Attachment to 

 
Guidance on Antiviral Product 
Development  Conducting 
and Submitting Virology 
Studies to the Agency 
 
 
 
Guidance for Submitting Influenza 

Resistance Data 

 
 
 
 
 
This guidance represents the Food and Drug Administrations (FDAs) current thinking on this topic.  It 
does not create or confer any rights for or on any  person and does not operate to bind FDA or the public.  
You can use an alternative approach if the approach satisfies the requirements of the applicable statutes 
and regulations.  If you want to discuss an alternative approach, contact the FDA staff responsible for 
implementing this guidance.  If you cannot identify the appropriate FDA staff, call the appropriate 
number listed on the title page of this guidance.  
 
 
 
 
U.S. Department of Health and Human Services 

Food and Drug Administration 

Center for Drug Evaluation and Research (CDER) 

 
June 2006 

Clinical Antimicrobial 
 
 
 
  Contains Nonbinding Recommendations 
GUIDANCE FOR SUBMITTING 

INFLUENZA RESISTANCE DATA 

 
Sponsors are encouraged to use the following sample format for submitting influenza resistance 
data for microbiology review.  Sponsors should begin these analyses in the earliest clinical stages 
of product development so that sample collection, storage, and analyses are well established at 
the time of the initiation of pivotal studies.  If sponsors wish to submit additional information, 
they are encouraged to discuss these suggestions with the division in advance.   
 
One dataset combines patient data, virologic data, genotypic data, and phenotypic data.1   
Selected clinical outcome data can also be included for exploratory analysis (we recommend 
discussion with the division to establish the format for including these data in the dataset).  There 
are a number of ways datasets can be subdivided (i.e., by clinical study1, baseline isolates, or 
designated later isolates) and this should be discussed with the division before submission. 
 
For each study, we recommend constructing datasets as SAS transport files containing the 
following information: 
 
	   One record (row) per patient per isolate. 
	   For treatment studies, a row should be included for the initial isolate obtained before starting 
study drug (baseline isolate), even if virologic studies (e.g., culture, PCR) are negative.  In 
cases where an assay was negative, insert <LLOQ (lower limit of quantification) or <LOD 
(limit of detection) where the specific numerical value of the LLOQ or LOD is inserted, as 
appropriate. Other isolates to be included for treatment studies, and inclusion and 
designation of isolates for prophylaxis studies, should be discussed with the division. 
	   Data in columns (with suggested column headings shown below)2 on all isolates. 
	   In studies where both treatment and prophylaxis are evaluated, a column should be included 
identifying the patient as treatment or prophylaxis group. 
	   In most studies it is anticipated that all isolates for virologic analysis will be obtained using 
the same methodology (e.g., nasal washing, nasopharyngeal swab, throat swab) that will be 
described in the protocol and study report.  If there is a reason for use of more than one 
method in the same study, discussion with the division is recommended. 
	   Genotypic data should be provided for (at a minimum) baseline isolates of all patients and 
the predetermined time points of isolate collection on the corresponding record for each 
patient isolate. 
	   Phenotypic data  should be provided for (at a minimum) baseline isolates and the 
predetermined time points of isolate collection on the corresponding record for each patient  
isolate. The FDA recognizes the difficulty of phenotypic analysis of influenza virus and the 
lack of clinical validation of current assays.  Sponsors are strongly encouraged to 
appropriately collect and store isolates for later analysis.  If the pathways to resistance as 
                                                           
1 For datasets containing multiple studies, a column should  be added to identify the relevant study in which the  
subject was enrolled. 
 
2 In the SAS transport files, column headings  can  be  given abbreviated column names to fit the SAS format; 
however, it is suggested that a description of  column names be provided to  the reviewer in the submission. 
1 
 Contains Nonbinding Recommendations 
defined by genotypic analysis are straightforward, phenotypic analysis, after consultation 
with the division, may not be necessary.   
	   Depending on the timing of serum specimens for antibody determination relative to isolates 
obtained for viral isolation, the most appropriate incorporation of serologic results into the 
dataset should be discussed with the division. 
 
Information to Include with Suggested Column Headings3   
 
I. Patient Data: 
 
	   Patient identification number (ID number should be unique to all clinical studies of the 
product) 
	   Isolate (e.g., baseline, day 2 (with day 0 being the start of product administration), 
discontinuation. Multiple isolates from the same visit should be numbered (e.g., baseline 1, 
baseline 2)). All isolates should be included even if negative for PCR and cell culture. 
	   Date of isolate 
	   Days of study product treatment on day isolate obtained 
	   Days off study product treatment on day isolate obtained 
	   Previous therapeutic products, if any 
	   Treatment group (e.g., specific dose, active control, placebo) 
	   Indication if data were censored (e.g., discontinuation because of adverse event) 
 
II. Virologic Data (culture and PCR results and quantification as appropriate): 
 
The protocol and study report should include a detailed description of assay methodology and 
explanation of units of measurement for any qualitative or quantitative assays used to identify 
viral isolates. Supporting information should be provided to allow review of assay performance; 
however, use of a specified assay in an antiviral product trial does not constitute FDA review, 
approval, or endorsement of the assay.   
 
	   Baseline measurement (e.g., log  influenza RNA copies/mL of nasal wash at baseline, log  
10 10 
TCID /mL).  (For therapeutic studies, after onset of illness and before receipt of study  
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product.) 
	   Measurements using the same units at predefined time points (e.g., day 2), one column for 
each time point including baseline (i.e., the measurement throughout the course of infection 
is repeated for each isolate)  
	   Measurements from additional time points can be included 
 
III. Genotypic Data (for baseline isolates of all patients and predetermined time points): 
 
	   Subtype for influenza A isolates (e.g., H1N1, H3N2); insert B for influenza B to confirm  
typing 
                                                           
3 In the SAS transport files, column headings  can  be  given abbreviated column names to fit the SAS format; 
however, it is suggested that a description of  column names be provided to  the reviewer in the submission. 
2 
 Contains Nonbinding Recommendations 
	   Genotype information for all the relevant coding regions sequenced; one amino acid per 
column with the wild-type (WT) amino acid as column heading identified using the one 
amino acid abbreviation.  Changes from WT  standard sequence indicated (i.e., blanks 
indicate no change). Known polymorphic amino acid residues should be flagged with an 
asterisk in the column heading.  For neuraminidase inhibitors, genotype information for both 
the neuraminidase and hemagglutinin proteins would be relevant.  
 
Example (Table 1 highlights how genotype information should be displayed but does not 
include all column headings previously suggested.) 
 
Table 1. Example of Genotype Information Display 
Patient #  Isolate  Subtype/Type  C-291  R292  D-293  N-294 
001  BL  H3N2         
001  Day  2  H3N2    K     
001  Day  5  H3N2    K     
002  BL  H1N1         
002  Day  2  H1N1         
002  Day 3   H1N1         
BL = baseline 
 
IV. Phenotypic Data (minimally for baseline isolates and predetermined time points): 
 
1.  Candidate product 
	   Baseline EC  value for candidate product 
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	   EC  value of reference strain for candidate product (the reference strain should be a 
50
widely available standard lab strain) 
	   Fold change of baseline EC  value compared to EC  value of reference strain of 

50 50
candidate product 

	   EC  value at time of subsequent assessment as appropriate for candidate product  
50
	   Fold change values in EC  value at time of subsequent assessment as appropriate 
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compared to reference strain for candidate product 
	   Fold change in EC  value at time of subsequent assessment as appropriate compared to 
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baseline for candidate product 
 
2. 	 Approved or investigational products in the same class 
	   Fold change in EC  value of baseline compared to reference strain for each of the 
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approved or investigational products in the same class  
	   Fold change in EC  value at time of subsequent assessment as appropriate compared to 
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reference strain for each of the approved or investigational products in the same class 
	   Fold change in the EC  value at time of subsequent assessment as appropriate compared 
50
to baseline for each of the approved or investigational products in the same class 
 
3 
 Contains Nonbinding Recommendations 
Example (Table 2 highlights how phenotype information should be displayed.) 
 
Table 2. Example of Phenotype Information Display 
    Other Products in 
  Product X  Same Product Class* 
 
  EC   Ref strain   resis   resis   resis   resis 
50 
  value  EC  value  from ref  from BL  from ref  from BL 
50
Isolate  Product X  Product X  Product X  Product X  Product Y  Product Y 
Baseline             
Day x               
Product  X = candidate product 
 
BL = baseline 

Day x = predefined time point for subsequent assessment as appropriate (e.g., day  2, day  5)
  
 resis = fold resistance change, e.g.: EC  value of baseline isolate with Product X 
 
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           EC  value of reference strain with Product X 

50 
Ref strain = reference strain (or  WT) 

*Note:  The   resis from ref and    resis from BL should be  included for all approved anti-influenza products. 

 
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