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Alcántara R, Peñaranda K, Mendoza-Rojas G, Nakamoto JA, Dueñas E, Alvarez D, Adaui V, Milón P. UnCovid: A versatile, low-cost, and open-source protocol for SARS-CoV-2 RNA detection. STAR Protoc 2021; 2:100878. [PMID: 34604812 PMCID: PMC8463329 DOI: 10.1016/j.xpro.2021.100878] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Here, we describe a detailed step-by-step protocol to detect SARS-CoV-2 RNA using RT-PCR-mediated amplification and CRISPR/Cas-based visualization. The optimized assay uses basic molecular biology equipment such as conventional thermocyclers and transilluminators for qualitative detection. Alternatively, a fluorescence plate reader can be used for quantitative measurements. The protocol detects two regions of the SARS-CoV-2 genome in addition to the human RNaseP sample control. Aiming to reach remote regions, this work was developed to use the portable molecular workstation from BentoLab. For complete details on the use and execution of this protocol, please refer to Alcántara et al., 2021.
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Affiliation(s)
- Roberto Alcántara
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Katherin Peñaranda
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Gabriel Mendoza-Rojas
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Jose A. Nakamoto
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Eva Dueñas
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Daniela Alvarez
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Vanessa Adaui
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
| | - Pohl Milón
- Centre for Research and Innovation, Health Sciences Faculty, Universidad Peruana de Ciencias Aplicadas (UPC), Lima 15023, Peru
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Kumar JS, Yadav PD, Shete AM, Majumdar T, Patil S, Dash PK. Development and evaluation of reverse transcription loop-mediated isothermal amplification for rapid and real-time detection of Kyasanur forest disease virus. Int J Infect Dis 2021; 112:346-351. [PMID: 33486011 DOI: 10.1016/j.ijid.2021.01.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/07/2021] [Accepted: 01/18/2021] [Indexed: 11/16/2022] Open
Abstract
SIGNIFICANCE Kyasanur forest disease (KFD), a re-emerging tick-borne viral disease, causes severe hemorrhagic fever in humans and nonhuman primates. KFD virus (KFDV) is a member of the genus Flavivirus. KFD is now increasingly reported outside its endemic zone in India. Rapid and specific detection of the KFDV plays a critical role in containment of the outbreak. The diagnosis of KFD currently relies on real-time RT-PCR, nested RT-PCR, end point RT-PCR, and serodiagnostic assay. These assays are tedious, time-consuming, and cannot be used as a routine screening platform. OBJECTIVE The present study was aimed to develop a one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for molecular diagnosis of KFD. DESIGN The gene amplification reaction was accomplished by incubation at a constant temperature of 63°C for 60min. RESULTS The limit of detection of RT-LAMP assay was 10 copies. KFD RT-LAMP assay was successfully evaluated with diverse host samples including humans, monkeys, and tick. The assay correctly picked up different KFD isolates indicating its applicability for divergent strains. Comparative evaluation of RT-LAMP assay with quantitative TaqMan real-time RT-PCR revealed 100% concordance. No cross-reaction with related flavi and other hemorrhagic fever viruses was observed, indicating its high specificity. CONCLUSION AND RELEVANCE The RT-LAMP test developed in this study will serve as a rapid, sensitive alternate detection method for KFDV infection and would be useful for high throughput screening of clinical samples in resource limited areas during outbreaks.
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Affiliation(s)
- Jyoti S Kumar
- Division of Virology, Defence Research and Development Establishment, Gwalior 474002, India
| | - Pragya D Yadav
- Indian Council of Medical Research, National Institute of Virology, Pune, 411021, India
| | - Anita M Shete
- Indian Council of Medical Research, National Institute of Virology, Pune, 411021, India
| | - Triparna Majumdar
- Indian Council of Medical Research, National Institute of Virology, Pune, 411021, India
| | - Savita Patil
- Indian Council of Medical Research, National Institute of Virology, Pune, 411021, India
| | - Paban Kumar Dash
- Division of Virology, Defence Research and Development Establishment, Gwalior 474002, India.
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Kyasanur Forest Disease and Alkhurma Hemorrhagic Fever Virus-Two Neglected Zoonotic Pathogens. Microorganisms 2020; 8:microorganisms8091406. [PMID: 32932653 PMCID: PMC7564883 DOI: 10.3390/microorganisms8091406] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/04/2020] [Accepted: 09/10/2020] [Indexed: 11/17/2022] Open
Abstract
Kyasanur Forest disease virus (KFDV) and Alkhurma hemorrhagic fever virus (AHFV) are tick-borne flaviviruses that cause life-threatening hemorrhagic fever in humans with case fatality rates of 3-5% for KFDV and 1-20% for AHFV, respectively. Both viruses are biosafety level 4 pathogens due to the severity of disease they cause and the lack of effective countermeasures. KFDV was discovered in India and is restricted to parts of the Indian subcontinent, whereas AHFV has been found in Saudi Arabia and Egypt. In recent years, both viruses have spread beyond their original endemic zones and the potential of AHFV to spread through ticks on migratory birds is a public health concern. While there is a vaccine with limited efficacy for KFDV used in India, there is no vaccine for AHFV nor are there any therapeutic concepts to combat infections with these viruses. In this review, we summarize the current knowledge about pathogenesis, vector distribution, virus spread, and infection control. We aim to bring attention to the potential public health threats posed by KFDV and AHFV and highlight the urgent need for the development of effective countermeasures.
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N S, Hewson R, Afrough B, Bewley K, Arunkumar G. Development of a quantitative real-time RT-PCR assay that differentiates between Kyasanur Forest disease virus and Alkhurma hemorrhagic fever virus. Ticks Tick Borne Dis 2020; 11:101381. [PMID: 32009000 DOI: 10.1016/j.ttbdis.2020.101381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 01/11/2020] [Accepted: 01/23/2020] [Indexed: 11/17/2022]
Abstract
Kyasanur Forest disease virus (KFDV) and Alkhurma hemorrhagic fever virus (AHFV) are enveloped, positive-stranded RNA viruses of clinical importance with complex enzootic life cycles involving hematophagous ticks which feed on small and large mammals. Humans and monkeys are dead-end hosts for these viruses. Recent trends in epidemiological data suggest both virus incidences are steadily increasing and their geographical distribution expanding out of previously known circulation regions. For the detection and discrimination of these two closely related flaviviruses, we have developed quantitative real-time RT-PCR assays with 100 % sensitivity and 100 % specificity for KFDV, 100 % sensitivity and 99.4 % specificity for AHFV as determined using 550 clinical samples collected between 2015-2018 from Western Ghats region of India. This rapid and sensitive assay will enable researchers to accurately diagnose the presence of the virus during viremia in human and animal blood samples, and also from tick specimens. Incorporation of these new tests into a routine diagnosis will help in the diagnosis of KFDV as well as AHFV in the endemic areas and also would provide an early warning of the spread of this virus to newer regions with similar epidemiology.
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Affiliation(s)
- Sudheesh N
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, India
| | - Roger Hewson
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Babak Afrough
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Kevin Bewley
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Govindakarnavar Arunkumar
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, India.
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Sarkale P, Shrivastava A, Mohandas S, Patil SL, Kore P, Soman V, Yadav PD. Growth Kinetics of Kyasanur Forest Disease Virus in Mammalian Cell Lines and Development of Plaque Reduction Neutralization Test. Vector Borne Zoonotic Dis 2019; 19:630-636. [PMID: 30994413 DOI: 10.1089/vbz.2018.2405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Kyasanur forest disease virus (KFDV) is a tick-borne flavivirus identified in 1957 in the Karnataka state of India causing fatalities in monkeys and humans. Even after the introduction of a vaccine in the endemic areas, hundreds of cases are reported every year. Being a high-risk category pathogen, the studies on this virus in India were limited till the past decade. The growth characteristics of this virus in various mammalian cell lines have not yet been studied. In this study, we have demonstrated the growth pattern of virus in BHK-21, Vero E6, Vero CCL81, rhabdomyosarcoma, porcine stable kidney, and Pipistrellus ceylonicus bat embryo cell lines, and found BHK-21 to be the best. We have developed KFDV plaque reduction neutralization test for the first time.
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Affiliation(s)
| | | | | | | | - Pravin Kore
- ICMR-National Institute of Virology, Pune, India
| | - Vinod Soman
- ICMR-National Institute of Virology, Pune, India
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Yadav PD, Nyayanit DA, Shete AM, Jain S, Majumdar TP, Chaubal GY, Shil P, Kore PM, Mourya DT. Complete genome sequencing of Kaisodi virus isolated from ticks in India belonging to Phlebovirus genus, family Phenuiviridae. Ticks Tick Borne Dis 2018; 10:23-33. [PMID: 30181094 DOI: 10.1016/j.ttbdis.2018.08.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/20/2018] [Accepted: 08/27/2018] [Indexed: 11/29/2022]
Abstract
An unknown virus was repeatedly isolated from hard tick (Haemaphysalis spinigera) during a proactive arbovirus survey in ticks conducted in 1957, in India. The virus remained uncharacterized for a long time. The passages of this virus in different vertebrate and invertebrate cells along with human and monkey-derived cell culture showed no cytopathic effect. It was identified later to be a member of Kaisodi group among Phlebovirus genus in the family Phenuiviridae (Order: Bunyavirales) by serological methods. Due to its genomic diversity, sequencing of this virus was a challenge for a while. In this study, we were able to sequence the complete genome of this virus isolate using next-generation sequencing (NGS) platform. The unknown virus was identified to be Kaisodi virus (KASDV) using NGS analysis. De novo genome assembly derived three genomic segments for the KASDV which encode for RNA-dependent RNA polymerase, glycoprotein precursor, and nucleoprotein. Functional as well as conserved domains for Kaisodi serogroup viruses were predicted and compared to a known representative of the genus Phlebovirus. The phylogenetic tree revealed its closeness to Silverwater virus, of Kaisodi serogroup with nucleotide (69%, 62%, and 61%) and amino acid (52%, 51%, and 62%) identity for L, M, and S segment, respectively. The study demonstrates the presence of a conserved motif (72TRGNK76) around the RNA binding motif region in tick-borne phleboviruses. The intergenic region encompassing the S segment of Kaisodi serogroup was GC-rich whereas the other Phlebovirus had AT-rich genome. KASDV has the largest intergenic region and larger loops, suggesting stem-loops formed due to larger loops as a possible factor for instability and cause of transcription termination. This paper also describes the real-time RT-PCR and RT-PCR assays developed and used for the detection of KASDV RNA in ticks from Karnataka, Kerala and Maharashtra State, India. The KASDV positivity observed in the recently collected tick pools indicates that the KASDV, isolated from Karnataka state in 1957, is also circulating in the adjoining Kerala state. On the basis of the current study, it should be possible to develop diagnostic assays which would facilitate an in-depth field survey exploring the veterinary and medical significance of KASDV.
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Affiliation(s)
- P D Yadav
- Maximum Containment Facility, Microbial Containment Complex, ICMR-National Institute of Virology, Sus Road, Pashan, Pune 411021, India
| | - D A Nyayanit
- Maximum Containment Facility, Microbial Containment Complex, ICMR-National Institute of Virology, Sus Road, Pashan, Pune 411021, India
| | - A M Shete
- Maximum Containment Facility, Microbial Containment Complex, ICMR-National Institute of Virology, Sus Road, Pashan, Pune 411021, India
| | - S Jain
- Maximum Containment Facility, Microbial Containment Complex, ICMR-National Institute of Virology, Sus Road, Pashan, Pune 411021, India
| | - T P Majumdar
- Maximum Containment Facility, Microbial Containment Complex, ICMR-National Institute of Virology, Sus Road, Pashan, Pune 411021, India
| | - G Y Chaubal
- Maximum Containment Facility, Microbial Containment Complex, ICMR-National Institute of Virology, Sus Road, Pashan, Pune 411021, India
| | - P Shil
- Maximum Containment Facility, Microbial Containment Complex, ICMR-National Institute of Virology, Sus Road, Pashan, Pune 411021, India
| | - P M Kore
- Maximum Containment Facility, Microbial Containment Complex, ICMR-National Institute of Virology, Sus Road, Pashan, Pune 411021, India
| | - D T Mourya
- Maximum Containment Facility, Microbial Containment Complex, ICMR-National Institute of Virology, Sus Road, Pashan, Pune 411021, India.
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