Minimum data fields for Experimental data – Detail document FINAL

Data Fields for Viral Isolates – Definitions, Curation and Examples FINAL _____________________________________________________________________________ This document contains the required minimum data fields for viral isolate characterization. The NIAID CEIRS centers must send these data sets to the NIAID public database in the format detailed below. Highlighted in yellow are fields that IRD will generate for the investigator based on the information provided. How to interpret the document: BOLD: Name of field ITALICS: Definition of field and format for values of this field.

General information about the influenza viral isolate 1. What is the strain name of the virus you are submitting data about? Format: Text Definition: The name of the viral isolate. Should comply with the WHO nomenclature for wild-type viruses or the CEIRS established nomenclature for the reverse genetic (RG) viruses. Curation: Valid strain format Examples: A/Vietnam/1203/2004 (example of wild type virus) A/Brevig Mission/1-CIP045_RG801/1918 (example of a RG virus – see CEIRS Short Nomenclature for Influenza Viruses Generated by Reverse Genetics ) 2. Please provide a unique laboratory identifier assigned to this virus by you (the investigator) Definition: Virus unique identifier. A unique laboratory identifier assigned to this virus by the collector/creator. Strain name is not enough in that they may not be unique. You can have various passages of the same virus, the same virus from different labs, etc. Format: Free form text up to 50 characters consisting of any combination of alphanumeric characters and all special characters except single quote, double quote, percent and period. Curation: No curation Example: 100245

3. What type of virus are you submitting data about? Format: Drop down menu: Wild-type virus, Reverse genetic (rg) virus, Reassortant virus (not rg derived), Animal adapted virus Definition: The type of viral isolate as determined by the investigator. Curation: Must click be one of the above selections *If Animal adapted virus answer the following questions (3a-3b),Other virus types go on to question 4: 3a. What is the host animal for adaptation? Format: Text Definition: The host animal that the adaptation experiments were performed in. Curation: No curation Example: Mouse

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3b What is the passage history for this virus? Format: Text Definition: Should provide the history of the passaging of the virus in cell culture, eggs and animals Curation: Must conform to the CDC established abbreviations Example: X5-E1-M4 4. Does this virus contain chimeric genes? Format: Yes/No Definition: Some viruses may contain chimeric genes where part of the gene segment is from one source virus and the other part of the gene segment is from another source virus. This field will capture this information. Curation: Must be Yes/No *If yes must answer 4a-4h. 4a. Which gene segments are chimeric? Format: Pull down menu, more than one gene can be selected: 1 PB1, 2 PB2, 3 PA, 4 HA, 5 NP, 6 NA, 7 M, 8 NS Definition: This field allows for identification of the genes that are chimeric. Curation: Must be one or more of the above selections 4b. For gene segment ________ what is the Genbank or IRD accession number for this chimeric gene? Format: Text/Not submitted Definition: This is the Genbank or IRD accession number for the sequence of the chimeric segment if it has been submitted. IRD accession numbers are assigned to RG mutated sequences submitted to BioHealthBase. Example: CY028858 4c For gene segment ________ how many source virus strains were used to generate the segment? Format: Number Definition: The gene segment can be made from several different source virus strains. This field will capture the number of strains that make up this virus. Example: 2 4d. For gene segment ________, what is the first source virus strain name? Format: Text Definition: The name of the viral isolate. Should comply with the WHO nomenclature for wild-type viruses or the CEIRS established nomenclature for the reverse genetic (RG) viruses. Curation: Valid strain format Examples: A/Vietnam/1203/2004 4e. For gene segment ________, what is the Genbank or IRD accession number for this first source virus strain? Format: Text/Not submitted/Unknown Definition: This is the Genbank or IRD accession number for the sequence of the first source virus strain for this chimeric gene segment if it has been submitted. Curation: Validate genbank number with strain name and gene segment Example: CY028858 4f. For gene segment ________, what are the nucleotide positions for the first source virus? Format: Numbers 7/30/09 Version 1.0 FINAL

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Definition: The nucleotide positions of the gene segment identified for the first source virus. Curation: No curation Example: 1-235 4g. Is the sequence for these nucleotide positions wild-type or have mutations been introduced? Format: Drop down menu: Wild type/Mutated Definition: Some reverse genetically derived chimeric viruses will have mutations introduced into the sequences. Curation: Must be Wild type or Mutated 4h. If mutated, describe the nucleotide alteration? Format: Text Definition: The changes that were generated in the gene segment Curation: No curation Example: a 627g, del 1025-1048 *Repeat questions 4d through 4h for the number of times identified in question 4c (the total number of source strains used to generate the segment. *Repeat questions 4b-4h for the next gene segment if more than one was identified in question 4a. *NOTE: Question 5 will now address details about the gene segments. If the virus being submitted is a chimeric virus, in question 5 only information for gene segments that have not already been submitted above should be requested. 5. For gene segment ________ please answer the following questions: 5a. What is the Genbank or IRD accession number? Format: Text Definition: This is the actual sequence of the virus that you are submitting. For reverse genetic viruses that include mutations, this sequence would have the mutations in it. Curation: Validate genbank or IRD number with strain name and gene segment Example: CY028858 *NOTE – wild type viruses repeat this question for each gene segment and then move on to question 6. 5b. What is the source virus strain name? Format: Text Definition: The name of the viral isolate. Should comply with the WHO nomenclature for wild-type viruses or the CEIRS established nomenclature for the reverse genetic (RG) viruses. Curation: Valid strain format Examples: A/Vietnam/1203/2004 5c. Is the sequence for these nucleotide positions wild-type or have mutations been introduced? Format: Drop down menu: Wild type/Mutated Definition: Some reverse genetically derived chimeric viruses will have mutations introduced into the sequences. Curation: Must be Wild type or Mutated *NOTE – if wild type should go to repeating question 5. If mutated should answer 5d & 5e. 7/30/09 Version 1.0 FINAL

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5d. If mutated, describe the nucleotide alteration? Format: Text Definition: The changes that were generated in the gene segment Curation: No curation Example: a 627g, del 1025-1048 5e. Please provide the Genbank or IRD accession number for the source virus strain (Parent strain). Format: Text Definition: This should be the source strain accession number. This would be your sequence without the mutations that were introduced. Curation: Validate genbank or IRD number with strain name and gene segment Example: CY028858 6. Sample Identifier: Definition: This identifier pertains to a single sample from a single host. If multiple samples are taken from the same host, each sample should have its own identifier. This Sample Identifier is the same identifier as used in the surveillance minimum data fields and it is essential that they be the same in order to track the samples and link them to the epi-data and sequence data. Format: Free form text, up to 50 characters consisting of any combination of alphanumeric characters and all special characters except single quote, double quote, percent and period. Curation: No curation 6a. Country: Definition: Country in which original sample was collected. Determined by strain name. Format: Value must be found on the approved list used by NCBI and found at the NCBI web site: http://www.ncbi.nlm.nih.gov/projects/collab/country.html Example: Viet Nam Curation: Must appear in NCBI country codes. IRD to fill in based on strain name. 6b. Collection Date Definition: Date on which the field sample was collected. This field would not be applicable for RG viruses Format: (d)d-first 3 letters of month-yyyy; NA = not applicable Eaxmple: 14-JAN-2009 Curation: Leading 0 of dd need not be provided; years must have four digits; month must match the first three (3) letters of the month of the alphabet; checked for out-ofrange dates. This ensures that there is no ambiguity with formats of dates from different regions of the world. IRD to fill in based on the sample identifier provided by investigator. 6c. Influenza type Definition: Influenza viruses are classified into three types. IRD will fill in based on strain name. Format: Text Example: A Curation: A, B or C

7.

Influenza A HA subtype Definition: Influenza A viruses are further classified by subtype on the basis of the two main surface glycoproteins. This field will identify the hemagglutinin (HA) subtype.

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Format: Example: Curation:

Drop down menu: H1, H2, H3, H4, H5, H6, H7, H8, H9, H10, H11, H12, H13, H14, H15, H16 H5 HA subtype should be the letter H followed by a number between 1-16 unless novel subtype is identified

7a. Influenza A HA subtype determined by: Definition: This field would specify how the influenza A HA subtype was determined. Format: Text Example: Sequence comparison Curation: No curation 8. Influenza A NA subtype Definition: Influenza A viruses are further classified by subtype on the basis of the two main surface glycoproteins. This field will identify the Neuraminidase (NA) subtype. Format: Text Example: N1 Curation: NA subtype should be the letter N followed by a number between 1-9 unless novel subtype is identified 8a. Influenza A NA subtype determined by: Definition: This field would specify how the influenza A HA subtype was determined. Format: Text Example: Sequence comparison Curation: None

9. WHO/OIE/FAO Clade (For HPAI H5N1 viruses): Definition: For highly pathogenic H5N1 viruses the WHO/OIE/FAO clade should be included. Note: as new viruses emerge and more information is collected this classification may change (example – a virus may go from being a clade 2 virus to being a clade 2.3) Reference:http://www.who.int/csr/disease/avian_influenza/guidelines/nomenclature/en/index. html Format: Text Example: 2.2 Curation: Number/Unknown/NA (Not applicable). IRD to fill out based on the reference website above. The investigator will have the opportunity to confirm/modify the assigned clade.

10. Institution of depositor Format: Text Definition: The institution and location of the person who is depositing the data. Example: St. Jude Children’s Research Hospital, TN, USA 11. Is this virus or reagents that you generated for this virus available to the scientific community? Format: Drop down menu: Yes/No Curation: One of the above If yes answer 11a and 11b, if no go to 12. 11a. What is the material that is available? Format: Text Definition: A description of the reagent or virus that is available to the scientific community upon request. 7/30/09 Version 1.0 FINAL

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Example: Curation:

Monoclonal antibodies No curation

11b. How can the material be requested (contact information)? Format Text Definition: A method for requesting the material should be provided. This could be an email address, a webpage link, etc. Curation: No curation 11c. Are any materials for this virus available in BEI Resources? Format: Yes/No Curation: IRD to determine by looking at strain name in BEI Resources. If the answer is YES – than it should be posted with a list of the types of reagents that are available (ie Monoclonal antibodies, recombinant HA protein, etc.

GENERAL QUESTIONS REGARDING PATHOGENICITY OF VIRAL ISOLATES

12. IRD will scan the sequences indicated for known pathogenicity markers including the polybasic HA cleavage site, PB2 E627K and PB2 D701N mutations. Are there other mutations of interest in your virus that effect pathogenicity? Format: Drop down menu: Yes/No/Unknown Curation: Must be Yes or No or Unknown. If yes – must answer 12 a. 12a. What is the gene segment, nucleotide number and mutation of interest? Format: Text Example: NS1 V149A Curation: No curation

12b. Polybasic HA cleavage site Definition: Cleavage of the HA is the first step in influenza entry into a cell. Highly pathogenic avian influenza (HPAI) has been found to have multiple basic amino acids at this site, which allows for cleavage by a variety of proteases expressed in various cell types, leading to an expanded tissue tropism. This field would define the polybasic amino acid cleavage site if present. The 5’ amino acid start of the cleavage site should be included. Format: Text if present/No/Unknown Curation: Text/No/Unknown References:Horimoto, T., and Y. Kawaoka. 1994. J. Virol. 68:3120-3128. Perdue, M. L. et al. 1997. Virus Res. 49:173-186 Senne, D. A. et al. 1996. Avian Dis. 40:425-437 Example: 339 RERRRKKR 12c. PB2 E627K mutation present Definition: For avian influenza viruses, mutation in PB2 at position 627 to Lys (K) has been found to be highly correlated with adaptation to mammals and to severe clinical infections in humans. Format: Yes/No/Unknown Curation: Yes/No/Unknown 12d. PB2 D701N mutation present

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Definition: For avian influenza viruses, mutation in PB2 at position 701 to Asn (N) has been found to be correlated with adaptation to mammals and to severe clinical infections in humans. Format: Yes/No/Unknown Curation: Yes/No/Unknown 13. Does the virus grow in cells without trypsin? Definition: Influenza viruses that are able to grow in culture without the addition of exogenous trypsin. Format: Yes/No/Unknown Curation: Yes/No/Unknown. If yes answer #11a. 13a. Which cell types will the virus grow in without trypsin? Definition: The cells types the virus will grow in without trypsin. Format: Text Curation: No curation. Example: MDCK

EXPERIMENTAL PATHOGENICITY DATA

14. Are you submitting experimental data for pathogenicity studies? Format: Drop down menu: Yes/No Curation: Must be Yes/No NOTE – If no proceed to # 15; If yes proceed to answer 14a-14p. 14a. Experiment #1 – Animal tested Format: Drop down menu: Chicken, Duck, Turkey, Quail, Passerine, Raptor, Guinea Pig, Mouse, Ferret, Other Curation: Must be one of the above. If the answer is other need to be able to fill in with text what it is. Note: Experiment # provided by IRD. Will change if investigator is submitting more than 1 experiment. 14b. Experiment #1 – Animal strain tested Format: Text Curation: No curation Example: BALB/c 14c. Experiment #1 – Age of animal tested Format: Text Curation: No curation Example: 6 weeks 14d. Experiment #1 – Route of inoculation Format: Drop down menu: Auricular (Otic), buccal, Cloacal, Conjunctival, Cutaneous, Dental, Electro-osmosis, Endocervical, Endosinusial, Endotracheal, Enteral, Epidural, Extra-amniotic, Extracorporeal, Hemodialysis, Infiltration, Inhaled, In Ovo, Interstital, Intra-abdominal, Intra-amniotic, Intra-arterial, Intra-articular, Intrabiliary, Intrabronchial, Intrabursal, Intracardiac, Intracartilaginous, Intracaudal, Intracavernous, Intracavitary, Intracerebral, Intracisteranal, Intracorneal, Intracoronal (dental), Intracoronary, Intracorporus cavernosum, Intradermal, Intradiscal, Intraductal, Intraduodenal, Intradural, Intraepidermal, Intraesophageal, Intragastric, Intragingival, Intraileal, Intralesional, Intraluminal, Intralymphatic, Intrameduallary, Intramenigeal, Intramuscular, Intraocular, 7/30/09 Version 1.0 FINAL

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Curation:

Intraovarian, Intrapericardial, Intraperitoneal, Intapleural, Intraprostatic, Intrapulmonary, Intrasinal, Intraspinal, Intrasynovial, Intratendinous, Intratesticular, Intratracheal, Intrathoracic, Intratubular, Intratumor, Intratympanic, Intrauterine, Intravascular, Intravenous, Intraventricular, Intravesical, Intravitreal, Iontophoresis, Irrigation, Laryngeal, Nasal, Nasogastric, Not applicable, Ophthalmic, Oral, Oropharyngeal, Other (Biologic), Other (Device), Other (Pharmaceutical), arenteral, Percutaneious, Periarticular, Peridural, Perineural, Periodontal, Rectal, Retrobulbar, Scarification, Subarachnoid, Subconjunctival, Subcutaneous, Sublingual, Submucosal, Topical, Transdermal, Transmucosal, Transtracheal, Transtympanic, Ureteral, Urethral, Vaginal Must be one of the above

14e. Experiment 1 –Were the animals sedated for inoculation? Format: Drop down menu: Yes/No/Unknown Curation: Must be one of the allowed selections ***If yes – must answer #14f, if no go one to 14g 14f. Experiment 1 – What were the animals sedated with? Format: Text Curation: No curation Example: Isofluorane 14g. Experiment 1 - Is the virus lethal for this animal strain tested? Format Drop down menu: Yes/No/Unknown Curation: Must be one of the above 14h. Experiment 1 – Total number of animals tested Format: Text Curation: No curation Example: 4 14i. Experiment 1 – Total number of animals that died from infection? Format: Text Curation: No curation Example: 2 14j. Experiment 1 – Total number of animals that were sick from infection? Format: Text Curation: No curation Example: 4 14k. Experiment 1 – What was the virus challenge dose? Format: Text Curation: No curation 6 Example: 10 EID50 14l. Experiment 1 – Did any of the animals seroconvert? Format: Drop down menu: Yes/No/Unknown Curation: Must be one of the allowed selections **If Yes go to question 14m. If no go to question 14n. 14m. Experiment 1 – At what timepoint after infection/challenge did the animals seroconvert? Format: Text Curation: No curation Example: 21 days

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14n. Experiment 1 – Other pathogenicity information? Example: HI data, receptor specificity, original isolation media, Lethal dose 50 data, etc. Definition: Text describing anything else of interest that the investigator would like to submit Format: Text/None Curation: None 14o. Experiment 1 – Was this data collected as part of a vaccine study? Format: Drop down menu: Yes/No Curation: One of the above 14p. Experiment 1 – Is this experimental data reported in a publication? Format: Drop down menu: No/Yes/Pending Curation Must be one of the allowed selections *IF Yes go to question 14o, If no or pending go to question 14p. 14q. Experiment 1 – Please list the PubMed ID of the publication Format: Text Curation: Validate that it is a function PubMed ID number. IRD to provide a direct link to the publication from the IRD website. Example: 17553873 14r. Would you like to submit data for another pathogenicity experiment? Format: Drop down menu: Yes/No *If yes, repeat Questions 14a-14r with the next number for experiment (PROVIDED BY IRD). If the answer is No go to question 15.

EXPERIMENTAL INFECTIVITY DATA

15. Are you submitting experimental data for infectivity studies? Format: Drop down menu: Yes/No Curation: Must be Yes/No NOTE – If no proceed to # 16; If yes proceed to answer 15a-15r. 15a. Experiment #1 – Animal tested Format: Drop down menu: Chicken, Duck, Turkey, Quail, Passerine, Raptor, Guinea Pig, Mouse, Ferret, Other Curation: Must be one of the above. If the answer is other need to be able to fill in with text what it is. 15b. Experiment #1 – Animal strain tested Format: Text Curation: No curation Example: BALB/c 15c. Experiment #1 – Age of animal tested Format: Text Curation: No curation Example: 6 weeks 15d. Experiment #1 – Route of inoculation Format: Drop down menu: Auricular (Otic), buccal, Cloacal, Conjunctival, Cutaneous, Dental, Electro-osmosis, Endocervical, Endosinusial, Endotracheal, Enteral, Epidural, Extra-amniotic, Extracorporeal, Hemodialysis, Infiltration, Inhaled, In Ovo, Interstital, Intra-abdominal, Intra-amniotic, Intra-arterial, Intra-articular, 7/30/09 Version 1.0 FINAL

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Curation:

Intrabiliary, Intrabronchial, Intrabursal, Intracardiac, Intracartilaginous, Intracaudal, Intracavernous, Intracavitary, Intracerebral, Intracisteranal, Intracorneal, Intracoronal (dental), Intracoronary, Intracorporus cavernosum, Intradermal, Intradiscal, Intraductal, Intraduodenal, Intradural, Intraepidermal, Intraesophageal, Intragastric, Intragingival, Intraileal, Intralesional, Intraluminal, Intralymphatic, Intrameduallary, Intramenigeal, Intramuscular, Intraocular, Intraovarian, Intrapericardial, Intraperitoneal, Intapleural, Intraprostatic, Intrapulmonary, Intrasinal, Intraspinal, Intrasynovial, Intratendinous, Intratesticular, Intratracheal, Intrathoracic, Intratubular, Intratumor, Intratympanic, Intrauterine, Intravascular, Intravenous, Intraventricular, Intravesical, Intravitreal, Iontophoresis, Irrigation, Laryngeal, Nasal, Nasogastric, Not applicable, Ophthalmic, Oral, Oropharyngeal, Other (Biologic), Other (Device), Other (Pharmaceutical), arenteral, Percutaneious, Periarticular, Peridural, Perineural, Periodontal, Rectal, Retrobulbar, Scarification, Subarachnoid, Subconjunctival, Subcutaneous, Sublingual, Submucosal, Topical, Transdermal, Transmucosal, Transtracheal, Transtympanic, Ureteral, Urethral, Vaginal Must be one of the above

15e. Experiment 1 –Were the animals sedated for inoculation? Format: Drop down menu: Yes/No/Unknown Curation: Must be one of the allowed selections ***If yes – must answer #15f, if no go on to 15g 15f. Experiment 1 – What were the animals sedated with? Format: Text Curation: No curation Example: Isofluorane 15g. Experiment 1 - Is the virus infectious for this animal strain tested? Format Drop down menu: Yes/No/Unknown Curation: Must be one of the above 15h. Experiment 1 – Total number of animals tested Format: Text Curation: No curation Example: 4 15i. Experiment 1 – Total number of animals that became infected? Format: Text Curation: No curation Example: 2 15j. Experiment 1 – Infectivity determined by? Format: Pull down menu: Serology, virus isolation, other Curation: Must be one of the above. If other need to be able to fill in. Must be able to select more than one 15k. Experiment 1 – What was the virus challenge dose? Format: Text Curation: No curation 6 Example: 10 EID50 15l. Experiment 1 – Did any of the animals seroconvert? Format: Drop down menu: Yes/No/Unknown Curation: Must be one of the allowed selections **If Yes go to question 15m. If no go to question 15n. 7/30/09 Version 1.0 FINAL

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15m. Experiment 1 – At what timepoint after infection/challenge did the animals seroconvert? Format: Text Curation: No curation Example: 21 days 15n. Experiment 1 – Other infectivity information? Example: HI data, receptor specificity, original isolation media, Lethal dose 50 data, etc. Definition: Text describing anything else of interest that the investigator would like to submit Format: Text/None Curation: None 15o. Experiment 1 – Was this data collected as part of a vaccine study? Format: Drop down menu: Yes/No Curation: One of the above 15p. Experiment 1 – Is this experimental data reported in a publication? Format: Drop down menu: No/Yes/Pending Curation Must be one of the allowed selections *IF Yes go to question 12o, If no or pending go to question 12p. 15q. Experiment 1 – Please list the PubMed ID of the publication Format: Text Curation: Validate that it is a function PubMed ID number. IRD to provide a direct link to the publication from the IRD website. Example: 17553873 15r. Would you like to submit data for another infectivity experiment? Format: Drop down menu: Yes/No *If yes, repeat Questions 15a-12r with the next number for experiment. If the answer is No go to question 16.

VIRUS TRANSMISSION DATA 16. Are you submitting experimental data for virus transmission studies? Format: Drop down menu: Yes/No Curation: Must be Yes/No NOTE – If no proceed to # 17; If yes proceed to answer 16a-16w. 16a. Experiment #1 – Infected animal tested Format: Drop down menu: Chicken, Duck, Turkey, Quail, Passerine, Raptor, Guinea Pig, Mouse, Ferret, Other Curation: Must be one of the above. If the answer is other need to be able to fill in with text what it is. 16b. Experiment #1 – Infected animal strain tested Format: Text Curation: No curation Example: BALB/c

16c. Experiment #1 –Contact animal species tested

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Format: Curation:

Drop down menu: Chicken, Duck, Turkey, Quail, Passerine, Raptor, Guinea Pig, Mouse, Ferret, Other Must be one of the above. If the answer is other need to be able to fill in with text what it is.

16d. Experiment #1 –Contact animal strain tested Format: Text Curation: No curation Example: BALB/c 16e. Experiment #1 – Age of infected animals tested Format: Text Curation: No curation Example: 6 weeks 16f. Experiment #1 – Age of contact animals tested Format: Text Curation: No curation Example: 6 weeks 16g. Experiment #1 – Route of inoculation Format: Drop down menu: Auricular (Otic), buccal, Cloacal, Conjunctival, Cutaneous, Dental, Electro-osmosis, Endocervical, Endosinusial, Endotracheal, Enteral, Epidural, Extra-amniotic, Extracorporeal, Hemodialysis, Infiltration, Inhaled, In Ovo, Interstital, Intra-abdominal, Intra-amniotic, Intra-arterial, Intra-articular, Intrabiliary, Intrabronchial, Intrabursal, Intracardiac, Intracartilaginous, Intracaudal, Intracavernous, Intracavitary, Intracerebral, Intracisteranal, Intracorneal, Intracoronal (dental), Intracoronary, Intracorporus cavernosum, Intradermal, Intradiscal, Intraductal, Intraduodenal, Intradural, Intraepidermal, Intraesophageal, Intragastric, Intragingival, Intraileal, Intralesional, Intraluminal, Intralymphatic, Intrameduallary, Intramenigeal, Intramuscular, Intraocular, Intraovarian, Intrapericardial, Intraperitoneal, Intapleural, Intraprostatic, Intrapulmonary, Intrasinal, Intraspinal, Intrasynovial, Intratendinous, Intratesticular, Intratracheal, Intrathoracic, Intratubular, Intratumor, Intratympanic, Intrauterine, Intravascular, Intravenous, Intraventricular, Intravesical, Intravitreal, Iontophoresis, Irrigation, Laryngeal, Nasal, Nasogastric, Not applicable, Ophthalmic, Oral, Oropharyngeal, Other (Biologic), Other (Device), Other (Pharmaceutical), arenteral, Percutaneious, Periarticular, Peridural, Perineural, Periodontal, Rectal, Retrobulbar, Scarification, Subarachnoid, Subconjunctival, Subcutaneous, Sublingual, Submucosal, Topical, Transdermal, Transmucosal, Transtracheal, Transtympanic, Ureteral, Urethral, Vaginal Curation: Must be one of the above 16h. Experiment 1 –Were the animals sedated for inoculation? Format: Drop down menu: Yes/No/Unknown Curation: Must be one of the allowed selections ***If yes – must answer #16i, if no go on to 16j 16i. Experiment 1 – What were the animals sedated with? Format: Text Curation: No curation Example: Isofluorane 16j. Experiment 1 - Does the virus transmit for this animal strain tested? Format Drop down menu: Yes/No/Unknown Curation: Must be one of the above 7/30/09 Version 1.0 FINAL

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16k. Experiment 1 – Total number of animals infected Format: Text Curation: No curation Example: 4 16l. Experiment 1 – Total number of contact animals? Format: Text Curation: No curation Example: 2 16m. Experiment 1 – Total number of contact animals that became infected? Format: Text Curation: No curation Example: 2 16n. Experiment 1 – Infectivity of contact animals determined by? Format: Pull down menu: Serology, virus isolation, other Curation: Must be one of the above. If other need to be able to fill in. Must be able to select more than one 16o. Experiment 1 – What was the virus challenge dose for the infected animals? Format: Text Curation: No curation 6 Example: 10 EID50 16p. Experiment 1 – What was the type of transmission? Format: Drop down menu: Aerosol, contact, Other, No transmission Curation: Must be one of the allowed selections; can select more than one. If other must specify 16q. Experiment 1 – Did any of the animals seroconvert? Format: Drop down menu: Yes/No/Unknown Curation: Must be one of the allowed selections **If Yes go to question 16r. If no go to question 16s. 16r. Experiment 1 – At what timepoint after infection/challenge did the animals seroconvert? Format: Text Curation: No curation Example: 21 days 16s. Experiment 1 – Other viral transmission information? Example: HI data, receptor specificity, original isolation media, Lethal dose 50 data, etc. Definition: Text describing anything else of interest that the investigator would like to submit Format: Text/None Curation: None 16t. Experiment 1 – Was this data collected as part of a vaccine study? Format: Drop down menu: Yes/No Curation: One of the above 16u. Experiment 1 – Is this experimental data reported in a publication? Format: Drop down menu: No/Yes/Pending Curation Must be one of the allowed selections *IF Yes go to question 16v, If no or pending go to question 16w. 7/30/09 Version 1.0 FINAL

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16v. Experiment 1 – Please list the PubMed ID of the publication Format: Text Curation: Validate that it is a function PubMed ID number. IRD to provide a direct link to the publication from the IRD website. Example: 17553873 16w. Would you like to submit data for another viral transmission experiment? Format: Drop down menu: Yes/No *If yes, repeat Questions 16a-16w with the next number for experiment. If the answer is No go to question 17.

ANTIVIRAL RESISTANCE DATA 17. Would you like to submit data on the antiviral resistance of this virus? Format: Drop down menu: Yes/No **If yes go on to questions 17a-17d; If no go to question 18. 17a. Name of the antiviral drug that you are submitting information about Format: Drop down menu: Amantadine, Oseltamivir, Peramivir, Rimantadine, Zanamivir Curation: Must be one of the above. 17b (IRD) Type of antiviral drug Format: M2 inhibitor, Neuraminidase inhibitor Curation: Oseltamivir, Zanamivir, Peramivir are NA inhibitors; Rimantadine and Amantadine are M2 inhibitors. 17c. Is the virus sensitive or resistant to this antiviral drug? Format: Drop down menu: Sensitive, Resistant Curation: Must be one of the above. 17d. Antiviral susceptibility/resistance determined by: Definition: Describe any evidence obtained to indicate that the virus isolate would be resistant/Sensitive to the antiviral inhibitor Format: Drop down menu; Sequence, phenotypic test, previous report Example: Susceptibility determined by sequence comparison with strain X; phenotypic test; both. Curation: One of the above. **If phenotypic test go to question 17h, If Previous report answer 17 e and 17f, if sequence answer 17g. 17e. Are there links to publications for the previous reports? Format: Drop down menu: Yes or No Curation: One of the above. If yes answer question 15f. 17f. What is the Pubmed ID for the publication? Format: Text Curation: Validate that it is a function PubMed ID number. IRD to provide a direct link to the publication from the IRD website. Example: 17553873 17g. What mutations are present that indicate resistance/sensitivity? Format: Text 7/30/09 Version 1.0 FINAL

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Minimum data fields for Experimental data – Detail document FINAL

Curation: Example:

No curation E119G

17h. Is this data reported in a publication? Format: Drop down menu: No/Yes/Pending Curation Must be one of the allowed selections *IF Yes go to question 17o, If no or pending go to question 17p. 17i. Please list the PubMed ID of the publication Format: Text Curation: Validate that it is a function PubMed ID number. IRD to provide a direct link to the publication from the IRD website. Example: 17553873 17j. Would you like to submit information for another antiviral drug? Format: Drop down menu: Yes/No *If yes, repeat Questions 17a-17j. If the answer is No go to question 18.

MICROARRAY DATA

18. Was a microarray done using this virus? Format: Drop down menu: Yes/No Curation: One of the above If yes answer 16a-16f, if no go to question 17. 18a. Experiment 1 - What is the host for this microarray? Format: Text Curation: No curation Example: Mouse 18b. Experiment 1 - How many microarrays have been done? Format: Text Curation: No curation Example: 2 18c. Experiment 1 - If the microarray data is currently deposited in a public database, please list a link to where the data is located. Format: Text/Not in database Curation: Validate that the link is functional 18d. Experiment 1 - Is this data reported in a publication? Format: Drop down menu: No/Yes/Pending Curation Must be one of the allowed selections *IF Yes go to question 18e, If no or pending go to question 18f. 18e. Please list the PubMed ID of the publication Format: Text Curation: Validate that it is a function PubMed ID number. IRD to provide a direct link to the publication from the IRD website. Example: 17553873 18f. Would you like to submit information for another microarray experiment? Format: Drop down menu: Yes/No *If yes, repeat Questions 18a-18j. If the answer is No THEY ARE DONE!!. 7/30/09 Version 1.0 FINAL

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