palmas 77016-330, TO, Brazil
| | - Emerson Luiz Lima Araújo
- General Coordination of Public Health, Laboratories of the Strategic Articulation, Department of the Health, Surveillance Secretariat, Ministry of Health (CGLAB/DAEVS/SVS-MS), Brasília 70719-040, DF, Brazil;
| | - Roozbeh Tahmasebi
- Departamento de Moléstias Infecciosas e Parasitárias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (R.M.); (M.B.); (V.d.S.M.); (R.T.); (S.S.W.); (E.C.S.); (A.C.d.C.)
| | - Steven S. Witkin
- Departamento de Moléstias Infecciosas e Parasitárias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (R.M.); (M.B.); (V.d.S.M.); (R.T.); (S.S.W.); (E.C.S.); (A.C.d.C.)
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94143, USA; (X.D.); (E.D.)
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94143, USA; (X.D.); (E.D.)
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Ester Cerdeira Sabino
- Departamento de Moléstias Infecciosas e Parasitárias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (R.M.); (M.B.); (V.d.S.M.); (R.T.); (S.S.W.); (E.C.S.); (A.C.d.C.)
| | | | - Élcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil;
- Correspondence:
| | - Antonio Charlys da Costa
- Departamento de Moléstias Infecciosas e Parasitárias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (R.M.); (M.B.); (V.d.S.M.); (R.T.); (S.S.W.); (E.C.S.); (A.C.d.C.)
| |
Collapse
|
24
|
Rocha LCD, Estofolete CF, Milhim BHGDA, Augusto MT, Zini N, Silva GCDD, Ferraz-Junior HC, Brienze VMS, Liso E, Cunha MS, Sabino EC, da Costa AC, Nogueira ML, Luchs A, Terzian ACB. Enteric viruses circulating in undiagnosed central nervous system infections at tertiary hospital in São José do Rio Preto, São Paulo, Brazil. J Med Virol 2021; 93:3539-3548. [PMID: 32579291 DOI: 10.1002/jmv.26216] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/15/2020] [Accepted: 06/20/2020] [Indexed: 12/18/2022]
Abstract
Enterovirus (EV) is commonly associated with central nervous system (CNS) syndromes. Recently, gastroenteric viruses, including rotavirus (RVA), human astrovirus (HAstV), and norovirus (NoV), have also been associated with CNS neurological disorders. The aim of the present study was to investigate the presence of EV, RVA, HAst, and NoV associated to CNS infections with undiagnosed etiology in Northwest region of São Paulo State, Brazil, and to conduct the molecular characterization of the positive samples detected. A total of 288 cerebrospinal fluid samples collected from July to December 2017 were tested for EV and NoV by quantitative real-time polymerase chain reaction (RT-qPCR), HAstV by conventional RT-PCR, and RVA by enzyme-linked immunosorbent assay. Positive-EV samples were inoculated in cells lines, amplified by RT-PCR and sequenced. RVA, NoV, and HAstV were not detected. EV infection was detected in 5.5% (16/288), and five samples successful genotyped: echovirus 3 (E3) (1/5), coxsackie virus A6 (CVA6) (1/5), and coxsackie virus B4 (CVB4) (3/5). Meningitis was the main syndrome observed (12/16; 75%). CVA6, CVB4, and E3 were identified associated with aseptic meningitis. Reports of CVA6 associated with aseptic meningitis are rare, E3 had not been previously reported in Brazil, and epidemiological data on CVB4 in the country is virtually unknown. The present investigation illustrates the circulation of diverse EV types in a small regional sample set and in a short period of time, highlighting the importance of an active EV surveillance system in CNS infections. Enhanced understanding of undiagnosed CNS infections will assist in public health and health care planning.
Collapse
Affiliation(s)
| | | | | | | | - Nathalia Zini
- São José do Rio Preto School of Medicine (FAMERP), São Paulo, Brazil
| | | | | | | | | | - Mariana Sequetin Cunha
- Vector Borne Disease Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | - Ester Cerdeira Sabino
- LIM/46, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
- Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil
| | | | | | - Adriana Luchs
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | | |
Collapse
|
25
|
Braz LMA, Tahmasebi R, da Costa AC, Witkin SS. Disparity between scientific accomplishment and biotechnology availability in Brazil. Sci Prog 2021; 104:368504211028373. [PMID: 34191659 PMCID: PMC10454951 DOI: 10.1177/00368504211028373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Despite being among the world's leaders in scientific output, Brazil ranks 66th among countries in the production of reagents and supplies needed for state-of-the-art scientific analyses. The production of needed reagents and equipment for experimental analyses and patient diagnostics is sorely lacking within Brazil and explicit in this pandemic period caused by SARS-CoV-2. A significant fraction of resources from Brazilian funding agencies is now being transferred to companies in other countries for the purchase of essential scientific-related products. Is this sustainable? Therefore it is necessary to draw the attention of all the world and Brazilian society about this situation.
Collapse
Affiliation(s)
- Lucia Maria Almeida Braz
- Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brasil
| | - Roozbeh Tahmasebi
- Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brasil
| | - Antonio Charlys da Costa
- Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brasil
| | - Steven S Witkin
- Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brasil
- Weill Cornell Medicine, New York, NY, USA
| |
Collapse
|
26
|
do Socorro Fôro Ramos E, Rosa UA, de Oliveira Ribeiro G, Villanova F, de Pádua Milagres FA, Brustulin R, Dos Santos Morais V, Bertanhe M, Marcatti R, Araújo ELL, Witkin SS, Delwart E, Luchs A, da Costa AC, Leal É. High Heterogeneity of Echoviruses in Brazilian Children with Acute Gastroenteritis. Viruses 2021; 13:v13040595. [PMID: 33807396 PMCID: PMC8067319 DOI: 10.3390/v13040595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/26/2021] [Accepted: 03/29/2021] [Indexed: 01/07/2023] Open
Abstract
Echoviruses (E) are a diverse group of viruses responsible for various pathological conditions in humans including aseptic meningitis, myocarditis, and acute flaccid paralysis. The detection and identification of echovirus genotypes in clinical samples is challenging due to its high genetic diversity. Here, we report the complete genome sequences of nine echoviruses, obtained by next-generation sequencing of 238 fecal samples from individuals with gastroenteritis in regions of Brazil. Detected viruses were classified into six genotypes: Three E1 sequences (BRA/TO-028, BRA/TO-069 and BRA/TO-236), one E3 (BRA/TO-018), one E11 (BRA/TO-086), one E20 (BRA/TO-016), two E29 (BRA/TO-030 and BRA/TO-193), and one E30 sequence (BRA/TO-032). Phylogenetic analysis indicated that the echoviruses E1 and E29 circulating in Brazil are divergent from strains circulating worldwide. The genotype diversity identified in our study may under-represent the total echovirus diversity in Brazil because of the small sample size and the restricted geographical distribution covered by the survey.
Collapse
Affiliation(s)
- Endrya do Socorro Fôro Ramos
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Pará, Brazil
| | - Ulisses Alves Rosa
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Pará, Brazil
| | - Geovani de Oliveira Ribeiro
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Pará, Brazil
| | - Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Pará, Brazil
| | - Flávio Augusto de Pádua Milagres
- Secretaria de Saúde do Tocantins, Palmas 77453-000, Tocantins, Brazil
- Laboratório Central de Saúde Pública do Tocantins (LACEN/TO), Palmas 77016-330, Tocantins, Brazil
| | - Rafael Brustulin
- Secretaria de Saúde do Tocantins, Palmas 77453-000, Tocantins, Brazil
| | - Vanessa Dos Santos Morais
- Departamento de Moléstias Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Mayara Bertanhe
- Departamento de Moléstias Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Roberta Marcatti
- Departamento de Moléstias Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Emerson Luiz Lima Araújo
- General Coordination of Public Health Laboratories of the Strategic Articulation, Department of the Health Surveillance Secretariat of the Ministry of Health (CGLAB/DAEVS/SVS-MS), Brasília 70719-040, Federal District, Brazil
| | - Steven S Witkin
- Departamento de Moléstias Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94143, USA
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Adriana Luchs
- Laboratório de Doenças Entéricas, Centro de Virologia, Instituto Adolfo Lutz, São Paulo 01246-000, Brazil
| | - Antonio Charlys da Costa
- Departamento de Moléstias Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Élcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Pará, Brazil
| |
Collapse
|
27
|
de Oliveira Ribeiro G, da Costa AC, Gill DE, Ribeiro ESD, Rego MODS, Monteiro FJC, Villanova F, Nogueira JS, Maeda AY, de Souza RP, Tahmasebi R, Morais VS, Pandey RP, Raj VS, Scandar SAS, da Silva Vasami FG, D'Agostino LG, Maiorka PC, Deng X, Nogueira ML, Sabino EC, Delwart E, Leal É, Cunha MS. Guapiaçu virus, a new insect-specific flavivirus isolated from two species of Aedes mosquitoes from Brazil. Sci Rep 2021; 11:4674. [PMID: 33633167 PMCID: PMC7907106 DOI: 10.1038/s41598-021-83879-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 02/03/2021] [Indexed: 12/18/2022] Open
Abstract
Classical insect-flaviviruses (cISFVs) and dual host-related insect-specific flavivirus (dISFV) are within the major group of insect-specific flavivirus. Remarkably dISFV are evolutionarily related to some of the pathogenic flavivirus, such as Zika and dengue viruses. The Evolutionary relatedness of dISFV to flavivirus allowed us to investigate the evolutionary principle of host adaptation. Additionally, dISFV can be used for the development of flavivirus vaccines and to explore underlying principles of mammalian pathogenicity. Here we describe the genetic characterization of a novel putative dISFV, termed Guapiaçu virus (GUAPV). Distinct strains of GUAPV were isolated from pools of Aedes terrens and Aedes scapularis mosquitoes. Additionally, we also detected viral GUAPV RNA in a plasma sample of an individual febrile from the Amazon region (North of Brazil). Although GUAPV did not replicate in tested mammalian cells, 3′UTR secondary structures duplication and codon usage index were similar to pathogenic flavivirus.
Collapse
Affiliation(s)
| | | | - Danielle Elise Gill
- Institute of Tropical Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil
| | - Edcelha Soares D'Athaide Ribeiro
- Public Health Laboratory of Amapa-LACEN/AP, Health Surveillance Superintendence of Amapa, Rua Tancredo Neves, 1.118, Macapá, AP, CEP 68905-230, Brazil
| | - Marlisson Octavio da S Rego
- Public Health Laboratory of Amapa-LACEN/AP, Health Surveillance Superintendence of Amapa, Rua Tancredo Neves, 1.118, Macapá, AP, CEP 68905-230, Brazil
| | - Fred Julio Costa Monteiro
- Public Health Laboratory of Amapa-LACEN/AP, Health Surveillance Superintendence of Amapa, Rua Tancredo Neves, 1.118, Macapá, AP, CEP 68905-230, Brazil
| | - Fabiola Villanova
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, 66075-000, Brazil
| | - Juliana Silva Nogueira
- Vector-Borne Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, SP, 01246-000, Brazil
| | - Adriana Yurika Maeda
- Vector-Borne Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, SP, 01246-000, Brazil
| | - Renato Pereira de Souza
- Vector-Borne Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, SP, 01246-000, Brazil
| | - Roozbeh Tahmasebi
- Institute of Tropical Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil
| | - Vanessa S Morais
- Institute of Tropical Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat, Haryana, India
| | - V Samuel Raj
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat, Haryana, India
| | | | | | | | - Paulo César Maiorka
- Department of Pathology, Faculty of Veterinary Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, 94118-4417, USA.,Department Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | | | - Ester Cerdeira Sabino
- Institute of Tropical Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, 94118-4417, USA. .,Department Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94143, USA.
| | - Élcio Leal
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, 66075-000, Brazil.
| | - Mariana Sequetin Cunha
- Institute of Tropical Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil. .,Vector-Borne Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, SP, 01246-000, Brazil.
| |
Collapse
|
28
|
Silva-Sales M, Leal E, Milagres FADP, Brustulin R, Morais VDS, Marcatti R, Araújo ELL, Witkin SS, Deng X, Sabino EC, Delwart E, Luchs A, Costa ACD. Genomic constellation of human Rotavirus A strains identified in Northern Brazil: a 6-year follow-up (2010-2016). Rev Inst Med Trop Sao Paulo 2020; 62:e98. [PMID: 33331517 PMCID: PMC7748031 DOI: 10.1590/s1678-9946202062098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 11/27/2020] [Indexed: 02/21/2023] Open
Abstract
Surveillance of Rotavirus A (RVA) throughout the national territory is important
to establish a more complete epidemiological-molecular scenario of this virus
circulation in Brazil. The aim of the present study was to investigate the
genetic diversity of RVA strains circulating in Tocantins State (Northern
Brazil) during six years of post-vaccination follow-up (2010-2016). A total of
248 stool samples were screened by next generation sequencing and 107 (43.1%)
nearly full length RVA genome sequences were obtained; one sample was
co-infected with two RVA strains (G2/G8P[4]). Six G and P genotypes combinations
were detected: G12P[8] strains (78.6%), as well as the G3P[8] (9.3%) and G1P[8]
(0.9%) were associated with a Wa-like genogroup backbone. All G2P[4] (5.6%) and
G8P[4] (2.8%) strains, including the mixed G2/G8P[4] infection (0.9%) showed the
DS-1-like genetic background. The two G12P[4] strains (1.9%) were associated
with distinct genetic backbones: Wa-like and DS-1-like. The phylogenetic
analysis revealed the circulation of lineages G1-I, G2-IV, G3-III, G8-I and
G12-III, and P[4]-V and P[8]-III of the VP7 and VP4 genes, respectively.
Conserved clustering pattern and low genetic diversity were observed regarding
VP1-VP3 and VP6, as well as NSP1-5 segments. We identified the same RVA
circulation pattern reported in other Brazilian regions in the period of
2010-2016, suggesting that rural and low-income areas may not have a different
RVA genotypic distribution compared to other parts of the country. The unique
presentation of whole-genome data of RVA strains detected in the Tocantins State
provides a baseline for monitoring variations in the genetic composition of RVA
in this area.
Collapse
Affiliation(s)
- Marcelle Silva-Sales
- Universidade Federal de Goiás, Instituto de Patologia Tropical e Saúde Pública, Laboratório de Virologia e Cultivo Celular, Goiânia, Goiás, Brazil
| | - Elcio Leal
- Universidade Federal do Pará, Instituto de Ciências Biológicas, Belém, Pará, Brazil
| | - Flavio Augusto de Pádua Milagres
- Universidade Federal do Tocantins, Palmas, Tocantins, Brazil.,Laboratório Central de Saúde Pública do Estado de Tocantins, Palmas, Tocantins, Brazil
| | - Rafael Brustulin
- Universidade Federal do Tocantins, Palmas, Tocantins, Brazil.,Laboratório Central de Saúde Pública do Estado de Tocantins, Palmas, Tocantins, Brazil
| | - Vanessa Dos Santos Morais
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Roberta Marcatti
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Emerson Luiz Lima Araújo
- Ministério da Saúde, Secretaria de Vigilância em Saúde, Departamento de Articulação Estratégica de Vigilância em Saúde, Coordenação Geral de Laboratórios de Saúde Pública, Brasília, Distrito Federal, Brazil
| | - Steven S Witkin
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil.,Weill Cornell Medicine, Department of Obstetrics and Gynecology, New York, New York, USA
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, California, USA.,University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, USA
| | - Ester Cerdeira Sabino
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, California, USA.,University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, USA
| | - Adriana Luchs
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, São Paulo, São Paulo, Brazil
| | - Antonio Charlys da Costa
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| |
Collapse
|
29
|
Tahmasebi R, Luchs A, Tardy K, Hefford PM, Tinker RJ, Eilami O, de Padua Milagres FA, Brustulin R, Teles MDAR, Dos Santos Morais V, Moreira CHV, Buccheri R, Araújo ELL, Villanova F, Deng X, Sabino EC, Delwart E, Leal É, Charlys da Costa A. Viral gastroenteritis in Tocantins, Brazil: characterizing the diversity of human adenovirus F through next-generation sequencing and bioinformatics. J Gen Virol 2020; 101:1280-1288. [PMID: 33044150 DOI: 10.1099/jgv.0.001500] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Human enteric adenovirus species F (HAdV-F) is one of the most common pathogens responsible for acute gastroenteritis worldwide. Brazil is a country with continental dimensions where continuous multiregional surveillance is vital to establish a more complete picture of the epidemiology of HAdV-F. The aim of the current study was to investigate the molecular epidemiology of HAdV-F using full-genome data in rural and low-income urban areas in northern Brazil. This will allow a genetic comparison between Brazilian and global HAdV-F strains. The frequency of HAdV-F infections in patients with gastroenteritis and molecular typing of positive samples within this period was also analysed. A total of 251 stool samples collected between 2010 and 2016 from patients with acute gastroenteritis were screened for HAdV-F using next-generation sequencing techniques. HAdV-F infection was detected in 57.8 % (145/251) of samples. A total of 137 positive samples belonged to HAdV-F41 and 7 to HAdV-F40. HAdV-F40/41 dual infection was found in one sample. Detection rates did not vary significantly according to the year. Single HAdV-F infections were detected in 21.9 % (55/251) of samples and mixed infections in 37.4 % (94/251), with RVA/HAdV-F being the most frequent association (21.5 %; 54/251). Genetic analysis indicated that the HAdV-F strains circulating in Brazil were closely related to worldwide strains, and the existence of some temporal order was not observed. This is the first large-scale HAdV-F study in Brazil in which whole-genome data and DNA sequence analyses were used to characterize HAdV-F strains. Expanding the viral genome database could improve overall genotyping success and assist the National Center for Biotechnology Information (NCBI)/GenBank in standardizing the HAdV genome records by providing a large set of annotated HAdV-F genomes.
Collapse
Affiliation(s)
- Roozbeh Tahmasebi
- Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo, Brazil.,Polytechnic School of University of Sao Paulo, Sao Paulo, Brazil
| | - Adriana Luchs
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | - Kaelan Tardy
- Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Rory J Tinker
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
| | - Owrang Eilami
- School of Medicine Social, Determinants of Health Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Flavio Augusto de Padua Milagres
- Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins, Brazil.,Secretary of Health of Tocantins, Tocantins, Brazil.,Institute of Biological Sciences, Federal University of Tocantins, Tocantins, Brazil
| | - Rafael Brustulin
- Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins, Brazil.,Institute of Biological Sciences, Federal University of Tocantins, Tocantins, Brazil.,Secretary of Health of Tocantins, Tocantins, Brazil
| | | | | | | | - Renata Buccheri
- Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Emerson Luiz Lima Araújo
- General Coordination of Public Health Laboratories of the Strategic Articulation Department of the Health Surveillance Secretariat of the Ministry of Health (CGLAB/DAEVS/SVS-MS), Brasília, DF, Brazil
| | - Fabiola Villanova
- Institute of Biological Sciences, Federal University of Para, Para, Brazil
| | - Xutao Deng
- Department Laboratory Medicine, University of California San Francisco, San Francisco, California, USA.,Vitalant Research Institute, San Francisco, California, USA
| | - Ester Cerdeira Sabino
- Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo, Brazil.,Polytechnic School of University of Sao Paulo, Sao Paulo, Brazil
| | - Eric Delwart
- Department Laboratory Medicine, University of California San Francisco, San Francisco, California, USA.,Vitalant Research Institute, San Francisco, California, USA
| | - Élcio Leal
- Institute of Biological Sciences, Federal University of Para, Para, Brazil
| | | |
Collapse
|
30
|
Ribeiro GDO, Morais VS, Monteiro FJC, Ribeiro ESD, Rego MODS, Souto RNP, Villanova F, Tahmasebi R, Hefford PM, Deng X, Delwart E, Cerdeira Sabino E, Fernandes LN, da Costa AC, Leal É. Aedes aegypti from Amazon Basin Harbor High Diversity of Novel Viral Species. Viruses 2020; 12:E866. [PMID: 32784421 PMCID: PMC7472207 DOI: 10.3390/v12080866] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/25/2020] [Accepted: 08/03/2020] [Indexed: 11/25/2022] Open
Abstract
Viruses are the most diverse and abundant microorganisms on earth, highly adaptive to a wide range of hosts. Viral diversity within invertebrate hosts has gained notoriety in recent years in public health as several such viruses have been of medical importance. Aedes aegypti serves as a vector for several viruses that have caused epidemics within the last year throughout Brazil; including Dengue, Zika and Chikungunya. This study aimed to identify new viral agents within Aedes aegypti mosquito in a city of the Amazonian region, where it is highly endemic. Metagenomic investigation was performed on 60 mosquito pools and viral RNA sequences present in their microbiota were characterized using genomic and phylogenetic tools. In total, we identified five putative novel virus species related to the Sobemovirus genus, Iflavirus genus and Permutatetraviridae family. These findings indicate a diverse taxonomy of viruses present in the mosquito microbiota of the Amazon, the region with the greatest invertebrate diversity in the world.
Collapse
Affiliation(s)
| | - Vanessa S Morais
- Institute of Tropical Medicine, University of São Paulo, São Paulo 05403-000, Brazil
| | - Fred Julio Costa Monteiro
- Public Health Laboratory of Amapa-LACEN/AP, Health Surveillance Superintendence of Amapa, Macapa 68905-230, Amapa, Brazil
| | | | - Marlisson Octavio da S Rego
- Public Health Laboratory of Amapa-LACEN/AP, Health Surveillance Superintendence of Amapa, Macapa 68905-230, Amapa, Brazil
| | | | - Fabiola Villanova
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, 66075-000, Brazil
| | - Roozbeh Tahmasebi
- Institute of Tropical Medicine, University of São Paulo, São Paulo 05403-000, Brazil
| | - Philip Michael Hefford
- University Hospitals Plymouth NHS Trust, Derriford Road, Crownhill, Plymouth PL6 8DH, UK
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94118-4417, USA
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94118-4417, USA
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Ester Cerdeira Sabino
- Institute of Tropical Medicine, University of São Paulo, São Paulo 05403-000, Brazil
| | - Licia Natal Fernandes
- Institute of Tropical Medicine, University of São Paulo, São Paulo 05403-000, Brazil
| | | | - Élcio Leal
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, 66075-000, Brazil
| |
Collapse
|
31
|
Tahmasebi R, da Costa AC, Tardy K, J. Tinker R, de Padua Milagres FA, Brustulin R, Rodrigues Teles MDA, Togisaki das Chagas R, de Deus Alves Soares CV, Sakurada Aranha Watanabe A, Salete Alencar C, Villanova F, Deng X, Delwart E, Luchs A, Leal É, Cerdeira Sabino E. Genomic Analyses of Potential Novel Recombinant Human Adenovirus C in Brazil. Viruses 2020; 12:v12050508. [PMID: 32375411 PMCID: PMC7290489 DOI: 10.3390/v12050508] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 12/31/2022] Open
Abstract
Human Adenovirus species C (HAdV-C) is the most common etiologic agent of respiratory disease. In the present study, we characterized the nearly full-length genome of one potential new HAdV-C recombinant strain constituted by Penton and Fiber proteins belonging to type 89 and a chimeric Hexon protein of types 1 and 89. By using viral metagenomics techniques, we screened out, in the states of Tocantins and Pará, Northern and North regions of Brazil, from 2010 to 2016, 251 fecal samples of children between 0.5 to 2.5 years old. These children were presenting acute diarrhea not associated with common pathogens (i.e., rotavirus, norovirus). We identified two HAdV-C strains in two distinct patients. Phylogenetic analysis performed using all complete genomes available at GenBank database indicated that one strain (HAdV-C BR-245) belonged to type 1. The phylogenetic analysis also indicated that the second strain (HAdV-C BR-211) was located at the base of the clade formed by the newly HAdV-C strains type 89. Recombination analysis revealed that strain HAdV-C BR-211 is a chimera in which the variable regions of Hexon gene combined HAdV-C1 and HAdV-C89 sequences. Therefore, HAdV-C BR-211 strain possesses a genomic backbone of type HAdV-C89 and a unique insertion of HAdV-C1 in the Hexon sequence. Recombination may play an important driving force in HAdV-C diversity and evolution. Studies employing complete genomic sequencing on circulating HAdV-C strains in Brazil are needed to understand the clinical significance of the presented data.
Collapse
Affiliation(s)
- Roozbeh Tahmasebi
- Polytechnic School of University of Sao Paulo, Sao Paulo 01246-903, Brazil;
- Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo 01246-903, Brazil;
- Correspondence: (R.T.); (A.C.d.C.); (É.L.)
| | - Antonio Charlys da Costa
- Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo 01246-903, Brazil;
- Correspondence: (R.T.); (A.C.d.C.); (É.L.)
| | - Kaelan Tardy
- Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo 01246-903, Brazil;
| | - Rory J. Tinker
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
| | - Flavio Augusto de Padua Milagres
- LIM/46, Faculty of Medicine, University of Sao Paulo, Sao Paulo 01246-903, Brazil; (F.A.d.P.M.); (R.B.)
- Secretary of Health of Tocantins, Tocantins 77453-000, Brazil; (M.d.A.R.T.); (R.T.d.C.); (C.V.d.D.A.S.)
- Institute of Biological Sciences, Federal University of Tocantins, Tocantins 77001-090, Brazil
- Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins 77016-330, Brazil
| | - Rafael Brustulin
- LIM/46, Faculty of Medicine, University of Sao Paulo, Sao Paulo 01246-903, Brazil; (F.A.d.P.M.); (R.B.)
- Secretary of Health of Tocantins, Tocantins 77453-000, Brazil; (M.d.A.R.T.); (R.T.d.C.); (C.V.d.D.A.S.)
- Institute of Biological Sciences, Federal University of Tocantins, Tocantins 77001-090, Brazil
| | - Maria da Aparecida Rodrigues Teles
- Secretary of Health of Tocantins, Tocantins 77453-000, Brazil; (M.d.A.R.T.); (R.T.d.C.); (C.V.d.D.A.S.)
- Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins 77016-330, Brazil
| | - Rogério Togisaki das Chagas
- Secretary of Health of Tocantins, Tocantins 77453-000, Brazil; (M.d.A.R.T.); (R.T.d.C.); (C.V.d.D.A.S.)
- Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins 77016-330, Brazil
| | - Cassia Vitória de Deus Alves Soares
- Secretary of Health of Tocantins, Tocantins 77453-000, Brazil; (M.d.A.R.T.); (R.T.d.C.); (C.V.d.D.A.S.)
- Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins 77016-330, Brazil
| | | | - Cecilia Salete Alencar
- Central Laboratory Division-DLC-HCSP, Clinical Laboratory and LIM 03-Department of Pathology, Clinical Hospital, University of Sao Paulo Medical School, Sao Paulo 01246-000, Brazil;
| | - Fabiola Villanova
- Institute of Biological Sciences, Federal University of Para, Para 66075-000, Brazil;
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94118-4417, USA; (X.D.); (E.D.)
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94118-4417, USA; (X.D.); (E.D.)
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Adriana Luchs
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo 01246-000, Brazil;
| | - Élcio Leal
- Institute of Biological Sciences, Federal University of Para, Para 66075-000, Brazil;
- Correspondence: (R.T.); (A.C.d.C.); (É.L.)
| | - Ester Cerdeira Sabino
- Polytechnic School of University of Sao Paulo, Sao Paulo 01246-903, Brazil;
- Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo 01246-903, Brazil;
- LIM/46, Faculty of Medicine, University of Sao Paulo, Sao Paulo 01246-903, Brazil; (F.A.d.P.M.); (R.B.)
| |
Collapse
|
32
|
Cunha MS, Luchs A, da Costa AC, Ribeiro GDO, Dos Santos FCP, Nogueira JS, Komninakis SV, Marinho RDSS, Witkin SS, Villanova F, Deng X, Sabino EC, Delwart E, Leal É, Nogueira ML, Maiorka PC. Detection and characterization of Ilheus and Iguape virus genomes in historical mosquito samples from Southern Brazil. Acta Trop 2020; 205:105401. [PMID: 32081658 DOI: 10.1016/j.actatropica.2020.105401] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/10/2020] [Accepted: 02/16/2020] [Indexed: 11/30/2022]
Abstract
In Brazil, flaviviruses have caused massive outbreaks. Surveillance programs designed to monitor virus activity in vectors provides a system for mapping disease distribution and for identifying specific vector species for targeted control. The present study aimed to describe the detection, whole genome characterization and phylogenetic analysis of Ilheus virus (ILHV) and Iguape virus (IGUV) strains obtained from historical mosquito's samples. Twelve isolates of pooled mosquito specimens (inoculated in neonate mouse brain) collected in the state of São Paulo, Brazil, in 1993, 1994 and 1997 were investigated. Viral RNA was extracted and analyzed by qRT-PCR using Flavivirus genus-specific primers. Positive samples were sequenced and underwent phylogenetic analyses. Flavivirus was detected in 50% of the specimens. Positive samples were successfully Sanger sequenced. Three Anopholes cruzii pools collected in 1994 were positive for IGUV. One Culex sp. pool, one Anopheles triannulatus pool, and one Coquillettidia juxtamansonia pool, collected in 1994, were positive for ILHV. Metagenomic sequencing successfully characterize one ILHV and four IGUV full genomes, and revealed a high degree of homology between the Brazilian ILHV and IGUV strains and isolates available in GenBank. Phylogenetic analysis of partial ILHV NS5 gene revealed three distinct lineages (clades), an indication of genetic heterogeneity in strains circulating in Brazil. Nucleotide insertions and a high-level of nucleotide diversity were observed in the NS1 protein and capsid region of IGUV strains, respectively. Detection of ILHV and IGUV in mosquitoes from Southeastern Brazil confirms the historical circulation of these viruses in this area. Furthermore, this first evidence of ILHV in Anopheles triannulatus suggests the potential importance of Anopheles mosquitoes in the IGUV transmission cycle. Genomic and phylogenetic analysis of these viruses provided insights into their diversity and evolution, which are important for the emergence patterns of flaviviruses and their evolutionary trends in Brazil, an endemic country for several arbovirus. in In-depth studies of ILHV and IGUV including vector competence and molecular studies are needed to shed light on their epidemiology and potential risk of future emergence.
Collapse
Affiliation(s)
- Mariana Sequetin Cunha
- Vector-Borne Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil.
| | - Adriana Luchs
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | | | | | | | - Juliana Silva Nogueira
- Vector-Borne Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | - Shirley Vasconcelos Komninakis
- Postgraduate Program in Health Science, Faculty of Medicine of ABC, Santo Andre, Brazil; Retrovirology Laboratory, Federal University of Sao Paulo, Sao Paulo, Brazil
| | | | - Steven S Witkin
- Tropical Medicine Institute of São Paulo, University of São Paulo, São Paulo, Brazil; Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, USA
| | - Fabiola Villanova
- Biological Sciences Institute, Federal University of Para, Belém, Brazil
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, USA; Department of Laboratory Medicine, University of California San Francisco, San Francisco, USA
| | - Ester Cerdeira Sabino
- Tropical Medicine Institute of São Paulo, University of São Paulo, São Paulo, Brazil; School of Medicine, LIM/46, University of São Paulo, Sao Paulo, Brazil
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, USA; Department of Laboratory Medicine, University of California San Francisco, San Francisco, USA
| | - Élcio Leal
- Biological Sciences Institute, Federal University of Para, Belém, Brazil
| | | | - Paulo César Maiorka
- Department of Pathology, School of Veterinary Medicine, University of Sao Paulo, Sao Paulo, Brazil
| |
Collapse
|
33
|
Rosa UA, Ribeiro GDO, Villanova F, Luchs A, Milagres FADP, Komninakis SV, Tahmasebi R, Lobato MCABS, Brustulin R, Chagas RTD, Abrão MDFNDS, Soares CVDDA, Tinker RJ, Pandey RP, Raj VS, Sabino EC, Deng X, Delwart E, Costa ACD, Leal É. First identification of mammalian orthoreovirus type 3 by gut virome analysis in diarrheic child in Brazil. Sci Rep 2019; 9:18599. [PMID: 31819139 PMCID: PMC6901473 DOI: 10.1038/s41598-019-55216-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 11/11/2019] [Indexed: 01/26/2023] Open
Abstract
Diarrhea remains one of the most common causes of deaths in children. Although many studies have investigated the prevalence of enteric pathogens around the globe some diarrheal episodes remain unexplained. It is possible that some yet-unidentified viral agents could be related to these cases of gastroenteritis. By using viral metagenomics techniques, we screened 251 fecal samples of children between 0.5 to 2.5-year-old with acute diarrhea not associated with common pathogens. These children live in rural areas and have different levels of contact with animals such as pigs, cows and bats. Here we report a complete genome of one mammalian orthoreovirus (MRV) type 3, denoted TO-151/BR, detected in a female child in the state of Tocantins (north of Brazil). Brazilian TO-151/BR strain was classified as MRV-3 based on S1 phylogeny and was closely related to porcine Asian strains. Phylogenetic analyses showed that other segments were more similar to MRV-3s of different geographic locations and hosts, including human and bats, highlighting genome reassortment and lack of host-specific barriers. This is the first report of MRV-3 in South America and a hypothesis of a silent long-term circulation of this virus in Brazil has been raised.
Collapse
Affiliation(s)
- Ulisses Alves Rosa
- Institute of Biological Sciences, Federal University of Para, Para, 66075-000, Brazil
| | | | - Fabiola Villanova
- Institute of Biological Sciences, Federal University of Para, Para, 66075-000, Brazil
| | - Adriana Luchs
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, 01246-000, Brazil
| | - Flávio Augusto de Pádua Milagres
- Secretary of Health of Tocantins, Tocantins, 77453-000, Brazil.,Institute of Biological Sciences, Federal University of Tocantins, Tocantins, 77001-090, Brazil.,Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins, 77016-330, Brazil
| | - Shirley Vasconcelos Komninakis
- Postgraduate Program in Health Science, Faculty of Medicine of ABC, Santo André, 09060-870, Brazil.,Retrovirology Laboratory, Federal University of São Paulo, São Paulo, 04023-062, Brazil
| | - Roozbeh Tahmasebi
- Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, 05403-000, Brazil.,Polytechnic School of University of Sao Paulo, Sao Paulo, Brazil
| | | | - Rafael Brustulin
- Secretary of Health of Tocantins, Tocantins, 77453-000, Brazil.,Institute of Biological Sciences, Federal University of Tocantins, Tocantins, 77001-090, Brazil.,Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins, 77016-330, Brazil
| | - Rogério Togisaki das Chagas
- Secretary of Health of Tocantins, Tocantins, 77453-000, Brazil.,Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins, 77016-330, Brazil
| | | | - Cassia Vitória de Deus Alves Soares
- Secretary of Health of Tocantins, Tocantins, 77453-000, Brazil.,Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins, 77016-330, Brazil
| | - Rory J Tinker
- Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, 05403-000, Brazil.,Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat, 131 029, Haryana, India
| | - V Samuel Raj
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat, 131 029, Haryana, India
| | - Ester Cerdeira Sabino
- Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, 05403-000, Brazil.,LIM/46, Faculdade de Medicina, Universidade de São Paulo, São Paulo, 01246-903, Brazil
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA, 94143, USA.,Department Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, 94143, USA.,Department Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | | | - Élcio Leal
- Institute of Biological Sciences, Federal University of Para, Para, 66075-000, Brazil.
| |
Collapse
|
34
|
Luchs A, Leal E, Tardy K, Milagres FADP, Komninakis SV, Brustulin R, Teles MDAR, Lobato MCABS, das Chagas RT, Abrão MDFNDS, Soares CVDDA, Deng X, Delwart E, Sabino EC, da Costa AC. The rare enterovirus c99 and echovirus 29 strains in Brazil: potential risks associated to silent circulation. Mem Inst Oswaldo Cruz 2019; 114:e190160. [PMID: 31411312 PMCID: PMC6690645 DOI: 10.1590/0074-02760190160] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/17/2019] [Indexed: 01/10/2023] Open
Abstract
Human enteroviruses (EVs) are associated with a wide spectrum of human diseases.
Here we report the complete genome sequences of one EV-C99 strain and one E29
strain obtained from children suffering from acute gastroenteritis, without
symptoms of enteroviral syndromes. This is the first report of EV-C99 in South
America, and the second E29 genome described worldwide. Continuous surveillance
on EVs is vital to provide further understanding of the circulation of new or
rare EV serotypes in the country. The present study also highlights the capacity
of EVs to remain in silent circulation in populations.
Collapse
Affiliation(s)
- Adriana Luchs
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, São Paulo, SP, Brasil
| | - Elcio Leal
- Universidade Federal do Pará, Instituto de Ciências Biológicas, Belém, PA, Brasil
| | - Kaelan Tardy
- Universidade de São Paulo, Instituto de Medicina Tropical, São Paulo, SP, Brasil.,Universidade de São Paulo, Faculdade de Medicina, LIM/46, São Paulo, SP, Brasil
| | - Flavio Augusto de Pádua Milagres
- Universidade Federal de Tocantins, Palmas, TO, Brasil.,Laboratório de Saúde Pública do Estado de Tocantins, Palmas, TO, Brasil.,Secretaria de Saúde de Tocantins, Palmas, TO, Brasil
| | - Shirley Vasconcelos Komninakis
- Faculdade de Medicina do ABC, Programa de Pós-Graduação em Ciências da Saúde, Santo André, SP, Brasil.,Universidade Federal de São Paulo, Laboratório de Retrovirologia, São Paulo, SP, Brasil
| | - Rafael Brustulin
- Universidade Federal de Tocantins, Palmas, TO, Brasil.,Laboratório de Saúde Pública do Estado de Tocantins, Palmas, TO, Brasil.,Secretaria de Saúde de Tocantins, Palmas, TO, Brasil
| | | | | | - Rogério Togisaki das Chagas
- Laboratório de Saúde Pública do Estado de Tocantins, Palmas, TO, Brasil.,Secretaria de Saúde de Tocantins, Palmas, TO, Brasil
| | | | | | - Xutao Deng
- Blood Systems Research Institute, San Francisco, USA.,University of California San Francisco, Department Laboratory Medicine, San Francisco, CA, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, USA.,University of California San Francisco, Department Laboratory Medicine, San Francisco, CA, USA
| | - Ester Cerdeira Sabino
- Universidade de São Paulo, Instituto de Medicina Tropical, São Paulo, SP, Brasil.,Universidade de São Paulo, Faculdade de Medicina, LIM/46, São Paulo, SP, Brasil
| | - Antonio Charlys da Costa
- Universidade de São Paulo, Instituto de Medicina Tropical, São Paulo, SP, Brasil.,Universidade de São Paulo, Faculdade de Medicina, LIM/46, São Paulo, SP, Brasil
| |
Collapse
|
35
|
Cilli A, Luchs A, Leal E, Gill D, Milagres FADP, Komninakis SV, Brustulin R, Teles MDAR, Lobato MCABS, Chagas RTD, Abrão MDFNDS, Soares CVDDA, Deng X, Delwart E, Sabino EC, Costa ACD. Human sapovirus GI.2 and GI.3 from children with acute gastroenteritis in northern Brazil. Mem Inst Oswaldo Cruz 2019; 114:e180574. [PMID: 30970051 PMCID: PMC6452520 DOI: 10.1590/0074-02760180574] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/18/2019] [Indexed: 01/04/2023] Open
Abstract
Human sapoviruses (HSaV) are considered important causative agents of acute
gastroenteritis in humans worldwide. However, knowledge of the genetic
characteristics of the whole genome of HSaV in Brazil is limited. Here we report
the complete genome sequences of six HSaVs GI.2 and two GI.3 strains obtained
from children with acute gastroenteritis in the Northern region of Brazil. Next
generation sequencing was used to obtain the full genome and molecular
characterization of the genome was performed. Phylogenetic analysis of the
genome was also performed. Only one complete HSaV GI.2 genome characterization
in the country precedes that of the present study. This is the first complete
genome sequence of genotype GI.3 in Brazil. The data obtained in this
investigation can contribute to the augmentation of the database on the
molecular diversity of HSaVs strains circulating in Brazil, and to the
improvement of current typing protocols.
Collapse
Affiliation(s)
- Audrey Cilli
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, São Paulo, SP, Brasil
| | - Adriana Luchs
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, São Paulo, SP, Brasil
| | - Elcio Leal
- Universidade Federal do Pará, Instituto de Ciências Biológicas, Belém, PA, Brasil
| | - Danielle Gill
- Universidade de São Paulo, Instituto de Medicina Tropical, São Paulo, SP, Brasil.,Universidade de São Paulo, Faculdade de Medicina, LIM/46, São Paulo, SP, Brasil
| | - Flavio Augusto de Pádua Milagres
- Universidade Federal de Tocantins, Palmas, TO, Brasil.,Laboratório Central de Saúde Pública do Tocantins, Palmas, TO, Brasil.,Secretaria da Saúde do Tocantins, Palmas, TO, Brasil
| | - Shirley Vasconcelos Komninakis
- Faculdade de Medicina do ABC, Programa de Pós-Graduação em Ciências da Saúde, Santo André, SP, Brasil.,Universidade Federal de São Paulo, Laboratório de Retrovirologia, São Paulo, SP, Brasil
| | - Rafael Brustulin
- Universidade Federal de Tocantins, Palmas, TO, Brasil.,Laboratório Central de Saúde Pública do Tocantins, Palmas, TO, Brasil.,Secretaria da Saúde do Tocantins, Palmas, TO, Brasil
| | | | | | - Rogério Togisaki das Chagas
- Laboratório Central de Saúde Pública do Tocantins, Palmas, TO, Brasil.,Secretaria da Saúde do Tocantins, Palmas, TO, Brasil
| | | | | | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA, USA.,University of California, Department Laboratory Medicine, San Francisco, CA, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA.,University of California, Department Laboratory Medicine, San Francisco, CA, USA
| | - Ester Cerdeira Sabino
- Universidade de São Paulo, Instituto de Medicina Tropical, São Paulo, SP, Brasil.,Universidade de São Paulo, Faculdade de Medicina, LIM/46, São Paulo, SP, Brasil
| | - Antonio Charlys da Costa
- Universidade de São Paulo, Instituto de Medicina Tropical, São Paulo, SP, Brasil.,Universidade de São Paulo, Faculdade de Medicina, LIM/46, São Paulo, SP, Brasil
| |
Collapse
|
36
|
Ribeiro GDO, Luchs A, Milagres FADP, Komninakis SV, Gill DE, Lobato MCABS, Brustulin R, Chagas RTD, Abrão MDFNDS, Soares CVDDA, Witkin SS, Villanova F, Deng X, Sabino EC, Delwart E, da Costa AC, Leal É. Detection and Characterization of Enterovirus B73 from a Child in Brazil. Viruses 2018; 11:v11010016. [PMID: 30597828 PMCID: PMC6357135 DOI: 10.3390/v11010016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/28/2018] [Accepted: 12/19/2018] [Indexed: 11/25/2022] Open
Abstract
Enterovirus B73 is a new member of the Enterovirus B species. First detected in the USA, it has been subsequently identified in China, India, Oman, and the Netherlands. In this study, we characterize the first B73 strain (named TO-127) to be detected in South America. TO-127 was obtained from a child with acute gastroenteritis living in a rural area in Northern Brazil. The subject was not infected with any known enteric pathogens such as norovirus, rotavirus, helminths, or enteric bacteria. Analysis of the nearly full-length TO-127 genome (6993 nt) indicated a 74–75% nucleotide similarity with EV-B73 strains from other countries. Evolutionary analysis suggests that B73 is endemic and widespread.
Collapse
Affiliation(s)
| | - Adriana Luchs
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo 01246-000, Brazil.
| | - Flávio Augusto de Pádua Milagres
- Secretary of Health of Tocantins, Tocantins 77453-000, Brazil.
- Institute of Biological Sciences, Federal University of Tocantins, Tocantins 77001-090, Brazil.
- Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins 77016-330, Brazil.
| | - Shirley Vasconcelos Komninakis
- Postgraduate Program in Health Science, Faculty of Medicine of ABC, Santo André 09060-870, Brazil.
- Retrovirology Laboratory, Federal University of São Paulo, São Paulo 04023-062, Brazil.
| | - Danielle Elise Gill
- Institute of Tropical Medicine, University of São Paulo, São Paulo 05403-000, Brazil.
| | - Márcia Cristina Alves Brito Sayão Lobato
- Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins 77016-330, Brazil.
- Postgraduate Program in Health Science, Faculty of Medicine of ABC, Santo André 09060-870, Brazil.
| | - Rafael Brustulin
- Secretary of Health of Tocantins, Tocantins 77453-000, Brazil.
- Institute of Biological Sciences, Federal University of Tocantins, Tocantins 77001-090, Brazil.
- Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins 77016-330, Brazil.
| | - Rogério Togisaki das Chagas
- Secretary of Health of Tocantins, Tocantins 77453-000, Brazil.
- Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins 77016-330, Brazil.
| | | | - Cassia Vitória de Deus Alves Soares
- Secretary of Health of Tocantins, Tocantins 77453-000, Brazil.
- Public Health Laboratory of Tocantins State (LACEN/TO), Tocantins 77016-330, Brazil.
| | - Steven S Witkin
- Institute of Tropical Medicine, University of São Paulo, São Paulo 05403-000, Brazil.
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Fabiola Villanova
- Institute of Biological Sciences, Federal University of Pará, Pará 66075-000, Brazil.
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA 94143, USA.
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Ester Cerdeira Sabino
- Institute of Tropical Medicine, University of São Paulo, São Paulo 05403-000, Brazil.
- LIM/46, Faculty of Medicine, University of São Paulo, São Paulo 01246-903, Brazil.
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA 94143, USA.
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA.
| | | | - Élcio Leal
- Institute of Biological Sciences, Federal University of Pará, Pará 66075-000, Brazil.
| |
Collapse
|
37
|
Luchs A, da Costa AC, Cilli A, Komninakis SCV, Carmona RDCC, Boen L, Morillo SG, Sabino EC, Timenetsky MDCST. Spread of the emerging equine-like G3P[8] DS-1-like genetic backbone rotavirus strain in Brazil and identification of potential genetic variants. J Gen Virol 2018; 100:7-25. [PMID: 30457517 DOI: 10.1099/jgv.0.001171] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In 2013, the equine-like G3P[8] DS-1-like rotavirus (RVA) strain emerged worldwide. In 2016, this strain was reported in northern Brazil. The aims of the study were to conduct a retrospective genetic investigation to identify the possible entry of these atypical strains in Brazil and to describe their distribution across a representative area of the country. From 2013 to 2017, a total of 4226 faecal samples were screened for RVA by ELISA, PAGE, RT-PCR and sequencing. G3P[8] represented 20.9 % (167/800) of all RVA-positive samples, further subdivided as equine-like G3P[8], DS-1-like (11.0 %; 88/800) and Wa-like G3P[8] (9.9 %; 79/800). Six equine-like G3P[8] DS-1-like samples were selected for whole-genome investigation, confirming the backbone I2-R2-C2-M2-A2-N2-T2-E2-H2. During 2013-2014, Wa-like G3P[8] was predominant and no equine-like G3P[8] DS-1-like was detected. Equine-like G3P[8] DS-1-like was first identified in Paraná in March/2015, suggesting that the strain entered Brazil through the Southern region. Equine-like G3P[8] rapidly spread across the area under surveillance and displayed a marked potential to replace Wa-like G3P[8] strains. Brazilian equine-like G3P[8] DS-1-like strains clustered with contemporary equine-like G3P[8] DS-1-like detected worldwide, but exhibited a distinct NSP2 genotype (N2) compared to the previously reported Amazon equine-like G3P[8] DS-1-like strain (N1). Two distinct NSP4 E2 genotype lineages were also identified. Taken together, these data suggest that different variants of equine-like G3P[8] DS-1-like strains might have been introduced into the country at distinct time points, and co-circulated in the period 2015-2017. The global emergence of equine-like G3P[8] DS-1-like strains, predominantly in countries using the Rotarix vaccine, raises the question of whether vaccines may be inducing selective pressures on zoonotic strains.
Collapse
Affiliation(s)
- Adriana Luchs
- 1Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | - Antonio Charlys da Costa
- 2LIM/46 - Laboratory of Medical Parasitology, Department of Infectious and Parasitic Diseases, College of Medicine, University of São Paulo, São Paulo, Brazil.,3Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil
| | - Audrey Cilli
- 1Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | - Shirley Cavalcante Vasconcelos Komninakis
- 4Postgraduate Program in Health Science, Faculty of Medicine of ABC, Santo André, Brazil.,5Retrovirology Laboratory, Federal University of São Paulo, São Paulo, São Paulo, Brazil
| | | | - Lais Boen
- 1Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | | | - Ester Cerdeira Sabino
- 2LIM/46 - Laboratory of Medical Parasitology, Department of Infectious and Parasitic Diseases, College of Medicine, University of São Paulo, São Paulo, Brazil.,3Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil
| | | |
Collapse
|
38
|
Charlys da Costa A, Thézé J, Komninakis SCV, Sanz-Duro RL, Felinto MRL, Moura LCC, Barroso IMDO, Santos LEC, Nunes MADL, Moura AA, Lourenço J, Deng X, Delwart EL, Guimarães MRDAS, Pybus OG, Sabino EC, Faria NR. Spread of Chikungunya Virus East/Central/South African Genotype in Northeast Brazil. Emerg Infect Dis 2018; 23:1742-1744. [PMID: 28930031 PMCID: PMC5621546 DOI: 10.3201/eid2310.170307] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We investigated an outbreak of exanthematous illness in Maceió by using molecular surveillance; 76% of samples tested positive for chikungunya virus. Genetic analysis of 23 newly generated genomes identified the East/Central/South African genotype, suggesting that this lineage has persisted since mid-2014 in Brazil and may spread in the Americas and beyond.
Collapse
|
39
|
Luchs A, Leal E, Komninakis SV, de Pádua Milagres FA, Brustulin R, da Aparecida Rodrigues Teles M, Gill DE, Deng X, Delwart E, Sabino EC, da Costa AC. Wuhan large pig roundworm virus identified in human feces in Brazil. Virus Genes 2018; 54:470-473. [PMID: 29594920 DOI: 10.1007/s11262-018-1557-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 03/16/2018] [Indexed: 12/23/2022]
Abstract
We report here the complete genome sequence of a bipartite virus, herein denoted WLPRV/human/BRA/TO-34/201, from a sample collected in 2015 from a two-year-old child in Brazil presenting acute gastroenteritis. The virus has 98-99% identity (segments 2 and 1, respectively) with the Wuhan large pig roundworm virus (unclassified RNA virus) that was recently discovered in the stomachs of pigs from China. This is the first report of a Wuhan large pig roundworm virus detected in human specimens, and the second genome described worldwide. However, the generation of more sequence data and further functional studies are required to fully understand the ecology, epidemiology, and evolution of this new unclassified virus.
Collapse
Affiliation(s)
- Adriana Luchs
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Av. Dr. Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil.
| | - Elcio Leal
- Institute of Biological Sciences, Federal University of Pará, Pará, Brazil
| | - Shirley Vasconcelos Komninakis
- Postgraduate Program in Health Science, Faculty of Medicine of ABC, Santo André, Brazil.,Retrovirology Laboratory, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Flavio Augusto de Pádua Milagres
- LIM/46, Faculty of Medicine, University of São Paulo, São Paulo, Brazil.,Federal University of Tocantins, Palmas, Tocantins, Brazil.,Public Health Laboratory of Tocantins State (LACEN/TO), Palmas, Brazil
| | - Rafael Brustulin
- Federal University of Tocantins, Palmas, Tocantins, Brazil.,Public Health Laboratory of Tocantins State (LACEN/TO), Palmas, Brazil
| | | | - Danielle Elise Gill
- Institute of Tropical Medicine, University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, USA.,Department Laboratory Medicine, University of California San Francisco, San Francisco, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, USA.,Department Laboratory Medicine, University of California San Francisco, San Francisco, USA
| | - Ester Cerdeira Sabino
- LIM/46, Faculty of Medicine, University of São Paulo, São Paulo, Brazil.,Institute of Tropical Medicine, University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil
| | - Antonio Charlys da Costa
- Institute of Tropical Medicine, University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil.
| |
Collapse
|
40
|
Faria NR, da Costa AC, Lourenço J, Loureiro P, Lopes ME, Ribeiro R, Alencar CS, Kraemer MUG, Villabona-Arenas CJ, Wu CH, Thézé J, Khan K, Brent SE, Romano C, Delwart E, Custer B, Busch MP, Pybus OG, Sabino EC. Genomic and epidemiological characterisation of a dengue virus outbreak among blood donors in Brazil. Sci Rep 2017; 7:15216. [PMID: 29123142 PMCID: PMC5680240 DOI: 10.1038/s41598-017-15152-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/20/2017] [Indexed: 01/20/2023] Open
Abstract
Outbreaks caused by Dengue, Zika and Chikungunya viruses can spread rapidly in immunologically naïve populations. By analysing 92 newly generated viral genome sequences from blood donors and recipients, we assess the dynamics of dengue virus serotype 4 during the 2012 outbreak in Rio de Janeiro. Phylogenetic analysis indicates that the outbreak was caused by genotype II, although two isolates of genotype I were also detected for the first time in Rio de Janeiro. Evolutionary analysis and modelling estimates are congruent, indicating a reproduction number above 1 between January and June, and at least two thirds of infections being unnoticed. Modelling analysis suggests that viral transmission started in early January, which is consistent with multiple introductions, most likely from the northern states of Brazil, and with an increase in within-country air travel to Rio de Janeiro. The combination of genetic and epidemiological data from blood donor banks may be useful to anticipate epidemic spread of arboviruses.
Collapse
Affiliation(s)
- Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, United Kingdom.
| | - Antonio Charlys da Costa
- Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, Brazil. .,LIM46, Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Paula Loureiro
- Faculdade de Ciências Médicas, Fundação Hemope, Recife, Brazil
| | | | - Roberto Ribeiro
- Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, Brazil.,LIM46, Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | - Chieh-Hsi Wu
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Julien Thézé
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Division of Infectious Diseases, University of Toronto, Toronto, Ontario, Canada
| | - Shannon E Brent
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Camila Romano
- Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, Brazil
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California, USA.,University of California San Francisco, San Francisco, California, USA
| | - Brian Custer
- Blood Systems Research Institute, San Francisco, California, USA.,University of California San Francisco, San Francisco, California, USA
| | - Michael P Busch
- Blood Systems Research Institute, San Francisco, California, USA.,University of California San Francisco, San Francisco, California, USA
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Ester C Sabino
- Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, Brazil. .,LIM46, Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.
| | | |
Collapse
|
41
|
Phan TG, Messacar K, Dominguez SR, da Costa AC, Deng X, Delwart E. A new densovirus in cerebrospinal fluid from a case of anti-NMDA-receptor encephalitis. Arch Virol 2016; 161:3231-5. [PMID: 27522586 DOI: 10.1007/s00705-016-3002-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/26/2016] [Indexed: 01/16/2023]
Abstract
We characterized the genome of a densovirus, tentatively called human CSF-associated densovirus 1 (HuCSFDV1), in cerebrospinal fluid (CSF) from a human case of encephalitis with antibodies against the N-methyl D-aspartate receptor. The presence of the viral genome in CSF was independently confirmed. This virus, which is proposed to be a member of a new species in the genus Iteradensovirus of the subfamily Densovirinae, showed the typical two ORFs encoding nonstructural and structural proteins with low-level identities of 22 and 16 % to the closest known densovirus relative. No other eukaryotic viral sequences were detected using deep sequencing. The replication and pathogenicity in humans of this virus, which belongs to a viral subfamily whose members are only known to replicate in invertebrates, remain to be demonstrated. Alternative explanations for the detection of densovirus DNA in CSF are discussed.
Collapse
Affiliation(s)
- Tung Gia Phan
- Blood Systems Research Institute, San Francisco, CA, 94118, USA.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA
| | - Kevin Messacar
- Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - Samuel R Dominguez
- Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - Antonio Charlys da Costa
- Blood Systems Research Institute, San Francisco, CA, 94118, USA.,Institute of Tropical Medicine, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA, 94118, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, 94118, USA. .,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA.
| |
Collapse
|
42
|
Phan TG, Dreno B, da Costa AC, Li L, Orlandi P, Deng X, Kapusinszky B, Siqueira J, Knol AC, Halary F, Dantal J, Alexander KA, Pesavento PA, Delwart E. A new protoparvovirus in human fecal samples and cutaneous T cell lymphomas (mycosis fungoides). Virology 2016; 496:299-305. [PMID: 27393975 DOI: 10.1016/j.virol.2016.06.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 02/07/2023]
Abstract
We genetically characterized seven nearly complete genomes in the protoparvovirus genus from the feces of children with diarrhea. The viruses, provisionally named cutaviruses (CutaV), varied by 1-6% nucleotides and shared ~76% and ~82% amino acid identity with the NS1 and VP1 of human bufaviruses, their closest relatives. Using PCR, cutavirus DNA was found in 1.6% (4/245) and 1% (1/100) of diarrhea samples from Brazil and Botswana respectively. In silico analysis of pre-existing metagenomics datasets then revealed closely related parvovirus genomes in skin biopsies from patients with epidermotropic cutaneous T-cell lymphoma (CTCL or mycosis fungoides). PCR of skin biopsies yielded cutavirus DNA in 4/17 CTCL, 0/10 skin carcinoma, and 0/21 normal or noncancerous skin biopsies. In situ hybridization of CTCL skin biopsies detected viral genome within rare individual cells in regions of neoplastic infiltrations. The influence of cutavirus infection on human enteric functions and possible oncolytic role in CTCL progression remain to be determined.
Collapse
Affiliation(s)
- Tung G Phan
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Brigitte Dreno
- Department of Dermatology, Nantes University Hospital, INSERM U 892, Nantes, France.
| | - Antonio Charlys da Costa
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Institute of Tropical Medicine, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Linlin Li
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA
| | | | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Beatrix Kapusinszky
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Juliana Siqueira
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Anne-Chantal Knol
- Department of Dermatology, Nantes University Hospital, INSERM U 892, Nantes, France
| | - Franck Halary
- Institute for Transplantation/Urology and Nephrology, Nantes University Hospital, Nantes F44093, France; INSERM, UMR 1064-Center for Research in Transplantation and Immunology, Nantes F44093, France; University of Nantes, Nantes F44093, France
| | - Jacques Dantal
- Department of Nephrology, Clinical Immunology, Transplantation, Nantes University Hospital, Nantes, France
| | - Kathleen A Alexander
- Department of Fisheries and Wildlife Conservation, Virginia Tech, Blacksburg, VA, USA; CARACAL, Centre for African Resources: Animals, Communities, and Land Use, Kasane, Botswana
| | - Patricia A Pesavento
- Department of Pathology, Microbiology and Immunology, University of California, Davis, CA, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA.
| |
Collapse
|
43
|
Ng TFF, Zhang W, Sachsenröder J, Kondov NO, da Costa AC, Vega E, Holtz LR, Wu G, Wang D, Stine CO, Antonio M, Mulvaney US, Muench MO, Deng X, Ambert-Balay K, Pothier P, Vinjé J, Delwart E. A diverse group of small circular ssDNA viral genomes in human and non-human primate stools. Virus Evol 2015; 1:vev017. [PMID: 27774288 PMCID: PMC5014484 DOI: 10.1093/ve/vev017] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Viral metagenomics sequencing of fecal samples from outbreaks of acute gastroenteritis from the US revealed the presence of small circular ssDNA viral genomes encoding a replication initiator protein (Rep). Viral genomes were ∼2.5 kb in length, with bi-directionally oriented Rep and capsid (Cap) encoding genes and a stem loop structure downstream of Rep. Several genomes showed evidence of recombination. By digital screening of an in-house virome database (1.04 billion reads) using BLAST, we identified closely related sequences from cases of unexplained diarrhea in France. Deep sequencing and PCR detected such genomes in 7 of 25 US (28 percent) and 14 of 21 French outbreaks (67 percent). One of eighty-five sporadic diarrhea cases in the Gambia was positive by PCR. Twenty-two complete genomes were characterized showing that viruses from patients in the same outbreaks were closely related suggesting common origins. Similar genomes were also characterized from the stools of captive chimpanzees, a gorilla, a black howler monkey, and a lemur that were more diverse than the human stool-associated genomes. The name smacovirus is proposed for this monophyletic viral clade. Possible tropism include mammalian enteric cells or ingested food components such as infected plants. No evidence of viral amplification was found in immunodeficient mice orally inoculated with smacovirus-positive stool supernatants. A role for smacoviruses in diarrhea, if any, remains to be demonstrated.
Collapse
Affiliation(s)
- Terry Fei Fan Ng
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Department of laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Wen Zhang
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Department of Microbiology, School of Medicine, Jiangsu University, Jiangsu, Zhenjiang, China
| | - Jana Sachsenröder
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Federal Institute for Risk Assessment, Berlin, Germany
| | - Nikola O Kondov
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA
| | - Antonio Charlys da Costa
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Institute of Tropical Medicine, University of Sao Paulo, São Paulo, Brazil
| | - Everardo Vega
- NCIRD, Polio and Picornavirus Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Guang Wu
- Department of Molecular Microbiology, and
| | - David Wang
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Colin O Stine
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Usha S Mulvaney
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA
| | - Marcus O Muench
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Department of laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Department of laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Katia Ambert-Balay
- National Reference Centre for enteric viruses, Dijon University Hospital, Dijon, France and
| | - Pierre Pothier
- National Reference Centre for enteric viruses, Dijon University Hospital, Dijon, France and
| | - Jan Vinjé
- NCIRD, National Calicivirus Laboratory, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Department of laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA
| |
Collapse
|
44
|
Abstract
A novel gyrovirus genome found in the feces of an adult with diarrhea is described. The genome shows the three expected main ORFs encoding a structural protein (VP1), nonstructural protein (VP2), and Apoptin protein (VP3), which shared identities of 41, 42, and 38 % with those of the most closely related gyrovirus proteins, respectively. Given the high divergence in its genome, this gyrovirus may be considered the prototype for a new viral species (GyV9) in the Gyrovirus genus. Because the closest relatives of this gyrovirus infect chicken, a possible dietary origin for the presence of this virus in human feces is discussed.
Collapse
Affiliation(s)
- Tung Gia Phan
- Blood Systems Research Institute, San Francisco, CA 94118, USA
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA
| | - Antonio Charlys da Costa
- Blood Systems Research Institute, San Francisco, CA 94118, USA
- Institute of Tropical Medicine, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Wen Zhang
- Blood Systems Research Institute, San Francisco, CA 94118, USA
- School of Medicine, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Pierre Pothier
- National Reference Centre for Enteric Viruses, University Hospital of Dijon, Dijon, France
| | - Katia Ambert-Balay
- National Reference Centre for Enteric Viruses, University Hospital of Dijon, Dijon, France
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA 94118, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA 94118, USA
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA
| |
Collapse
|
45
|
Sanabani SS, Nukui Y, Pereira J, da Costa AC, de Oliveira ACS, Pessôa R, Leal FE, Segurado AC, Kallas EG, Sabino EC. Lack of evidence to support the association of a single IL28B genotype SNP rs12979860 with the HTLV-1 clinical outcomes and proviral load. BMC Infect Dis 2012; 12:374. [PMID: 23259930 PMCID: PMC3547796 DOI: 10.1186/1471-2334-12-374] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 12/20/2012] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The Interleukin 28B (IL28B) rs12979860 polymorphisms was recently reported to be associated with the human T-cell leukemia virus type 1 (HTLV-1) proviral load (PvL) and the development of the HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). METHODS In an attempt to examine this hypothesis, we assessed the association of the rs12979860 genotypes with HTLV-1 PvL levels and clinical status in 112 unrelated Brazilian subjects (81 HTLV-1 asymptomatic carriers, 24 individuals with HAM/TSP and 7 with Adult T cell Leukemia/Lymphoma (ATLL)). RESULTS All 112 samples were successfully genotyped and their PvLs compared. Neither the homozygote TT nor the heterozygote CT mutations nor the combination genotypes (TT/CT) were associated with a greater PvL. We also observed no significant difference in allele distribution between asymptomatic carriers and patients with HTLV-1 associated HAM/TSP. CONCLUSIONS Our study failed to support the previously reported positive association between the IL28B rs12979860 polymorphisms and an increased risk of developing HAM/TSP in the Brazilian population.
Collapse
Affiliation(s)
- Sabri Saeed Sanabani
- Clinical Laboratory, Department of Pathology, LIM 03, Hospital das Clínicas (HC), School of Medicine, University of São Paulo, São Paulo, Brazil
- São Paulo Inistitute of Tropical Medicine, São Paulo, Brazil
| | - Youko Nukui
- Department of Hematology, University of São Paulo, São Paulo, Brazil
| | - Juliana Pereira
- Department of Hematology, University of São Paulo, São Paulo, Brazil
| | - Antonio Charlys da Costa
- Clinical Laboratory, Department of Pathology, LIM 03, Hospital das Clínicas (HC), School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Ana Carolina Soares de Oliveira
- Clinical Laboratory, Department of Pathology, LIM 03, Hospital das Clínicas (HC), School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Rodrigo Pessôa
- Clinical Laboratory, Department of Pathology, LIM 03, Hospital das Clínicas (HC), School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Fabio Eudes Leal
- Division of Clinical Immunology and Allergy, University of Sao Paulo Medical School, São Paulo, Brazil
| | - Aluisio C Segurado
- Deparment of Infectious Diseases, School of Medicine, University of Sao Paulo, São Paulo, Brazil
| | - Esper Georges Kallas
- Division of Clinical Immunology and Allergy, University of Sao Paulo Medical School, São Paulo, Brazil
| | - Ester Cerdeira Sabino
- Deparment of Infectious Diseases, School of Medicine, University of Sao Paulo, São Paulo, Brazil
| |
Collapse
|
46
|
Soares de Oliveira AC, da Costa AC, Martinez VP, Maidana MT, Celia de Menezes Succi GR, Sabino Esper EC, Kallas G, Sanabani SS. Genetic variability and high proportion of HIV-1 BF1 recombinant strains among vertically infected children in São Paulo, Brazil. Retrovirology 2012. [PMCID: PMC3360345 DOI: 10.1186/1742-4690-9-s1-p4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
|
47
|
Soares de Oliveira AC, Pessôa de Farias R, da Costa AC, Sauer MM, Bassichetto KC, Oliveira SMS, Costa PR, Tomiyama C, Tomiyama HTI, Sabino EC, Kallas EG, Sanabani SS. Frequency of subtype B and F1 dual infection in HIV-1 positive, Brazilian men who have sex with men. Virol J 2012; 9:223. [PMID: 23021203 PMCID: PMC3499372 DOI: 10.1186/1743-422x-9-223] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 09/27/2012] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Because various HIV vaccination studies are in progress, it is important to understand how often inter- and intra-subtype co/superinfection occurs in different HIV-infected high-risk groups. This knowledge would aid in the development of future prevention programs. In this cross-sectional study, we report the frequency of subtype B and F1 co-infection in a clinical group of 41 recently HIV-1 infected men who have sex with men (MSM) in São Paulo, Brazil. METHODOLOGY Proviral HIV-1 DNA was isolated from subject's peripheral blood polymorphonuclear leukocytes that were obtained at the time of enrollment. Each subject was known to be infected with a subtype B virus as determined in a previous study. A small fragment of the integrase gene (nucleotide 4255-4478 of HXB2) was amplified by nested polymerase chain reaction (PCR) using subclade F1 specific primers. The PCR results were further confirmed by phylogenetic analysis. Viral load (VL) data were extrapolated from the medical records of each patient. RESULTS For the 41 samples from MSM who were recently infected with subtype B virus, it was possible to detect subclade F1 proviral DNA in five patients, which represents a co-infection rate of 12.2%. In subjects with dual infection, the median VL was 5.3 × 10(4) copies/ML, whereas in MSM that were infected with only subtype B virus the median VL was 3.8 × 10(4) copies/ML (p > 0.8). CONCLUSIONS This study indicated that subtype B and F1 co-infection occurs frequently within the HIV-positive MSM population as suggested by large number of BF1 recombinant viruses reported in Brazil. This finding will help us track the epidemic and provide support for the development of immunization strategies against the HIV.
Collapse
|
48
|
Sanabani SS, Soares de Oliveira AC, da Costa AC, Melillo M, Cristina Bassichetto Solange SK, Oliveira MS, Costa PR, Tomiyama C, Tomiyama HTI, Cerdeira E, Esper S, Kal G. Frequency of subtype B and F1 dual infection in HIV-1 positive, Brazilian men who have sex with men. Retrovirology 2012. [PMCID: PMC3360350 DOI: 10.1186/1742-4690-9-s1-p31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
| | | | | | - Mariana Melillo
- Instituto de Medicina Tropical de São Paulo, São Paulo, Brazil
| | | | | | | | | | | | - Ester Cerdeira
- Instituto de Medicina Tropical de São Paulo, São Paulo, Brazil
| | - Sabino Esper
- Instituto de Medicina Tropical de São Paulo, São Paulo, Brazil
| | - Georges Kal
- Instituto de Medicina Tropical de São Paulo, São Paulo, Brazil
| |
Collapse
|
49
|
Sanabani SS, Pastena ÉRDS, da Costa AC, Martinez VP, Kleine-Neto W, de Oliveira ACS, Sauer MM, Bassichetto KC, Oliveira SMS, Tomiyama HTI, Sabino EC, Kallas EG. Characterization of partial and near full-length genomes of HIV-1 strains sampled from recently infected individuals in São Paulo, Brazil. PLoS One 2011; 6:e25869. [PMID: 22022460 PMCID: PMC3193532 DOI: 10.1371/journal.pone.0025869] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 09/13/2011] [Indexed: 12/03/2022] Open
Abstract
Background Genetic variability is a major feature of human immunodeficiency virus type 1 (HIV-1) and is considered the key factor frustrating efforts to halt the HIV epidemic. A proper understanding of HIV-1 genomic diversity is a fundamental prerequisite for proper epidemiology, genetic diagnosis, and successful drugs and vaccines design. Here, we report on the partial and near full-length genomic (NFLG) variability of HIV-1 isolates from a well-characterized cohort of recently infected patients in São Paul, Brazil. Methodology HIV-1 proviral DNA was extracted from the peripheral blood mononuclear cells of 113 participants. The NFLG and partial fragments were determined by overlapping nested PCR and direct sequencing. The data were phylogenetically analyzed. Results Of the 113 samples (90.3% male; median age 31 years; 79.6% homosexual men) studied, 77 (68.1%) NFLGs and 32 (29.3%) partial fragments were successfully subtyped. Of the successfully subtyped sequences, 88 (80.7%) were subtype B sequences, 12 (11%) BF1 recombinants, 3 (2.8%) subtype C sequences, 2 (1.8%) BC recombinants and subclade F1 each, 1 (0.9%) CRF02 AG, and 1 (0.9%) CRF31 BC. Primary drug resistance mutations were observed in 14/101 (13.9%) of samples, with 5.9% being resistant to protease inhibitors and nucleoside reverse transcriptase inhibitors (NRTI) and 4.9% resistant to non-NRTIs. Predictions of viral tropism were determined for 86 individuals. X4 or X4 dual or mixed-tropic viruses (X4/DM) were seen in 26 (30.2%) of subjects. The proportion of X4 viruses in homosexuals was detected in 19/69 (27.5%). Conclusions Our results confirm the existence of various HIV-1 subtypes circulating in São Paulo, and indicate that subtype B account for the majority of infections. Antiretroviral (ARV) drug resistance is relatively common among recently infected patients. The proportion of X4 viruses in homosexuals was significantly higher than the proportion seen in other study populations.
Collapse
Affiliation(s)
- Sabri Saeed Sanabani
- Division of Clinical Immunology and Allergy, Faculty of Medicine, University of São Paulo, São Paulo, Brazil.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|