Biomaterial Database

Development and Validation of Real-Time RT-LAMP Assays for the Specific Detection of Zika Virus. 2020

Benjamin Lopez-Jimena, and Mohammed Bakheit, and Michaël Bekaert, and Graham Harold, and Sieghard Frischmann, and Cheikh Fall, and Cheikh Tidiane Diagne, and Oumar Faye, and Ousmane Faye, and Amadou Alpha Sall, and Manfred Weidmann

Institute of Aquaculture, University of Stirling, Scotland, UK. benjamin.lopez-jimena@lifearc.org.

Two one-step real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for the detection of Zika virus (ZIKV) were developed, based on two different primer design approaches: (1) open source, based on a combination of sequence diversity clustering (phylogeny and principal component analysis) and LAVA algorithm, using 45 whole genome ZIKV sequences retrieved from the National Center for Biotechnology Information (NCBI) database; (2) standard software for LAMP primer design (Primer Explorer V4), using 59 sequences of the ZIKV 3' UTR. The assays were firstly evaluated with External Quality Assessment panels from INSTAND e.V. (Germany) and EVD-LabNet (The Netherlands) including 4 and 12 unknown samples, respectively, and secondly, with 9 human, mosquito, and monkey ZIKV isolates from Africa (Senegal, Ivory Coast, and Uganda) and America (Brazil). The limit of detection as determined by probit analysis was 181 molecules for both RT-LAMP assays, and 100% reproducibility in the assays was obtained for 103 molecules (4/8 repetitions were positive for 102 molecules). Both assays were specific, amplifying only ZIKV RNA and not cross-detecting other arboviruses included in this study.

UI	MeSH Term	Description	Entries
D009033	Culicidae	A family of the order DIPTERA that comprises the mosquitoes. The larval stages are aquatic, and the adults can be recognized by the characteristic WINGS, ANIMAL venation, the scales along the wing veins, and the long proboscis. Many species are of particular medical importance.	Mosquitoes,Mosquitos,Mosquito
D009426	Netherlands	Country located in EUROPE. It is bordered by the NORTH SEA, BELGIUM, and GERMANY. Constituent areas are Aruba, Curacao, and Sint Maarten, formerly included in the NETHERLANDS ANTILLES.	Holland,Kingdom of the Netherlands
D001938	Brazil	A country located on the eastern coast of South America, located between Colombia and Peru, that borders the Atlantic Ocean. It is bordered on the north by Venezuela, Guyana, Suriname, and French Guiana, on the south by Uruguay, and on the west by Argentina. The capital is Brasilia.
D002478	Cells, Cultured	Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.	Cultured Cells,Cell, Cultured,Cultured Cell
D005858	Germany	A country in central Europe, bordering the Baltic Sea and the North Sea, between the Netherlands and Poland, south of Denmark. The capital is Berlin.
D006801	Humans	Members of the species Homo sapiens.	Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D000071243	Zika Virus Infection	A viral disease transmitted by the bite of AEDES mosquitoes infected with ZIKA VIRUS. Its mild DENGUE-like symptoms include fever, rash, headaches and ARTHRALGIA. The viral infection during pregnancy, in rare cases, is associated with congenital brain and ocular abnormalities, called Congenital Zika Syndrome, including MICROCEPHALY and may also lead to GUILLAIN-BARRE SYNDROME.	Congenital Zika Syndrome,Congenital Zika Virus Infection,Fever, Zika,ZikV Infection,Zika Fever,Zika Virus Disease,Disease, Zika Virus,Infection, ZikV,Infection, Zika Virus,Virus Disease, Zika,Virus Infection, Zika
D000071244	Zika Virus	An arbovirus in the FLAVIVIRUS genus of the family FLAVIVIRIDAE. Originally isolated in the Zika Forest of UGANDA it has been introduced to Asia and the Americas.	Virus, Zika,ZikV
D000349	Africa	The continent south of EUROPE, east of the ATLANTIC OCEAN and west of the INDIAN OCEAN.
D000465	Algorithms	A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.	Algorithm