Most of the genetic studies of wild-type rubella viruses have been conducted by sequencing the full length or portions of the coding region of the E1 envelope protein. Sequencing other regions of the rubella virus genome for molecular epidemiology has been considered, but no compelling arguments for altering the target from the E1 region of the rubella genome have been forthcoming. However, different regions (windows) within the E1 coding region have been utilized for genetic characterization. Following an evaluation of the alternative windows within the E1 region, the currently recommended target region consists of 739 nucleotides (E-739) from 8731-9469. The CDC protocol for amplification of two overlapping fragments that can be used to sequence the E1 region for sequencing rubella viruses is provided in Annex 7.5.
7.8 Overview and methods for determination of rubella genotypes
- Manual introduction
- Chapter 1. Measles and rubella: An overview
- 1.1 The structure and biology of measles virus
- 1.2 The clinical description and complications of measles
- 1.3 Infection, immune response and laboratory diagnosis of measles
- 1.4 Epidemiologic features of measles
- 1.5 The structure and biology of rubella virus
- 1.6 The clinical description of rubella and congenital rubella syndrome
- 1.7 Infection, immune response and laboratory diagnosis of rubella and CRS
- 1.8 Epidemiologic features of rubella and CRS
- Bibliography to Chapter 1
- Chapter 2. The Global Measles and Rubella Laboratory Network
- Chapter 3. Clinical specimens for the laboratory diagnosis and molecular epidemiology of measles, rubella, and CRS
- 3.1 Guidelines for the preparation and transport of clinical specimens
- 3.2 Safety procedures for incoming clinical specimens
- 3.3 Best practices for quality serum specimens for measles and rubella IgM detection
- 3.4 Alternative specimens for IgM antibody testing
- 3.5 Clinical specimens for molecular testing and virus isolation
- 3.6 Serologic and clinical specimens for confirmation of congenital rubella syndrome (CRS)
- Bibliography to Chapter 3
- Chapter 4. Antibody detection methods for laboratory confirmation of measles, rubella, and CRS
- 4.1 Selection and comparison of EIAs for IgM detection
- 4.2 Interpretation of IgM results for case classification of measles and rubella
- 4.3 Interpretation of IgM results among suspected cases with recent vaccine history
- 4.4 Alternative specimens for IgM detection
- 4.5 IgG assays and interpretation for case classification
- 4.6 Determination of measles- or rubella-specific IgG avidity
- 4.7 Interpretation of IgG avidity results
- 4.8 Serologic confirmation of suspected CRS cases
- 4.9 New serological techniques and methodologies
- Bibliography to Chapter 4
- Chapter 5. Virus isolation and identification of measles and rubella in cell culture
- 5.1 Recommended cell line for measles and rubella virus isolation
- 5.2 Propagation of Vero-hSLAM cells
- 5.5 Provision of virus isolates for molecular surveillance and the strain bank
- 5.3 Measles virus isolation and confirmation
- 5.4 Rubella virus isolation and confirmation
- 5.6 Methods to ship virus isolates
- Bibliography to Chapter 5
- Chapter 6. Detection of viral RNA by RT-PCR for the confirmation of measles and rubella infection
- 6.1 Best practices for collection and processing clinical specimens and extraction of RNA
- 6.2 Considerations for the use of molecular diagnostic methods
- 6.3 Measles RNA detection by RT-PCR
- 6.4 Vaccine-specific RT-PCR for identification of measles vaccine strains
- 6.5 Rubella RNA detection by RT-PCR
- 6.6 Quality assurance and quality control for RT-PCR
- 6.7 Test validity, data interpretation and assay limitations
- Bibliography to chapter 6
- Chapter 7. Molecular epidemiology of measles and rubella
- 7.1 Phylogenetic diversity and nomenclature for measles genotypes
- 7.2 Integration of measles molecular and epidemiological data
- 7.3 Overview and methods for determination of measles genotypes
- 7.4 Guidelines for reporting a new measles genotype and use of data from MeaNS
- 7.5 The measles nucleotide surveillance (MeaNS) database
- 7.6 Phylogenetic diversity and nomenclature for rubella genotypes
- 7.7 Integration of rubella molecular and epidemiological data
- 7.8 Overview and methods for determination of rubella genotypes
- 7.9 Guidelines for reporting a new rubella genotype
- 7.10 The rubella nucleotide surveillance (RubeNS) database
- 7.11 Methods and prospects for enhancing resolution of sequence data for molecular epidemiology
- 7.12 GMRLN guidance for use of extended sequencing of measles virus for the verification of elimination (February 2024)
- Bibliography to chapter 7
- Chapter 8. Laboratory testing in support of measles and rubella surveillance in elimination settings
- 8.1 Challenges for accurate case classification in elimination settings
- 8.2 Utility and limitations for molecular testing in elimination settings
- 8.3 Difficult cases and situations that may require additional testing
- 8.4 Additional testing to aid case classification
- 8.5 Measles reinfections: characteristics and case confirmation
- Bibliography to Chapter 8
- Chapter 9. Laboratory testing for determination of population immune status
- Chapter 10. Laboratory support for the verification of elimination of measles and rubella
- Chapter 11. Data management and reporting of laboratory results
- Chapter 12. Quality assurance, quality control, and assessment of laboratory capacity and performance
- 12.1 The establishment and benefits of a quality management system
- 12.2 Technical elements of QMS
- 12.3 Key objectives of laboratory quality assurance
- 12.4 Monitoring IgM assay performance
- 12.5 The WHO external quality assessment programme
- 12.6 Process of WHO assessment and accreditation
- Bibliography to Chapter 12
- List of Annexes
- Chapter 1. Measles and rubella: An overview
- Manual introduction
- Chapter 1. Measles and rubella: An overview
- 1.1 The structure and biology of measles virus
- 1.2 The clinical description and complications of measles
- 1.3 Infection, immune response and laboratory diagnosis of measles
- 1.4 Epidemiologic features of measles
- 1.5 The structure and biology of rubella virus
- 1.6 The clinical description of rubella and congenital rubella syndrome
- 1.7 Infection, immune response and laboratory diagnosis of rubella and CRS
- 1.8 Epidemiologic features of rubella and CRS
- Bibliography to Chapter 1
- Chapter 2. The Global Measles and Rubella Laboratory Network
- Chapter 3. Clinical specimens for the laboratory diagnosis and molecular epidemiology of measles, rubella, and CRS
- 3.1 Guidelines for the preparation and transport of clinical specimens
- 3.2 Safety procedures for incoming clinical specimens
- 3.3 Best practices for quality serum specimens for measles and rubella IgM detection
- 3.4 Alternative specimens for IgM antibody testing
- 3.5 Clinical specimens for molecular testing and virus isolation
- 3.6 Serologic and clinical specimens for confirmation of congenital rubella syndrome (CRS)
- Bibliography to Chapter 3
- Chapter 4. Antibody detection methods for laboratory confirmation of measles, rubella, and CRS
- 4.1 Selection and comparison of EIAs for IgM detection
- 4.2 Interpretation of IgM results for case classification of measles and rubella
- 4.3 Interpretation of IgM results among suspected cases with recent vaccine history
- 4.4 Alternative specimens for IgM detection
- 4.5 IgG assays and interpretation for case classification
- 4.6 Determination of measles- or rubella-specific IgG avidity
- 4.7 Interpretation of IgG avidity results
- 4.8 Serologic confirmation of suspected CRS cases
- 4.9 New serological techniques and methodologies
- Bibliography to Chapter 4
- Chapter 5. Virus isolation and identification of measles and rubella in cell culture
- 5.1 Recommended cell line for measles and rubella virus isolation
- 5.2 Propagation of Vero-hSLAM cells
- 5.5 Provision of virus isolates for molecular surveillance and the strain bank
- 5.3 Measles virus isolation and confirmation
- 5.4 Rubella virus isolation and confirmation
- 5.6 Methods to ship virus isolates
- Bibliography to Chapter 5
- Chapter 6. Detection of viral RNA by RT-PCR for the confirmation of measles and rubella infection
- 6.1 Best practices for collection and processing clinical specimens and extraction of RNA
- 6.2 Considerations for the use of molecular diagnostic methods
- 6.3 Measles RNA detection by RT-PCR
- 6.4 Vaccine-specific RT-PCR for identification of measles vaccine strains
- 6.5 Rubella RNA detection by RT-PCR
- 6.6 Quality assurance and quality control for RT-PCR
- 6.7 Test validity, data interpretation and assay limitations
- Bibliography to chapter 6
- Chapter 7. Molecular epidemiology of measles and rubella
- 7.1 Phylogenetic diversity and nomenclature for measles genotypes
- 7.2 Integration of measles molecular and epidemiological data
- 7.3 Overview and methods for determination of measles genotypes
- 7.4 Guidelines for reporting a new measles genotype and use of data from MeaNS
- 7.5 The measles nucleotide surveillance (MeaNS) database
- 7.6 Phylogenetic diversity and nomenclature for rubella genotypes
- 7.7 Integration of rubella molecular and epidemiological data
- 7.8 Overview and methods for determination of rubella genotypes
- 7.9 Guidelines for reporting a new rubella genotype
- 7.10 The rubella nucleotide surveillance (RubeNS) database
- 7.11 Methods and prospects for enhancing resolution of sequence data for molecular epidemiology
- 7.12 GMRLN guidance for use of extended sequencing of measles virus for the verification of elimination (February 2024)
- Bibliography to chapter 7
- Chapter 8. Laboratory testing in support of measles and rubella surveillance in elimination settings
- 8.1 Challenges for accurate case classification in elimination settings
- 8.2 Utility and limitations for molecular testing in elimination settings
- 8.3 Difficult cases and situations that may require additional testing
- 8.4 Additional testing to aid case classification
- 8.5 Measles reinfections: characteristics and case confirmation
- Bibliography to Chapter 8
- Chapter 9. Laboratory testing for determination of population immune status
- Chapter 10. Laboratory support for the verification of elimination of measles and rubella
- Chapter 11. Data management and reporting of laboratory results
- Chapter 12. Quality assurance, quality control, and assessment of laboratory capacity and performance
- 12.1 The establishment and benefits of a quality management system
- 12.2 Technical elements of QMS
- 12.3 Key objectives of laboratory quality assurance
- 12.4 Monitoring IgM assay performance
- 12.5 The WHO external quality assessment programme
- 12.6 Process of WHO assessment and accreditation
- Bibliography to Chapter 12
- List of Annexes
- Chapter 1. Measles and rubella: An overview