Molecular clock software#
Molecular clock code#

WGS is also used for other types of cells such as human cells or viruses but these applications are not relevant to this handbook. WGS is a process whereby all, or most of, the sequence of genomic material (Deoxyribonucleic acid ( DNA)) from bacterial organisms, such as Mycobacterium species, is determined.

Molecular clock code#

1.2 Background 1.2.1 Whole-genome sequencing ( WGS)Ī genome contains all the genetic information of an organism as a nucleotide sequence that includes code for specific genes and some noncoding regions. Cases may be linked epidemiologically without WGS where clinical samples do not exist and will require follow-up as a cluster. Note: WGS is only available on culture positive TB cases, not latent TB infections ( LTBI) diagnosed by Interferon-Gamma Release Assay ( IGRA) or cases diagnosed clinically or those with negative cultures. It is primarily intended for regional health protection teams to support the management of TB cases and incidents. The handbook will remain an evolving document subject to modification to reflect current knowledge. This handbook gives an overview of the end-to-end processes of WGS for the investigation and management of TB cases and shares good practice. WGS is now used routinely to identify clusters of TB and potential transmission chains to reduce the incidence of TB in the UK. It provides guidance for UK Health Security Agency ( UKHSA) staff and public health teams following the introduction of WGS into national diagnostic service as a tool for TB cluster investigation. This handbook supports the use of tuberculosis ( TB) whole-genome sequencing ( WGS) data for TB diagnosis and investigation of TB clusters. Langham, Surinder Tamne, Prof Grace Smith UKHSAįield Services: Dr Charles Beck (CB), Andy Burkitt, Neil Macdonald Version control Versionġ Introduction 1.1 Purpose of the handbook UKHSA National TB Unit: Dr Dona Foster (DF), Dr Suzanne Coles (SC), Dr David Wyllie, Dr Esther Robinson, Dr Lauren Ahyow, Dr Sharon Cox, Dr Martin Deadicoat, Tracey L. Special thanks are extended to the health protection teams, for their essential collaboration in the ongoing investigation of TB transmission. We also thank all who contribute information on TB notifications in England, including physicians, nurses, microbiologists, scientists, and administrative staff. We thank all the NHS TB teams and laboratories for isolation and submission of TB cultures.

Molecular clock software#

We gratefully acknowledge all those in the National Mycobacterial Reference laboratories and UKHSA bioinformaticians and software engineers who undertake whole-genome sequence sample preparation and processing and maintenance of the computational systems respectively.