Analysis workflow.

<p>Input sequences were processed through a “dual-BLASTn” pipeline in order to select for the most conserved and at the same time specific molecular markers.</p

List of selected targets and real-time PCR primer pairs designed for different viral species employed in this study.

<p>List of selected targets and real-time PCR primer pairs designed for different viral species employed in this study.</p

Real-time PCR assays of members from the <i>Flavivirida</i>e and <i>Bunyaviridae</i> families.

<p>Amplification and melting curves for five different flaviviruses species are shown. Each sample was tested undiluted, with a 10-fold dilution and with a 100-fold dilution. (A) St. Louis encephalitis virus (SLEV). (B) Usutu virus (USUV). (C) Tick-borne encephalitis virus (TBEV). (D) Japanese encephalitis virus (JPEV). (E) West Nile virus (WNV; 2 strains, NY99 and Dakar). The right half of the panel shows the amplification and melting curves of the different genomic segments of the members from the <i>Bunyaviridae</i> family tested in this study. (F) Crimean-Congo hemorrhagic fever virus (CCHFV). (G) Rift Valley fever virus (RVFV). (H) Seoul virus (SEOV). NTC, no template control; RFU, relative fluorescence units; C_t, cycle threshold; Dil., dilution; Seg., Segment.</p

Testing cross-reactions between a set of close relatives from the <i>Flaviviridae</i> family.

<p>West Nile virus (WNV), Japanese encephalitis virus (JPEV), and Usutu virus (USUV) were tested. (A) Phylogenetic analysis of a subset of 6–10 sequences from members of the <i>Flaviviridae</i> family. (B) Real-time amplification of viruses with master mixes containing different primer pairs. RFU, relative fluorescence units; C_<i>t</i>, cycle threshold.</p

Loop-mediated isothermal amplification of Usutu virus (USUV) and St. Louis encephalitis virus (SLEV).

<p>NTC, no template control; RFU, relative fluorescence units; C_<i>t</i>, cycle threshold.</p

Ambiguity-based comparison of consensus sequences generated using various amounts of Crimean-Congo hemorrhagic fever virus (CCHFV) or Japanese encephalitis virus (JPEV) genomes.

<p>Ambiguity-based comparison of consensus sequences generated using various amounts of Crimean-Congo hemorrhagic fever virus (CCHFV) or Japanese encephalitis virus (JPEV) genomes.</p

Country-specific enrolment characteristics of patients and controls in the NIDIAG study on persistent digestive disorders.

<p>Country-specific enrolment characteristics of patients and controls in the NIDIAG study on persistent digestive disorders.</p

Principal elements of the NIDIAG digestive study and the respective standard operating procedures (SOPs) used.

<p>Principal elements of the NIDIAG digestive study and the respective standard operating procedures (SOPs) used.</p

Set of standard operating procedures (SOPs) used in the NIDIAG study on persistent digestive disorders.

<p>Set of standard operating procedures (SOPs) used in the NIDIAG study on persistent digestive disorders.</p

Diagnostic challenges encountered during the NIDIAG study on persistent digestive disorders and proposed solutions.

<p>Diagnostic challenges encountered during the NIDIAG study on persistent digestive disorders and proposed solutions.</p