National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention 

Division of Tuberculosis Elimination

Since the start of the National Tuberculosis (TB) Genotyping Service (NTGS) in 2004, TB genotypes have been 

defined as a unique combination of spoligotype and 12-locus MIRU-VNTR results. Each result combination has been 

assigned a PCRType. PCRType is designated as “PCR” followed by give digits. PCRTypes are assigned sequentially 

to every genotype identified in the United States. For example, the spoligotype result 000000000003771 with the 

12-locus MIRU-VNTR result 223325173533 was the second genotype seen in the United States and was designated as 

PCR00002.

In April 2009, MIRU-VNTR analysis was expanded from 12 loci to 24 loci. The complete set of 24 loci is referred to 

as ‘24-locus MIRU-VNTR.’ The additional 12 loci (reported in TB GIMS as “MIRU2”) increase our ability to distinguish 

between strains of M. tuberculosis and better identify chains of transmission. In order to fully integrate 24-locus 

MIRU-VNTR into routine use, a new national naming system, GENType, has been developed. 

What is a GENType and how is it assigned?

• Each unique combination of spoligotype and 24-locus MIRU-VNTR results has been assigned a GENType, 

formatted as “G” followed by five digits. For example, G00010 refers to the unique combination of spoligotype: 

000000000003771 and 24 locus MIRU-VNTR: 223325173533 444534423428.

• Unique combinations of spoligotype and 24-locus MIRU-VNTR results will be routinely and sequentially assigned 

GENTypes as they are identified. 

• GENTypes are not assigned to isolates without 24-locus MIRU-VNTR results. (This includes most isolates that were 

genotyped before April 2009.)

• A single PCRType may have multiple GENTypes assigned, since a single PCRType can include multiple 24-locus 

MIRU-VNTR patterns. However, each GENType has only one PCRType. (See Table below.) For example, Line #1 and 

Line #3 are both PCR00002, but represent two different GENTypes (G00010 and G00012) due to different 24-locus 

MIRU-VNTR results.

CS232896

GENType: New Genotyping Terminology to Integrate 24-locus MIRU-VNTR

Line# GENType† PCRType Spoligotype

1 G00010 PCR00002 000000000003771 223325173533 444534423428

2 G00011 PCR00015 777776777760601 224325153323 444234423337

3 G00012 PCR00002 000000000003771 223325173533 445644423328

4 G00013 PCR00016 700036777760731 222325143223 434534412334

5 G00014 PCR00051 776037777760771 223125163324 242434223525

24-locus MIRU-VNTR

Comparative Examples for GENType and PCRType

 † Unique combination of spoligotype and 24-locus MIRU-VNTR

How is GENType pronounced?

• GENType is pronounced like the woman’s name ‘Jen’ followed by the word ‘type.’ 

What is a meant by a percent sign (%) or a dash (-) in a MIRU-VNTR result?

• A percent sign (%) at a particular locus means that the result could be one of two possible results (e.g., a 

laboratory testing identifies an isolate with two possible MIRU2 results: 443324232614 or 443324232514; 

therefore the result will be shown as 443324232%14). This type of mixed result used to be represented by an 

asterisk (*).

• A dash (-) at a particular locus means that the result is unknown or cannot be determined 

(e.g., the MIRU-VNTR result would be: 44332-423261).

8/16/2012
What happens to GENType when MIRU-VNTR results include a percent sign (%) or a dash (-)?

• GENTypes are assigned for all isolates with 24-locus MIRU-VNTR results, even if they contain a percent sign 

or dash.

How is a “genotype cluster” defined using GENType?

• A genotype cluster should be defined on the basis of GENType.

• All patients with a single GENType are part of the same genotype cluster. 

• Patients with the same PCRType, but multiple GENTypes, should not be considered part of the same genotype 

cluster; they are not likely to represent a single chain of transmission.

Is PCRType still available? 

• PCRTypes will continue to be assigned to Spoligotype and 12-locus MIRU-VNTR patterns until the use of GENType 

becomes routine practice.

• Both GENType and PCRType are available in TB GIMS for searches, reports, and maps. 

• A table is available in TB GIMS to cross-reference GENTypes and PCRTypes; the format is similar to the example 

table above. 

How do I find out the GENTypes for the clusters in my jurisdiction?

• There are several ways in TB GIMS that you can find the GENType for a specific cluster or generate a list of all the 

GENTypes in your jurisdiction.

• Go to the Genotype or Patient Results searches and search by a PCRType or Cluster Name. The GENType is shown 

in the line list in the column right before PCRType.

• Go to “Training Resources” and scroll down to “Additional Resources.” The Excel file “GENType Reference Table” 

includes all GENTypes and their corresponding PCRTypes. Of note, this file will only be updated with each new TB 

GIMS release; thus, it may not be completely up to date. 

• Go to “Generate Reports” and select “State List of GENTypes.” This report shows all the GENTypes in the state and 

their corresponding PCRType and Cluster Name2. 

Additional information

• For general information on TB genotyping, please see the TB genotyping fact sheet: 

http://www.cdc.gov/tb/publications/factsheets/statistics/genotyping.htm

• For information on TB GIMS, please see the TB GIMS fact sheet: 

http://www.cdc.gov/tb/publications/factsheets/statistics/gims.htm

• For more information on TB genotyping, please contact tbgenotyping@cdc.gov