1
|
Silva SJRD, Magalhães JJFD, Matthews Q, Divarzak ALL, Mendes RPG, Santos BNR, Cabral DGDA, Silva JBD, Kohl A, Pardee K, Pena L. Development and field validation of a reverse transcription loop-mediated isothermal amplification assay (RT-LAMP) for the rapid detection of chikungunya virus in patient and mosquito samples. Clin Microbiol Infect 2024:S1198-743X(24)00116-2. [PMID: 38460820 DOI: 10.1016/j.cmi.2024.03.004] [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: 09/03/2023] [Revised: 03/02/2024] [Accepted: 03/04/2024] [Indexed: 03/11/2024]
Abstract
OBJECTIVES We aimed to develop a reverse transcription loop-mediated isothermal amplification (RT-LAMP) platform for the rapid detection of chikungunya virus (CHIKV) in both patient and mosquito samples from Brazil. METHODS We optimized an RT-LAMP assay and then evaluated the specificity and sensitivity using visual detection. In comparison with the RT-qPCR reference method, we validated the utility of this assay as a molecular diagnostic test in a reference laboratory for arbovirus diagnostics using 100 serum samples collected from suspected CHIKV cases. RESULTS Our RT-LAMP assay specifically detected CHIKV without cross-reactivity against other arboviruses. The limit of detection of our RT-LAMP was estimated in -1.18 PFU (confidence interval [CI] ranging from -2.08 to 0.45), resulting in a similar analytical sensitivity when directly compared with the reference standard RT-qPCR assay. Then, we demonstrate the ability of our RT-LAMP assay to detect the virus in different human specimens (serum, urine, and saliva), and crude lysate of Aedes aegypti mosquitoes in as little as 20-30 minutes and without a separate RNA isolation step. Lastly, we showed that our RT-LAMP assay could be lyophilized and reactivated by adding water, indicating potential for room-temperature storage. Our RT-LAMP had a clinical sensitivity of 100% (95% CI, 90.97-100.00%), clinical specificity of 96.72% (95% CI, 88.65-99.60%), and overall accuracy of 98.00% (95% CI, 92.96-99.76%). DISCUSSION Taken together, these findings indicate that the RT-LAMP assay reported here solves important practical drawbacks to the deployment of molecular diagnostics in the field and can be used to improve testing capacity, particularly in low- and middle-income countries.
Collapse
Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Laboratory of Virology and Experimental Therapy (Lavite), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil; Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada.
| | - Jurandy Júnior Ferraz de Magalhães
- Laboratory of Virology and Experimental Therapy (Lavite), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil; Department of Virology, Pernambuco State Central Laboratory (LACEN/PE), Recife, Pernambuco, Brazil; University of Pernambuco (UPE), Serra Talhada Campus, Serra Talhada, Pernambuco, Brazil; Public Health Laboratory of the XI Regional Health, Pernambuco, Brazil
| | - Quinn Matthews
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | | | - Renata Pessôa Germano Mendes
- Laboratory of Virology and Experimental Therapy (Lavite), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil
| | - Bárbara Nazly Rodrigues Santos
- Laboratory of Virology and Experimental Therapy (Lavite), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil
| | | | | | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Department of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada; Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON, Canada
| | - Lindomar Pena
- Laboratory of Virology and Experimental Therapy (Lavite), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil.
| |
Collapse
|
2
|
da Silva SJR, do Nascimento JCF, Germano Mendes RP, Guarines KM, Targino Alves da Silva C, da Silva PG, de Magalhães JJF, Vigar JRJ, Silva-Júnior A, Kohl A, Pardee K, Pena L. Two Years into the COVID-19 Pandemic: Lessons Learned. ACS Infect Dis 2022; 8:1758-1814. [PMID: 35940589 PMCID: PMC9380879 DOI: 10.1021/acsinfecdis.2c00204] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [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: 01/29/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible and virulent human-infecting coronavirus that emerged in late December 2019 in Wuhan, China, causing a respiratory disease called coronavirus disease 2019 (COVID-19), which has massively impacted global public health and caused widespread disruption to daily life. The crisis caused by COVID-19 has mobilized scientists and public health authorities across the world to rapidly improve our knowledge about this devastating disease, shedding light on its management and control, and spawned the development of new countermeasures. Here we provide an overview of the state of the art of knowledge gained in the last 2 years about the virus and COVID-19, including its origin and natural reservoir hosts, viral etiology, epidemiology, modes of transmission, clinical manifestations, pathophysiology, diagnosis, treatment, prevention, emerging variants, and vaccines, highlighting important differences from previously known highly pathogenic coronaviruses. We also discuss selected key discoveries from each topic and underline the gaps of knowledge for future investigations.
Collapse
Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil.,Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Jessica Catarine Frutuoso do Nascimento
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Renata Pessôa Germano Mendes
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Klarissa Miranda Guarines
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Caroline Targino Alves da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Poliana Gomes da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Jurandy Júnior Ferraz de Magalhães
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil.,Department of Virology, Pernambuco State Central Laboratory (LACEN/PE), 52171-011 Recife, Pernambuco, Brazil.,University of Pernambuco (UPE), Serra Talhada Campus, 56909-335 Serra Talhada, Pernambuco, Brazil.,Public Health Laboratory of the XI Regional Health, 56912-160 Serra Talhada, Pernambuco, Brazil
| | - Justin R J Vigar
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Abelardo Silva-Júnior
- Institute of Biological and Health Sciences, Federal University of Alagoas (UFAL), 57072-900 Maceió, Alagoas, Brazil
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, United Kingdom
| | - Keith Pardee
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada.,Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Lindomar Pena
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| |
Collapse
|
3
|
da Silva SJR, do Nascimento JCF, Dos Santos Reis WPM, da Silva CTA, da Silva PG, Mendes RPG, Mendonça AA, Santos BNR, de Magalhães JJF, Kohl A, Pena L. Widespread Contamination of SARS-CoV-2 on Highly Touched Surfaces in Brazil During the Second Wave of the COVID-19 Pandemic. Environ Microbiol 2021; 23:7382-7395. [PMID: 34863010 PMCID: PMC9303906 DOI: 10.1111/1462-2920.15855] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 08/04/2021] [Accepted: 11/18/2021] [Indexed: 12/04/2022]
Abstract
Although SARS‐CoV‐2 surface contamination has been investigated in health care settings, little is known about the SARS‐CoV‐2 surface contamination in public urban areas, particularly in tropical countries. Here, we investigated the presence of SARS‐CoV‐2 on high‐touch surfaces in a large city in Brazil, one of the most affected countries by the COVID‐19 pandemic in the world. A total of 400 surface samples were collected in February 2021 in the City of Recife, Northeastern Brazil. A total of 97 samples (24.2%) tested positive for SARS‐CoV‐2 by RT‐qPCR using the CDC‐USA protocol. All the collection sites, except one (18/19, 94.7%) had at least one environmental surface sample contaminated. SARS‐CoV‐2 positivity was higher in public transport terminals (47/84, 55.9%), followed by health care units (26/84, 30.9%), beach areas (4/21, 19.0%), public parks (14/105, 13.3%), supply centre (2/21, 9.5%), and public markets (4/85, 4.7%). Toilets, ATMs, handrails, playgrounds and outdoor gyms were identified as fomites with the highest rates of SARS‐CoV‐2 detection. Taken together, our data provide a real‐world picture of SARS‐CoV‐2 dispersion in highly populated tropical areas and identify critical control points that need to be targeted to break SARS‐CoV‐2 transmission chains.
Collapse
Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM) , Oswaldo Cruz Foundation (Fiocruz), 50670-420, Recife, Pernambuco, Brazil
| | - Jéssica Catarine Frutuoso do Nascimento
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM) , Oswaldo Cruz Foundation (Fiocruz), 50670-420, Recife, Pernambuco, Brazil
| | - Wendell Palôma Maria Dos Santos Reis
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM) , Oswaldo Cruz Foundation (Fiocruz), 50670-420, Recife, Pernambuco, Brazil
| | - Caroline Targino Alves da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM) , Oswaldo Cruz Foundation (Fiocruz), 50670-420, Recife, Pernambuco, Brazil
| | - Poliana Gomes da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM) , Oswaldo Cruz Foundation (Fiocruz), 50670-420, Recife, Pernambuco, Brazil
| | - Renata Pessôa Germano Mendes
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM) , Oswaldo Cruz Foundation (Fiocruz), 50670-420, Recife, Pernambuco, Brazil
| | - Allyson Andrade Mendonça
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM) , Oswaldo Cruz Foundation (Fiocruz), 50670-420, Recife, Pernambuco, Brazil
| | - Bárbara Nazly Rodrigues Santos
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM) , Oswaldo Cruz Foundation (Fiocruz), 50670-420, Recife, Pernambuco, Brazil
| | - Jurandy Júnior Ferraz de Magalhães
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM) , Oswaldo Cruz Foundation (Fiocruz), 50670-420, Recife, Pernambuco, Brazil.,Department of Virology, Pernambuco State Central Laboratory (LACEN/PE), Recife, Pernambuco, Brazil.,Serra Talhada Campus, University of Pernambuco (UPE), Serra Talhada, Pernambuco, Brazil
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, G61 1QH,, UK
| | - Lindomar Pena
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM) , Oswaldo Cruz Foundation (Fiocruz), 50670-420, Recife, Pernambuco, Brazil
| |
Collapse
|
4
|
Paiva MHS, Guedes DRD, Docena C, Bezerra MF, Dezordi FZ, Machado LC, Krokovsky L, Helvecio E, da Silva AF, Vasconcelos LRS, Rezende AM, da Silva SJR, Sales KGDS, de Sá BSLF, da Cruz DL, Cavalcanti CE, Neto ADM, da Silva CTA, Mendes RPG, da Silva MAL, Gräf T, Resende PC, Bello G, Barros MDS, do Nascimento WRC, Arcoverde RML, Bezerra LCA, Brandão-Filho SP, Ayres CFJ, Wallau GL. Multiple Introductions Followed by Ongoing Community Spread of SARS-CoV-2 at One of the Largest Metropolitan Areas of Northeast Brazil. Viruses 2020; 12:v12121414. [PMID: 33316947 PMCID: PMC7763515 DOI: 10.3390/v12121414] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [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: 10/17/2020] [Revised: 11/16/2020] [Accepted: 11/22/2020] [Indexed: 01/08/2023] Open
Abstract
Multiple epicenters of the SARS-CoV-2 pandemic have emerged since the first pneumonia cases in Wuhan, China, such as Italy, USA, and Brazil. Brazil is the third-most affected country worldwide, but genomic sequences of SARS-CoV-2 strains are mostly restricted to states from the Southeast region. Pernambuco state, located in the Northeast region, is the sixth most affected Brazilian state, but very few genomic sequences from the strains circulating in this region are available. We sequenced 101 strains of SARS-CoV-2 from patients presenting Covid-19 symptoms that reside in Pernambuco. Phylogenetic reconstructions revealed that all genomes belong to the B lineage and most of the samples (88%) were classified as lineage B.1.1. We detected multiple viral introductions from abroad (likely from Europe) as well as six local B.1.1 clades composed by Pernambuco only strains. Local clades comprise sequences from the capital city (Recife) and other country-side cities, corroborating the community spread between different municipalities of the state. These findings demonstrate that different from Southeastern Brazilian states where the epidemics were majorly driven by one dominant lineage (B.1.1.28 or B.1.1.33), the early epidemic phase at the Pernambuco state was driven by multiple B.1.1 lineages seeded through both national and international traveling.
Collapse
Affiliation(s)
- Marcelo Henrique Santos Paiva
- Núcleo de Ciências da Vida, Universidade Federal de Pernambuco (UFPE), Centro Acadêmico do Agreste-Rodovia BR-104, km 59-Nova Caruaru, Caruaru 55002-970, Brazil;
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (D.R.D.G.); (F.Z.D.); (L.C.M.); (L.K.); (E.H.); (A.F.d.S.); (D.L.d.C.); (C.F.J.A.)
| | - Duschinka Ribeiro Duarte Guedes
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (D.R.D.G.); (F.Z.D.); (L.C.M.); (L.K.); (E.H.); (A.F.d.S.); (D.L.d.C.); (C.F.J.A.)
| | - Cássia Docena
- Núcleo de Plataformas Tecnológicas (NPT), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil;
| | - Matheus Filgueira Bezerra
- Departamento de Microbiologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (M.F.B.); (A.M.R.); (B.S.L.F.d.S.)
| | - Filipe Zimmer Dezordi
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (D.R.D.G.); (F.Z.D.); (L.C.M.); (L.K.); (E.H.); (A.F.d.S.); (D.L.d.C.); (C.F.J.A.)
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil
| | - Laís Ceschini Machado
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (D.R.D.G.); (F.Z.D.); (L.C.M.); (L.K.); (E.H.); (A.F.d.S.); (D.L.d.C.); (C.F.J.A.)
| | - Larissa Krokovsky
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (D.R.D.G.); (F.Z.D.); (L.C.M.); (L.K.); (E.H.); (A.F.d.S.); (D.L.d.C.); (C.F.J.A.)
| | - Elisama Helvecio
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (D.R.D.G.); (F.Z.D.); (L.C.M.); (L.K.); (E.H.); (A.F.d.S.); (D.L.d.C.); (C.F.J.A.)
| | - Alexandre Freitas da Silva
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (D.R.D.G.); (F.Z.D.); (L.C.M.); (L.K.); (E.H.); (A.F.d.S.); (D.L.d.C.); (C.F.J.A.)
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil
| | - Luydson Richardson Silva Vasconcelos
- Departamento de Parasitologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (L.R.S.V.); (A.d.M.N.); (C.T.A.d.S.); (R.P.G.M.); (M.A.L.d.S.); (W.R.C.d.N.); (R.M.L.A.); (S.P.B.-F.)
| | - Antonio Mauro Rezende
- Departamento de Microbiologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (M.F.B.); (A.M.R.); (B.S.L.F.d.S.)
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil
| | - Severino Jefferson Ribeiro da Silva
- Laboratório de Virologia e Terapia Experimental (LAVITE), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (S.J.R.d.S.); (C.E.C.)
| | - Kamila Gaudêncio da Silva Sales
- Departamento de Imunologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (K.G.d.S.S.); (M.d.S.B.)
| | - Bruna Santos Lima Figueiredo de Sá
- Departamento de Microbiologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (M.F.B.); (A.M.R.); (B.S.L.F.d.S.)
| | - Derciliano Lopes da Cruz
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (D.R.D.G.); (F.Z.D.); (L.C.M.); (L.K.); (E.H.); (A.F.d.S.); (D.L.d.C.); (C.F.J.A.)
| | - Claudio Eduardo Cavalcanti
- Laboratório de Virologia e Terapia Experimental (LAVITE), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (S.J.R.d.S.); (C.E.C.)
| | - Armando de Menezes Neto
- Departamento de Parasitologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (L.R.S.V.); (A.d.M.N.); (C.T.A.d.S.); (R.P.G.M.); (M.A.L.d.S.); (W.R.C.d.N.); (R.M.L.A.); (S.P.B.-F.)
| | - Caroline Targino Alves da Silva
- Departamento de Parasitologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (L.R.S.V.); (A.d.M.N.); (C.T.A.d.S.); (R.P.G.M.); (M.A.L.d.S.); (W.R.C.d.N.); (R.M.L.A.); (S.P.B.-F.)
| | - Renata Pessôa Germano Mendes
- Departamento de Parasitologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (L.R.S.V.); (A.d.M.N.); (C.T.A.d.S.); (R.P.G.M.); (M.A.L.d.S.); (W.R.C.d.N.); (R.M.L.A.); (S.P.B.-F.)
| | - Maria Almerice Lopes da Silva
- Departamento de Parasitologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (L.R.S.V.); (A.d.M.N.); (C.T.A.d.S.); (R.P.G.M.); (M.A.L.d.S.); (W.R.C.d.N.); (R.M.L.A.); (S.P.B.-F.)
| | - Tiago Gräf
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil;
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, Brazil;
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro 21040-900, Brazil;
| | - Michelle da Silva Barros
- Departamento de Imunologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (K.G.d.S.S.); (M.d.S.B.)
| | - Wheverton Ricardo Correia do Nascimento
- Departamento de Parasitologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (L.R.S.V.); (A.d.M.N.); (C.T.A.d.S.); (R.P.G.M.); (M.A.L.d.S.); (W.R.C.d.N.); (R.M.L.A.); (S.P.B.-F.)
- Departamento de Medicina Tropical, Centro de Ciências Médicas, Universidade Federal de Pernambuco (UFPE), Recife 50670-901, Brazil
| | - Rodrigo Moraes Loyo Arcoverde
- Departamento de Parasitologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (L.R.S.V.); (A.d.M.N.); (C.T.A.d.S.); (R.P.G.M.); (M.A.L.d.S.); (W.R.C.d.N.); (R.M.L.A.); (S.P.B.-F.)
| | | | - Sinval Pinto Brandão-Filho
- Departamento de Parasitologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (L.R.S.V.); (A.d.M.N.); (C.T.A.d.S.); (R.P.G.M.); (M.A.L.d.S.); (W.R.C.d.N.); (R.M.L.A.); (S.P.B.-F.)
| | - Constância Flávia Junqueira Ayres
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (D.R.D.G.); (F.Z.D.); (L.C.M.); (L.K.); (E.H.); (A.F.d.S.); (D.L.d.C.); (C.F.J.A.)
| | - Gabriel Luz Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (D.R.D.G.); (F.Z.D.); (L.C.M.); (L.K.); (E.H.); (A.F.d.S.); (D.L.d.C.); (C.F.J.A.)
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil
- Correspondence:
| |
Collapse
|
5
|
da Silva SJR, Germano Mendes RP, Alves da Silva CT, Lorusso A, Kohl A, Pena L. Insights into SARS-CoV-2, the Coronavirus Underlying COVID-19: Recent Genomic Data and the Development of Reverse Genetics Systems. J Gen Virol 2020; 101:1021-1024. [PMID: 32579100 PMCID: PMC7660456 DOI: 10.1099/jgv.0.001458] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/01/2020] [Indexed: 12/13/2022] Open
Abstract
The emergence and rapid worldwide spread of a novel pandemic of acute respiratory disease - eventually named coronavirus disease 2019 (COVID-19) by the World Health Organization (WHO) - across the human population has raised great concerns. It prompted a mobilization around the globe to study the underlying pathogen, a close relative of severe acute respiratory syndrome coronavirus (SARS-CoV) called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Numerous genome sequences of SARS-CoV-2 are now available and in-depth analyses are advancing. These will allow detailed characterization of sequence and protein functions, including comparative studies. Care should be taken when inferring function from sequence information alone, and reverse genetics systems can be used to unequivocally identify key features. For example, the molecular markers of virulence, host range and transmissibility of SARS-CoV-2 can be compared to those of related viruses in order to shed light on the biology of this emerging pathogen. Here, we summarize some recent insights from genomic studies and strategies for reverse genetics systems to generate recombinant viruses, which will be useful to investigate viral genome properties and evolution.
Collapse
Affiliation(s)
| | - Renata Pessôa Germano Mendes
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420, Recife Pernambuco, Brazil
| | - Caroline Targino Alves da Silva
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420, Recife Pernambuco, Brazil
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise (IZSAM), Teramo, Italy
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland G61 1QH, UK
| | - Lindomar Pena
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420, Recife Pernambuco, Brazil
| |
Collapse
|
6
|
Guarines KM, Mendes RPG, Cordeiro MT, Miagostovich MP, Gil LHVG, Green KY, Pena LJ. Absence of norovirus contamination in shellfish harvested and commercialized in the Northeast coast of Brazil. ACTA ACUST UNITED AC 2020; 53:e9529. [PMID: 32965324 PMCID: PMC7510241 DOI: 10.1590/1414-431x20209529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 01/19/2020] [Accepted: 07/16/2020] [Indexed: 11/22/2022]
Abstract
Norovirus (NoV) is the main cause of gastroenteritis outbreaks worldwide. Although NoV spreads mainly from person to person, it is estimated that a large proportion of NoV outbreaks are caused by foodborne transmission. Bivalve mollusks are one of the most important foods involved in NoV transmission to humans. Little is known about NoV prevalence in shellfish harvested and commercialized in Brazil. The aim of this study was to map, for the first time, the distribution of NoV contamination in oysters and mussels harvested and commercialized in the coast of Pernambuco state, northeast Brazil. A total of 380 mollusks (260 oysters and 120 mussels) were collected between February and August 2017 either directly from harvesting areas or obtained from beach vendors at 17 sites in Pernambuco. Samples were processed and tested for NoV contamination using a SYBR Green real-time PCR assay. All samples were negative for NoV GI or GII contamination, suggesting a low risk of NoV contamination from this food source during the study period. Additional surveys in different areas of the Brazilian coast are warranted to monitor the risk of NoV infection upon seafood consumption.
Collapse
Affiliation(s)
- K M Guarines
- Departamento de Virologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brasil
| | - R P G Mendes
- Departamento de Virologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brasil
| | - M T Cordeiro
- Departamento de Virologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brasil
| | - M P Miagostovich
- Laboratório de Virologia Comparativa e Ambiental, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - L H V G Gil
- Departamento de Virologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brasil
| | - K Y Green
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - L J Pena
- Departamento de Virologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brasil
| |
Collapse
|
7
|
da Silva SJR, Silva CTAD, Guarines KM, Mendes RPG, Pardee K, Kohl A, Pena L. Clinical and Laboratory Diagnosis of SARS-CoV-2, the Virus Causing COVID-19. ACS Infect Dis 2020; 6:2319-2336. [PMID: 32786280 PMCID: PMC7441751 DOI: 10.1021/acsinfecdis.0c00274] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [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: 05/04/2020] [Indexed: 01/08/2023]
Abstract
In December 2019, a novel beta (β) coronavirus eventually named SARS-CoV-2 emerged in Wuhan, Hubei province, China, causing an outbreak of severe and even fatal pneumonia in humans. The virus has spread very rapidly to many countries across the world, resulting in the World Health Organization (WHO) to declare a pandemic on March 11, 2020. Clinically, the diagnosis of this unprecedented illness, called coronavirus disease-2019 (COVID-19), becomes difficult because it shares many symptoms with other respiratory pathogens, including influenza and parainfluenza viruses. Therefore, laboratory diagnosis is crucial for the clinical management of patients and the implementation of disease control strategies to contain SARS-CoV-2 at clinical and population level. Here, we summarize the main clinical and imaging findings of COVID-19 patients and discuss the advances, features, advantages, and limitations of different laboratory methods used for SARS-CoV-2 diagnosis.
Collapse
Affiliation(s)
| | - Caroline Targino Alves da Silva
- Department of Virology, Aggeu
Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz),
50670-420, Recife, Pernambuco, Brazil
| | - Klarissa Miranda Guarines
- Department of Virology, Aggeu
Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz),
50670-420, Recife, Pernambuco, Brazil
| | - Renata Pessôa Germano Mendes
- Department of Virology, Aggeu
Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz),
50670-420, Recife, Pernambuco, Brazil
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy,
University of Toronto, Toronto, ON M5S 3M2,
Canada
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus
Research, Glasgow, Scotland G61 1QH, U.K.
| | - Lindomar Pena
- Department of Virology, Aggeu
Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz),
50670-420, Recife, Pernambuco, Brazil
| |
Collapse
|
8
|
Silva SJRD, Magalhães JJFD, Mendes RPG, Pena LJ. Has Zika Virus Established a Sylvatic Cycle in South America? Acta Trop 2020; 209:105525. [PMID: 32447030 DOI: 10.1016/j.actatropica.2020.105525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/21/2020] [Accepted: 05/02/2020] [Indexed: 02/05/2023]
Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Avenida Professor Moraes Rego 50670-420, Recife, Pernambuco, Brazil
| | - Jurandy Júnior Ferraz de Magalhães
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Avenida Professor Moraes Rego 50670-420, Recife, Pernambuco, Brazil
| | - Renata Pessôa Germano Mendes
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Avenida Professor Moraes Rego 50670-420, Recife, Pernambuco, Brazil
| | - Lindomar José Pena
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Avenida Professor Moraes Rego 50670-420, Recife, Pernambuco, Brazil.
| |
Collapse
|
9
|
da Silva SJR, Alves da Silva CT, Mendes RPG, Pena L. Role of nonstructural proteins in the pathogenesis of SARS-CoV-2. J Med Virol 2020; 92:1427-1429. [PMID: 32270884 PMCID: PMC7262198 DOI: 10.1002/jmv.25858] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 04/08/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Department of Virology, Aggeu Magalhaes Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Avenida Professor Moraes Rego, Recife, Pernambuco, Brazil
| | - Caroline Targino Alves da Silva
- Department of Virology, Aggeu Magalhaes Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Avenida Professor Moraes Rego, Recife, Pernambuco, Brazil
| | - Renata Pessôa Germano Mendes
- Department of Virology, Aggeu Magalhaes Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Avenida Professor Moraes Rego, Recife, Pernambuco, Brazil
| | - Lindomar Pena
- Department of Virology, Aggeu Magalhaes Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Avenida Professor Moraes Rego, Recife, Pernambuco, Brazil
| |
Collapse
|