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Article ; Online: Loop-mediated isothermal amplification (LAMP): An effective molecular point-of-care technique for the rapid diagnosis of coronavirus SARS-CoV-2.

Chaouch, Melek

2021 Volume 31, Issue 6, Page(s) e2215

Abstract: The novel coronavirus disease-2019 (Covid-19) public health emergency has caused enormous loss around the world. This pandemic is a concrete example of the existing gap between availability of advanced diagnostics and current need for cost-effective ... ...

Abstract	The novel coronavirus disease-2019 (Covid-19) public health emergency has caused enormous loss around the world. This pandemic is a concrete example of the existing gap between availability of advanced diagnostics and current need for cost-effective methodology. The advent of the loop-mediated isothermal amplification (LAMP) assay provided an innovative tool for establishing a rapid diagnostic technique based on the molecular amplification of pathogen RNA or DNA. In this review, we explore the applications, diagnostic effectiveness of LAMP test for molecular diagnosis and surveillance of severe acute respiratory syndrome coronavirus 2. Our results show that LAMP can be considered as an effective point-of-care test for the diagnosis of Covid-19 in endemic areas, especially for low- and middle-income countries.
MeSH term(s)	Bibliometrics ; COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19/pathology ; COVID-19/virology ; COVID-19 Nucleic Acid Testing/economics ; COVID-19 Nucleic Acid Testing/instrumentation ; COVID-19 Nucleic Acid Testing/methods ; Humans ; Molecular Diagnostic Techniques/economics ; Molecular Diagnostic Techniques/instrumentation ; Molecular Diagnostic Techniques/methods ; Nucleic Acid Amplification Techniques/economics ; Nucleic Acid Amplification Techniques/instrumentation ; Nucleic Acid Amplification Techniques/methods ; Point-of-Care Testing/economics ; Point-of-Care Testing/organization & administration ; RNA, Viral/genetics ; SARS-CoV-2/genetics ; SARS-CoV-2/pathogenicity ; Sensitivity and Specificity
Chemical Substances	RNA, Viral
Language	English
Publishing date	2021-01-21
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1086043-5
ISSN	1099-1654 ; 1052-9276
ISSN (online)	1099-1654
ISSN	1052-9276
DOI	10.1002/rmv.2215
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Article: Retrospective Phylodynamic and Phylogeographic Analysis of the Bluetongue Virus in Tunisia.

Souiai, Oussema / Arbi, Marwa / Hanachi, Mariem / Sallami, Ameny / Larbi, Imen / Chaouch, Melek / Harigua-Souiai, Emna / Benkahla, Alia

Evolutionary bioinformatics online

2023 Volume 19, Page(s) 11769343231212266

Abstract: Bluetongue virus (BTV) is an arbovirus considered as a major threat for the global livestock economy. Since 1999, Tunisia has experienced several incursions of BTV, during which numerous cases of infection and mortality have been reported. However, the ... ...

Abstract	Bluetongue virus (BTV) is an arbovirus considered as a major threat for the global livestock economy. Since 1999, Tunisia has experienced several incursions of BTV, during which numerous cases of infection and mortality have been reported. However, the geographical origin and epidemiological characteristics of these incursions remained unclear. To understand the evolutionary history of BTV emergence in Tunisia, we extracted from Genbank the segment 6 sequences of 7 BTV strains isolated in Tunisia during the period 2000 to 2017 and blasted them to obtain a final dataset of 67 sequences. We subjected the dataset to a Bayesian phylogeography framework inferring geographical origin and serotype as phylodynamic models. Our results suggest that BTV-2 was first introduced in Tunisia in the 1960s and that since 1990s, the country has witnessed the emergence of other typical and atypical BTV serotypes notably BTV-1, BTV-3 and BTV-Y. The reported serotypes have a diverse geographical origin and have been transmitted to Tunisia from countries in the Mediterranean Basin. Interserotype reassortments have been identified among BTV-1, BTV-2 and BTV-Y. This study has provided new insights on the temporal and geographical origin of BTV in Tunisia, suggesting the contribution of animal trade and environment conditions in virus spread.
Language	English
Publishing date	2023-11-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	2227610-5
ISSN	1176-9343
ISSN	1176-9343
DOI	10.1177/11769343231212266
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Article ; Online: Development and evaluation of an easy to use real-time reverse-transcription loop-mediated isothermal amplification assay for clinical diagnosis of West Nile virus.

Khedhiri, Marwa / Chaouch, Melek / Ayouni, Kaouther / Chouikha, Anissa / Gdoura, Mariem / Touzi, Henda / Hogga, Nahed / Benkahla, Alia / Fares, Wasfi / Triki, Henda

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

2023 Volume 170, Page(s) 105633

Abstract: West Nile Virus (WNV) causes a serious public health concern in many countries around the world. Virus detection in pathological samples is a key component of WNV infection diagnostic, classically performed by real-time PCR. In outbreak situation, rapid ... ...

Abstract	West Nile Virus (WNV) causes a serious public health concern in many countries around the world. Virus detection in pathological samples is a key component of WNV infection diagnostic, classically performed by real-time PCR. In outbreak situation, rapid detection of the virus, in peripheral laboratories or at point of care, is crucial to guide decision makers and for the establishment of adequate action plans to prevent virus dissemination. Here, we evaluate a Loop-mediated isothermal amplification (LAMP) tool for WNV detection. Amplifications were performed comparatively on extracted viral RNA and on crude samples using a classical thermal cycler and a portable device (pebble device). qRT-PCR was used as gold standard and two sets of urine samples (n = 62 and n = 74) were used to evaluate the retained amplification protocols and assess their sensitivity and specificity. RT-LAMP on RNA extracts and crude samples showed a sensitivity of 90 % and 87 %, respectively. The specificity was 100 % for extracts and 97 % for crude samples. Using the device, the RT-LAMP on extracted RNA was comparable to the gold standard results (100 % sensitivity and specificity) and it was a bit lower on crude samples (65 % sensitivity and 94 % specificity). These results show that RT-LAMP is an efficient technique to detect WNV. RT-LAMP provides a rapid, sensitive, high-throughput and portable tool for accurate WNV detection and has potentials to facilitate diagnostic and surveillance efforts both in the laboratory and in the field, especially in developing countries.
MeSH term(s)	Humans ; West Nile virus/genetics ; Nucleic Acid Amplification Techniques/methods ; Molecular Diagnostic Techniques ; Sensitivity and Specificity ; RNA, Viral/genetics
Chemical Substances	RNA, Viral
Language	English
Publishing date	2023-12-07
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1446080-4
ISSN	1873-5967 ; 1386-6532
ISSN (online)	1873-5967
ISSN	1386-6532
DOI	10.1016/j.jcv.2023.105633
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Zs.A 3790: Show issues

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ab Jg. 2022: Lesesaal (EG)

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Article ; Online: ITS1 and cpb genetic polymorphisms in Algerian and Tunisian Leishmania infantum isolates from humans and dogs

Benikhlef, Razika / Chaouch, Melek / Abid, Meriem Ben / Aoun, Karim / Harrat, Zoubir / Bouratbine, Aida / BenAbderrazak, Souha

Zoonoses and Public Health. 2023 May, v. 70, no. 3 p.201-212

2023

Abstract: Leishmania (L.) infantum strains, isolated from varying hosts and clinical manifestations (cutaneous, visceral and canine leishmaniasis), were investigated in order to understand the genetic polymorphisms within this species in Algeria and Tunisia. Two ... ...

Abstract	Leishmania (L.) infantum strains, isolated from varying hosts and clinical manifestations (cutaneous, visceral and canine leishmaniasis), were investigated in order to understand the genetic polymorphisms within this species in Algeria and Tunisia. Two DNA‐based typing methods were tested in order to evaluate their effectiveness against Multilocus enzyme electrophoresis (MLEE), widely considered as the reference method for Leishmania parasite typing. On the other hand, MLEE is cumbersome, high‐cost, time consuming and frequently does not detect intra‐species genetic polymorphisms. In this work, we used two molecular target regions to discriminate L. infantum strains, Internal transcribed spacer 1 (ITS1) and the cysteine proteinase B (cpb). The ITS1 region offers good resolution for Leishmania discrimination but does not spotlight intra‐species polymorphisms. In contrast, cpbE and cpbF PCR‐Sequencing demonstrated a certain variability within CL and VL Algerian and Tunisian L. infantum isolates. Following phylogenetic analyses of 44 L. infantum isolates, two main groups were identified, a group with 39 bp deletion in the cpb sequence, composed of cutaneous, visceral and canine isolates from both countries with no significant clinical or geographic distribution; these samples were typed as MON‐1, MON‐24, and MON‐80 zymodemes. A second group which presents a clear clusterization of Tunisian cutaneous strains belonging to the L. infantum MON‐24. This group, with no deletion in the mature domain of the cpb gene sequence, should be further explored with a higher number of samples.
Keywords	Leishmania infantum ; cysteine proteinases ; dogs ; electrophoresis ; geographical distribution ; internal transcribed spacers ; leishmaniasis ; parasites ; phylogeny ; public health ; zoonoses ; Algeria ; Tunisia
Language	English
Dates of publication	2023-05
Size	p. 201-212.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2271118-1
ISSN	1863-2378 ; 1863-1959
ISSN (online)	1863-2378
ISSN	1863-1959
DOI	10.1111/zph.13016
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Investigation of natural infection of Phlebotomine (Diptera: Psychodidae) by

Chaouch, Melek / Chaabane, Amal / Ayari, Chiraz / Ben Othman, Souad / Sereno, Denis / Chemkhi, Jomaa / BenAbderrazak, Souha

Parasite epidemiology and control

2021 Volume 14, Page(s) e00212

Abstract: Leishmaniases are caused by protozoan parasites of the ... ...

Abstract	Leishmaniases are caused by protozoan parasites of the genus
Language	English
Publishing date	2021-04-17
Publishing country	Netherlands
Document type	Journal Article
ISSN	2405-6731
ISSN (online)	2405-6731
DOI	10.1016/j.parepi.2021.e00212
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: First Report of Two

Ghawar, Wissem / Chaouch, Melek / Ben Salah, Afif / Snoussi, Mohamed Ali / Salem, Sadok / Kharroubi, Ghassen / Chouchen, Said / Bouaoun, Amor / Laouini, Dhafer / Bettaieb, Jihene / Ben Abderrazak, Souha

Microorganisms

2022 Volume 10, Issue 8

Abstract: This study shows, for the first time, ... ...

Abstract	This study shows, for the first time, natural
Language	English
Publishing date	2022-07-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms10081502
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Article: Evaluation of the Taxonomic Status of Lesser Egyptian Jerboa,

Ghawar, Wissem / Chaouch, Melek / Ben Abderrazak, Souha / Snoussi, Mohammed Ali / Salem, Sadok / Chouchen, Said / Bouaoun, Amor / Ben Salah, Afif / Bettaieb, Jihene

Animals : an open access journal from MDPI

2022 Volume 12, Issue 6

Abstract: The taxonomy of the Lesser Egyptian jerboa, ...

Abstract	The taxonomy of the Lesser Egyptian jerboa,
Language	English
Publishing date	2022-03-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606558-7
ISSN	2076-2615
ISSN	2076-2615
DOI	10.3390/ani12060758
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Article ; Online: ITS1 and cpb genetic polymorphisms in Algerian and Tunisian Leishmania infantum isolates from humans and dogs.

Benikhlef, Razika / Chaouch, Melek / Abid, Meriem Ben / Aoun, Karim / Harrat, Zoubir / Bouratbine, Aida / BenAbderrazak, Souha

Zoonoses and public health

2022 Volume 70, Issue 3, Page(s) 201–212

Abstract	Leishmania (L.) infantum strains, isolated from varying hosts and clinical manifestations (cutaneous, visceral and canine leishmaniasis), were investigated in order to understand the genetic polymorphisms within this species in Algeria and Tunisia. Two DNA-based typing methods were tested in order to evaluate their effectiveness against Multilocus enzyme electrophoresis (MLEE), widely considered as the reference method for Leishmania parasite typing. On the other hand, MLEE is cumbersome, high-cost, time consuming and frequently does not detect intra-species genetic polymorphisms. In this work, we used two molecular target regions to discriminate L. infantum strains, Internal transcribed spacer 1 (ITS1) and the cysteine proteinase B (cpb). The ITS1 region offers good resolution for Leishmania discrimination but does not spotlight intra-species polymorphisms. In contrast, cpbE and cpbF PCR-Sequencing demonstrated a certain variability within CL and VL Algerian and Tunisian L. infantum isolates. Following phylogenetic analyses of 44 L. infantum isolates, two main groups were identified, a group with 39 bp deletion in the cpb sequence, composed of cutaneous, visceral and canine isolates from both countries with no significant clinical or geographic distribution; these samples were typed as MON-1, MON-24, and MON-80 zymodemes. A second group which presents a clear clusterization of Tunisian cutaneous strains belonging to the L. infantum MON-24. This group, with no deletion in the mature domain of the cpb gene sequence, should be further explored with a higher number of samples.
MeSH term(s)	Humans ; Animals ; Dogs ; Leishmania infantum/genetics ; Leishmaniasis, Visceral/epidemiology ; Leishmaniasis, Visceral/veterinary ; Leishmaniasis, Visceral/parasitology ; Phylogeny ; Polymorphism, Genetic ; Skin ; Dog Diseases/epidemiology ; Dog Diseases/parasitology
Language	English
Publishing date	2022-11-28
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2271118-1
ISSN	1863-2378 ; 1863-1959
ISSN (online)	1863-2378
ISSN	1863-1959
DOI	10.1111/zph.13016
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Investigation of natural infection of Phlebotomine (Diptera: Psychodidae) by Leishmania in Tunisian endemic regions

Chaouch, Melek / Chaabane, Amal / Ayari, Chiraz / Ben Othman, Souad / Sereno, Denis / Chemkhi, Jomaa / BenAbderrazak, Souha

Parasite epidemiology and control. 2021 Aug., v. 14

2021

Abstract: Leishmaniases are caused by protozoan parasites of the genus Leishmania transmitted by females blood-feeding phlebotomine insects (Diptera: Psychodidae). In Tunisia, cutaneous and visceral leishmaniases are of public health concern. In Tunisia, 17 ... ...

Abstract	Leishmaniases are caused by protozoan parasites of the genus Leishmania transmitted by females blood-feeding phlebotomine insects (Diptera: Psychodidae). In Tunisia, cutaneous and visceral leishmaniases are of public health concern. In Tunisia, 17 species of phlebotomine sand flies are described. Here we investigate natural infection in Tunisian mixed foci regions of leishmaniases. We trap female sandflies during the Leishmania transmission season in the country's central-eastern and northern parts. We investigate Leishmania infection using PCR-RFLP targeting the ITS1 ribosomal DNA, followed by enzymatic digestion with HaeIII; then, we identify sand flies using molecular methodologies. We confirm the presence of Phlebotomus papatasi and Phlebotomus perniciosus infected by L. major and L. infantum parasites in Tunisia.
Keywords	Phlebotomus papatasi ; Phlebotomus perniciosus ; epidemiology ; females ; hematophagy ; parasites ; public health ; ribosomal DNA ; sand ; visceral leishmaniasis ; Tunisia
Language	English
Dates of publication	2021-08
Publishing place	Elsevier Ltd
Document type	Article
Note	NAL-AP-2-clean
ISSN	2405-6731
DOI	10.1016/j.parepi.2021.e00212
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Data Management Plans in the genomics research revolution of Africa: Challenges and recommendations.

Fadlelmola, Faisal M / Zass, Lyndon / Chaouch, Melek / Samtal, Chaimae / Ras, Verena / Kumuthini, Judit / Panji, Sumir / Mulder, Nicola

Journal of biomedical informatics

2021 Volume 122, Page(s) 103900

Abstract: Drafting and writing a data management plan (DMP) is increasingly seen as a key part of the academic research process. A DMP is a document that describes how a researcher will collect, document, describe, share, and preserve the data that will be ... ...

Abstract	Drafting and writing a data management plan (DMP) is increasingly seen as a key part of the academic research process. A DMP is a document that describes how a researcher will collect, document, describe, share, and preserve the data that will be generated as part of a research project. The DMP illustrates the importance of utilizing best practices through all stages of working with data while ensuring accessibility, quality, and longevity of the data. The benefits of writing a DMP include compliance with funder and institutional mandates; making research more transparent (for reproduction and validation purposes); and FAIR (findable, accessible, interoperable, reusable); protecting data subjects and compliance with the General Data Protection Regulation (GDPR) and/or local data protection policies. In this review, we highlight the importance of a DMP in modern biomedical research, explaining both the rationale and current best practices associated with DMPs. In addition, we outline various funders' requirements concerning DMPs and discuss open-source tools that facilitate the development and implementation of a DMP. Finally, we discuss DMPs in the context of African research, and the considerations that need to be made in this regard.
MeSH term(s)	Africa ; Biomedical Research ; Data Management ; Genomics ; Humans ; Research Design
Language	English
Publishing date	2021-09-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	2057141-0
ISSN	1532-0480 ; 1532-0464
ISSN (online)	1532-0480
ISSN	1532-0464
DOI	10.1016/j.jbi.2021.103900
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