MeaNS (www.who-measles.org) was initiated as a joint project between the Health Protection Agency, London, United Kingdom (now Public Health England, PHE) and WHO. This database is comprised of measles sequences and associated data that are submitted primarily by the GMRLN or downloaded from GenBank. Most of the measles sequences that are submitted to MeaNS are N-450 sequences, which is the recommended minimum sequence window for genotyping measles viruses.
Initial navigation to the MeaNS website will display options that are available without logging in to the site. The login box and registration button are located on the top-right of the site and various information and aggregate data pages are displayed in a menu bar near the top of the page. Access to the data in MeaNS requires that users register with the website, whereupon registrants are promoted to users by system administrators. The default (public) level of access allows users to view data in MeaNS that is available in GenBank. GMRLN staff are granted submitter access which enables users to submit sequences and view sequences submitted by other users (non-public data). All users are required to acknowledge that they have read and agreed to the terms and conditions of the site on initial login.
7.5.1 Submission of sequences to MeaNS
Submission of measles virus sequences to MeaNS can be completed through a simple web interface and requires an appropriate region of sequence and a minimal epidemiological dataset. Users with submitter access can submit wild-type measles sequences to the MeaNS database and are encouraged to submit all sequences rather than a representative subset. Users should not submit sequences from a case that had a rash due to a vaccine reaction (sequence identified as clade A, vaccine strain).
While most of the submissions consist of N-450 sequences, the sequences that encode the complete hemagglutinin gene (H-gene) and the complete N-gene are also commonly submitted. MeaNS is designed to accept coding sequence from any complete gene, as well as whole genomes.
MVi and MVs sequences from different cases should have different isolate/sequence numbers in instances in which the date and location are identical. It is recommended that only one sequence for N and/or H genes be reported to the databases from each case even if sequence data are available from multiple specimens. Each sequence submitted is assigned a distinct sequence ID in MeaNS in addition to the WHO name.
The information required to generate a standard WHO name and additional epidemiologic data are entered into appropriate fields for each sequence. Guidelines and detailed instructions for entering the data for submission of sequences (new record) to MeaNS are available on the website home page in the form of a training video and FAQs and are included in Annex 7.4, Instructions for entering data and navigating MeaNS for sequence submission.
7.5.2 Sequence data and analysis tools available in MeaNS
Upon login to MeaNS, the menu bar expands to include additional tabs. In addition to submission of sequences (NEW RECORD), clicking the DATA tab reveals three other additional menu choices on tabs entitled LIST, SEARCH, and NAMED STRAINS.
The LIST tab presents users with a list of records stored within MeaNS, the top portion of this page contains a series of filters (geographical, temporal, genotype) that can be completed to narrow the selection of sequences that are displayed. The data fields in the listed table are sortable by clicking the table headers. The WHO name for each record serves as a hyperlink to the individual record entry.
The SEARCH tab presents the user with a series of labelled text boxes that allow users to enter fields that can be used to search for specific records within the database. It is worth noting that there is no fuzzy or wild-card matching and search fields must be entered as they are stored within the database. A successful search will return a single MeaNS sample record and all of the sequences associated with that sample.
The NAMED STRAINS tab links to a page that details WHO reference and named strains for each genotype.
By clicking the menu tab, SEQUENCE ANALYSIS, several tools and options are available:
1. SEQUENCE MATCHING tool. The first option is to search for exact match. By selecting this option, a search is initiated for sequences identical to the input sequence. The search results are displayed in a table showing the WHO name and associated information about identical sequences. This list can be sorted, filtered and downloaded from the website. If the selected sequence matches a named strain, that record will be displayed with a red background at the top of the matching sequences list. A match with a WHO reference sequence will be shown in green at the top of the matching sequences list. Alternatively, users can also use the BLAST algorithm to search the MeaNS database for identical and similar sequences.
2. GENOTYPING tool. Users can check the genotype of their sequence by running the genotype tool within MeaNS. This option is only available for N-450 or H sequence. Genotype is assigned based on sequence similarity to the closest WHO reference sequence.
3. PHYLO tool. This option plots a phylogeny (tree) of the displayed sequence, the WHO reference set and sequences designated as named strains. The Sequence Analysis tab allows the user to obtain aggregate data on submitted genotypes in different formats. The monthly summary tab provides genotype data on a monthly basis by year and WHO region chosen by the user. The remaining 2 options are only available to National Laboratories to summarize country data and for generation of annual reports.
4. NL LISTING tool. This tool allows producing annual tables of all sequences reported to MeaNS for a given country (see Figure 7.2 below). The output is a line listing of comprehensive information on genotypes, named strains, distinct sequence IDs provided in a useful format for the regional verification process, when applicable.
7.5.3 Sequence data obtained on MeaNS and determination of the source of virus
The analysis of sequence data available from the MeaNS database can be useful to describe the molecular epidemiology of circulating measles viruses, but it is important to understand the limitations that exist for inferring an epidemiologic relationship (e.g., a common source or transmission chain) based on identity of N-450 sequences. Some virus strains circulate over a wide geographic area, which limits the conclusions that can be drawn regarding the source of virus. In addition, the travel history (origin or destination) of a case may be coincidental, as the exposure may have occurred while in transit.
If the travel history for a case suggests an importation from a specific country but a search in MeaNS reveals no similar sequences for that country, or the timeframe for the circulation of the matching sequences located in MeaNS makes the possibility of co-circulation unlikely, it may be advisable to contact the country laboratory to inquire whether additional information on the status of measles in their country is available to substantiate the possible importation.
Therefore, the source of infection for a case of measles may be classified as unknown even if a genotype is identified and similar sequences have been identified in MeaNS [1]. For the source of a case to be designated as either imported or importation-related, the investigation must identify an epidemiologic link to an imported case or association with a contemporaneous outbreak traced to an imported case (see Table below). However, demonstration of a genetic match to the outbreak and possible exposure through travel or work-related exposure may support an import-related classification.
Categories for designation of the source for confirmed measles or rubella cases
(adapted from Table 1, Framework for verifying elimination of measles and rubella, Weekly Epidemiological Record, 2013, 88: 89-100
Imported measles, or rubella, case
A case exposed to measles, or rubella, outside the region or country during the 7–21 days (12–23 days for rubella) prior to rash onset and supported by epidemiological or virologic evidence, or both
Note: For cases that were outside the region or country for only a part of the 7–21-day interval (12–23-day interval for rubella) prior to rash onset, additional evidence including a thorough investigation of contacts of the case is needed to exclude a local source of infection.
Importation-related measles, or rubella case
A locally acquired infection occurring as part of a chain of transmission originating from an imported case as supported by epidemiologic or virologic evidence, or both Note: If transmission of measles, or rubella, from cases related to importation persists for ≥12 months, cases are no longer considered import-related but endemic.
Unknown source measles, or rubella, case
A confirmed case for which an epidemiological or virologic link to importation or to endemic transmission cannot be established after a thorough investigation.
A large number of virus sequences generated by a database search by country does not necessarily reflect the size of the outbreak or indicate high levels of measles transmission since some countries may report sequences from all cases from smaller outbreaks, while only a small proportion of sequences may be reported from a large, focalized outbreak. Although the recommendation is that all measles sequence information should be submitted to MeaNS, the actual practices depend on the approach to conducting virologic surveillance, the extent of measles activity and epidemiologic setting, and the capacity for collecting and processing specimens that exist in different countries and different laboratories.
There is a similar limitation due to timeliness of reporting, since there have been substantial delays (up to a year or more) in reporting sequences from some countries. Therefore, the data within MeaNS is incomplete and biased towards those countries with fewer/smaller outbreaks, laboratories that perform more intensive (comprehensive) sequencing, and those that report sequences in a timely manner.