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The use of whole genome sequencing (WGS) as a method for supporting outbreak investigations, studying Salmonella microbial populations and improving understanding of pathogenicity has been well-described (1–3). However, performing WGS on a discrete dataset does not pose the same challenges as implementing WGS as a routine, reference microbiology service for public health surveillance. Challenges include translating WGS data into a useable format for laboratory reporting, clinical case management, Salmonella surveillance, and outbreak investigation as well as meeting the requirement to communicate that information in an understandable and universal language for clinical and public health action. Public Health England have been routinely sequencing all referred presumptive Salmonella isolates since 2014 which has transformed our approach to reference microbiology and surveillance. Here we describe an overview of the integrated methods for cross-disciplinary working, describe the challenges and provide a perspective on how WGS has impacted the laboratory and surveillance processes in England and Wales.

The 3-terminal sequences of hepatitis C virus (HCV) positive-and negative-strand RNAs contribute cis-acting functions essential for viral replication. The secondary structure and protein-binding properties of these highly conserved regions are of interest not only for the further elucidation of HCV molecular biology, but also for the design of antisense therapeutic constructs. The RNA structure of the positive-strand 3 untranslated region has been shown previously to influence binding by various host and viral proteins and is thus thought to promote HCV RNA synthesis and genome stability. Recent studies have attributed analogous functions to the negative-strand 3 terminus. We evaluated the HCV negative-strand secondary structure by enzymatic probing with single-strand-specific RNases and thermodynamic modeling of RNA folding. The accessibility of both 3-terminal sequences to hybridization by antisense constructs was evaluated by RNase H cleavage mapping in the presence of combinatorial oligodeoxynucleotide libraries. The mapping results facilitated identification of antisense oligodeoxynucleotides and a 10-23 deoxyribozyme active against the positivestrand 3-X region RNA in vitro.The untranslated regions (UTRs) of the hepatitis C virus (HCV) positive-strand genome and negative-strand intermediate contain cis-acting sequences essential for viral translation and RNA replication. The 341-nucleotide (nt) 5Ј-UTR of the positive strand acts as an internal ribosome entry site (IRES) to direct cap-independent translation of the single ϳ3,000-codon-long HCV open reading frame (38, 40). The tripartite 3Ј-UTR consists of a short upstream variable region, a central poly(U)-polypyrimidine stretch of variable length, and a terminal highly conserved 98-nt sequence (38). With the exception of the variable region, all sequence elements in the 3Ј-UTR are necessary for intracellular replication of HCV RNA (16,29,56).A number of in vitro studies (26,35,36,39,58) have established that the terminal 98-nt X region sequence can serve as a minimal template for de novo initiation of negative-strand synthesis by the viral RNA-dependent RNA polymerase, NS5B. The 3Ј terminus of the HCV negative strand reportedly plays an analogous role in positive-strand RNA synthesis (25,36,39). The binding of HCV 3Ј termini to various host proteins may exert subtle effects on IRES-mediated translation (16,23,34,55) or protect viral transcripts from degradation by cytoplasmic RNases (15,48,49).The replicative and protein-binding functions of heteropolymeric regions in the HCV 3Ј termini are, in many instances, dependent on the ability of the primary sequence to fold into higher-order RNA structure. In vitro, the X region sequence is capable of adopting a three-stem-loop structure, with the 3Ј-terminal 46 nt forming a thermodynamically stable stem-loop, SL I (6). Mutational analysis indicates that the duplex structure forming the base of SL I influences both the site and efficiency of de novo initiation by NS5B (26,35). Preservation of the interior stem-loo...