Geographical variability affects CCHFV detection by RT-PCR : a tool for in-silico evaluation of molecular assays

Gruber, Cesare E. M. (avtor), Bartolini, Barbara (avtor), Castilletti, Concetta (avtor), Mirazimi, Ali (avtor), Hewson, Roger (avtor), Christova, Iva (avtor), Avšič-Županc, Tatjana (avtor), Grunow, Roland (avtor), Papa, Anna (avtor), Sánchez-Seco, María P. (avtor), Koopmans, Marion (avtor), Ippolito, Giuseppe (avtor), Capobianchi, Maria Rosaria (avtor), Reusken, Chantal B. E. M. (avtor), Di Caro, Antonino (avtor)

The Crimean-Congo hemorrhagic fever virus (CCHFV) is considered to be a major emerging infectious threat, according to the WHO R&D blueprint. A wide range of CCHFV molecular assays have been developed, employing varied primer/probe combinations. The high genetic variability of CCHFV often hampers the efficacy of available molecular tests and can affect their diagnostic potential. Recently, increasing numbers of complete CCHFV genomic sequences have become available, allowing a better appreciation of the genomic evolution of this virus. We summarized the current knowledge on molecular methods and developed a new bioinformatics tool to evaluate the existing assays for CCHFV detection, with a special focus on strains circulating in different geographical areas. Twenty-two molecular methods and 181 sequences of CCHFV were collected, respectively, from PubMed and GenBank databases. Up to 28 mismatches between primers and probes of each assay and CCHFV strains were detected through in-silico PCR analysis. Combinations of up to three molecular methods markedly decreased the number of mismatches within most geographic areas. These results supported the good practice of CCHFV detection of performing more than one assay, aimed for different sequence targets. The choice of the most appropriate tests must take into account patient's travel history and geographic distribution of the different CCHFV strains.

• Jezik: Angleški jezik
• Ključne besede: Crimean-Congo hemorrhagic fever, molecular detection, CCHFV, Crimean–Congo hemorrhagic fever virus, arthropod-borne virus, laboratory preparedness, emerging diseases
• Vrsta gradiva: Članek v reviji
• Tipologija: 1.01 - Izvirni znanstveni članek
• Organizacija: MF - Medicinska fakulteta
• Status publikacije: Objavljeno
• Različica publikacije: Objavljena publikacija
• Leto izida: 2019
• Št. strani: 14 str.
• Številčenje: Vol. 11, iss. 10, art. 953
• PID: 20.500.12556/RUL-133136
• UDK: 616.9
• ISSN pri članku: 1999-4915
• DOI: 10.3390/v11100953
• COBISS.SI-ID: 34533081
• Datum objave v RUL: 12.11.2021

Gradivo je del revije

• Naslov: Viruses
• Skrajšan naslov: Viruses
• Založnik: MDPI
• ISSN: 1999-4915
• COBISS.SI-ID: 517597977

Licence

• Licenca: CC BY 4.0, Creative Commons Priznanje avtorstva 4.0 Mednarodna
• Povezava: http://creativecommons.org/licenses/by/4.0/deed.sl
• Opis: To je standardna licenca Creative Commons, ki daje uporabnikom največ možnosti za nadaljnjo uporabo dela, pri čemer morajo navesti avtorja.
• Začetek licenciranja: 16.10.2019

Sekundarni jezik

• Jezik: Slovenski jezik
• Ključne besede: krimsko-kongoška hemoragična mrzlica, molekularno odkrivanje, arbovirus