ENA virus pathogen reporting standard checklist

Conditions at which sample was stored, usually storage temperature, duration and location. In soil context: Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other).

Exposure of the subject to infected human or animals, such as poultry, wild bird or swine. If multiple exposures are applicable, please state them separated by semicolon. Example: poultry; wild bird

Setting within which the subject is exposed to animals, such as farm, slaughterhouse, food preparation. If multiple exposures are applicable, please state their type in the same order in which you reported the exposure in the field 'subject exposure'. Example: backyard flock; confined animal feeding operation

Use of personal protective equipment, such as gloves, gowns, during any type of exposure. Example: mask

Was the subject confined to a hospital as a result of virus infection or problems occurring secondary to virus infection?

The number of days the illness lasted. Example: 4

The symptoms that have been reported in relation to the illness, such as cough, diarrhea, fever, headache, malaise, myalgia, nausea, runny_nose, shortness_of_breath, sore_throat. If multiple exposures are applicable, please state them separated by semicolon.

The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008.

The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system

The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system

The geographical origin of the sample as defined by the specific region name followed by the locality name.

Duration of the exposure of the subject to an infected human or animal. If multiple exposures are applicable, please state their duration in the same order in which you reported the exposure in the field 'subject exposure'. Example: 1 day; 0.33 days

Reason for the sample collection.

The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).

Disease outcome in the host.

common name of the host, e.g. human

a unique identifier by which each subject can be referred to, de-identified, e.g. #131

age of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees

Health status of the host at the time of sample collection.

Gender or sex of the host.

scientific name of the laboratory host used to propagate the source organism from which the sample was obtained

Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.

Unique laboratory identifier assigned to the virus by the investigator. Strain name is not sufficient since it might not be unique due to various passsages of the same virus. Format: up to 50 alphanumeric characters

Name of the person who collected the specimen. Example: John Smith

Name of the institution to which the person collecting the specimen belongs. Format: Institute Name, Institute Address

Date on which the sample was received. Format:YYYY-MM-DD. Please provide the highest precision possible. If the sample was received by the institution and not collected, the 'receipt date' must be provided instead. Either the 'collection date' or 'receipt date' must be provided. If available, provide both dates.

The cut off value used by an investigatior in determining that a sample was seropositive.

Serological variety of a species characterised by its antigenic properties. For Influenza, HA subtype should be the letter H followed by a number between 1-16 unless novel subtype is identified and the NA subtype should be the letter N followed by a number between 1-9 unless novel subtype is identified. If only one of the subtypes have been tested then use the format H5Nx or HxN1. Example: H1N1

individual isolate from which the sample was obtained

Name of the strain from which the sample was obtained.

Natural habitat of the avian or mammalian host.

Name of host tissue or organ sampled for analysis. Example: tracheal tissue

Other descriptive information relating to the host.

Whether or not the subject is gravid. If so, report date due or date post-conception and specify which of these two dates is being reported.

Natural behaviour of the host.

Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived. Example: soil