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Virginia - low path H5N1 outbreak in Shenandoah county

M

Mamabird

Well-known member
In a report filed with OIE today, the US did not exactly release any sequences, but it did reveal the HA cleavage site on the low pathogenic H5N1 detected in Virginia turkeys back in March. To the relief of all, it looks like the 1975 and 1981 varieties previously detected in the US (NVPQRETR*GLFGAI). Wouldn't it be interesting to see what additional characteristics this virus might reveal if we had all the genetic information posed to GenBank?

http://www.oie.int/wahid-prod/public.php?page=weekly_report_index&admin=0
 
Re: US Reveals Genetic Information on its LP H5N1

Re: US Reveals Genetic Information on its LP H5N1

Mamabird said:
In a report filed with OIE today, the US did not exactly release any sequences, but it did reveal the HA cleavage site on the low pathogenic H5N1 detected in Virginia turkeys back in March. To the relief of all, it looks like the 1975 and 1981 varieties previously detected in the US (NVPQRETR*GLFGAI). Wouldn't it be interesting to see what additional characteristics this virus might reveal if we had all the genetic information posed to GenBank?

http://www.oie.int/wahid-prod/public.php?page=weekly_report_index&admin=0
Click to expand...
Actually, they released the sequence of the HA cleavage site on July 23:

Information received on 23/07/2007 from Dr John Clifford, Deputy Administrator, Animal and Plant Health Inspection Service, United States Department of Agriculture, Washington, United States of America
Summary
<TABLE class=rep_table cellPadding=0 width="100%" border=0 cellmargin="0"><TBODY><TR><TD class=rep_item width=200>Report type</TD><TD class=rep_data width=*>Immediate notification</TD></TR><TR><TD class=rep_item width=200>Start date</TD><TD class=rep_data width=*>07/07/2007</TD></TR><TR><TD class=rep_item width=200>Date of confirmation of event</TD><TD class=rep_data width=*>20/07/2007</TD></TR><TR><TD class=rep_item width=200>Report date</TD><TD class=rep_data width=*>23/07/2007</TD></TR><TR><TD class=rep_item width=200>Date submitted to OIE</TD><TD class=rep_data width=*>23/07/2007</TD></TR><TR><TD class=rep_item width=200>Reason for notification</TD><TD class=rep_data width=*>Reoccurrence of a listed disease</TD></TR><TR><TD class=rep_item width=200>Date of previous occurrence</TD><TD class=rep_data width=*>03/04/2007</TD></TR><TR><TD class=rep_item width=200>Manifestation of disease</TD><TD class=rep_data width=*>Sub-clinical infection</TD></TR><TR><TD class=rep_item width=200>Causal agent</TD><TD class=rep_data width=*>Low pathogenic avian influenza virus</TD></TR><TR><TD class=rep_item width=200>Serotype</TD><TD class=rep_data width=*>H5N1</TD></TR><TR><TD class=rep_item width=200>Nature of diagnosis</TD><TD class=rep_data width=*>Laboratory (basic), Laboratory (advanced)</TD></TR><TR><TD class=rep_item width=200>Report pertains to</TD><TD class=rep_data width=*>Entire country</TD></TR><TR><TD class=rep_item width=200>Related reports</TD><TD class=rep_data width=*>
</TD></TR></TBODY></TABLE>

New outbreaks <TABLE class=rep_table width="100%" border=0><TBODY><TR><TD class=rep_item_ob width=200>Outbreak 1 </TD><TD class=rep_data_ob width=*>Shenandoah County, Shenandoah, VIRGINIA</TD></TR><TR><TD class=rep_item width=200>Date of start of outbreak</TD><TD class=rep_data width=*>07/07/2007</TD></TR><TR><TD class=rep_item width=200>Outbreak status</TD><TD class=rep_data width=*>Resolved (04/08/2007)</TD></TR><TR><TD class=rep_item width=200>Epidemiological unit</TD><TD class=rep_data width=*>Farm</TD></TR><TR><TD class=rep_item width=200>Affected animals</TD><TD><TABLE class=rep_sub_table width="100%" border=0><TBODY><TR><TD class=rep_sub_item width="20%">Species</TD><TD class=rep_sub_item width="16%">Susceptible</TD><TD class=rep_sub_item width="16%">Cases</TD><TD class=rep_sub_item width="16%">Deaths</TD><TD class=rep_sub_item width="16%">Destroyed</TD><TD class=rep_sub_item width="16%">Slaughtered</TD></TR><TR vAlign=top><TD class=rep_sub_data>Birds</TD><TD class=rep_sub_data>54000</TD><TD class=rep_sub_data>0</TD><TD class=rep_sub_data>0</TD><TD class=rep_sub_data>54000</TD><TD class=rep_sub_data>0</TD></TR></TBODY></TABLE></TD></TR><TR><TD class=rep_item width=200>Affected population</TD><TD class=rep_data width=*>• The index farm is a commercial turkey farm with nine houses containing a total of 54,000 birds. • The turkeys did not show any clinical signs of sickness or diseases. </TD></TR><TR><TD class=rep_item_ob width=200>Summary of outbreaks</TD><TD class=rep_data_ob width=*>Total outbreaks: 1</TD></TR><TR><TD class=rep_item width=200>Outbreak statistics</TD><TD class=rep_data><TABLE class=rep_sub_table width="100%" border=0><TBODY><TR><TD class=rep_sub_item width="20%">Species</TD><TD class=rep_sub_item width="20%">Apparent morbidity rate</TD><TD class=rep_sub_item width="20%">Apparent mortality rate</TD><TD class=rep_sub_item width="20%">Apparent case fatality rate</TD><TD class=rep_sub_item width="20%">Proportion susceptible removed* </TD></TR><TR vAlign=top><TD class=rep_sub_data>Birds</TD><TD class=rep_sub_data>0.00%</TD><TD class=rep_sub_data>0.00%</TD><TD class=rep_sub_data>-</TD><TD class=rep_sub_data>100.00%</TD></TR></TBODY></TABLE>* Removed from the susceptible population either through death, destruction or slaughter</TD></TR></TBODY></TABLE>
Epidemiology <TABLE class=rep_table width="100%" border=0><TBODY><TR><TD class=rep_item width=200>Source of infection</TD><TD class=rep_data width=*>
  • Unknown or inconclusive
</TD></TR><TR><TD class=rep_item width=200>Epidemiological comments</TD><TD class=rep_data width=*>• On 7 July 2007, the National Veterinary Services Laboratory (NVSL) confirmed positive serology for H5 antibodies on hemagglutinin inhibition testing (HI).
• The samples that were taken were routine samples collected from market-age birds during pre-slaughter under the national surveillance program for notifiable avian influenza (NAI).
• The birds were healthy and showed no signs of illness.
• On 11 July 2007, the NVSL confirmed positive serology for N1 antibodies on neuroaminidase inhibition (NI) testing.
• On 11-14 July 2007, the turkeys on the affected farm were depopulated followed by cleaning and disinfection of the facilities.
• On 19 July 2007, the NVSL isolated virus from samples taken from birds that were depopulated (prior to this date, results had only yielded positive serology).
• All commercial flocks within 3 Km and 10 Km of the index farm and all epidemiologically linked flocks have been sampled and all have tested negative.
• Backyard flocks within 10 Km of the index flock have also been sampled and have tested negative.
• No additional affected farms have been found either within 10 Km of the index flock or in the 17 county region.
• On 21 July, the NVSL completed gene sequence testing – the isolate subtype H5N1 is compatible with the low pathogenic North American strain (NVPQRETR GLFGAI).
• Enhanced surveillance within the 17 county region will continue through 7 August 2007, in accordance with the State plan for NAI surveillance.

</TD></TR></TBODY></TABLE>
Control measures <TABLE class=rep_table width="100%" border=0><TBODY><TR><TD class=rep_item width=200>Measures already applied</TD><TD class=rep_data width=*>
  • <LI class=rep_list>Movement control inside the country <LI class=rep_list>Screening <LI class=rep_list>Disinfection of infected premises/establishment(s) <LI class=rep_list>Quarantine <LI class=rep_list>Stamping out <LI class=rep_list>Vaccination prohibited
  • No treatment of affected animals
</TD></TR><TR><TD class=rep_item width=200>Measures to be applied</TD><TD class=rep_data width=*>
  • None specified
</TD></TR></TBODY></TABLE>Diagnostic test results <TABLE class=rep_table width="100%" border=0><TBODY><TR><TD class=rep_item width=200>Laboratory name and type</TD><TD class=rep_data width=*>Virginia, Harrisonburg Laboratory (Local laboratory)</TD></TR><TR><TD class=rep_item width=200>Tests and results</TD><TD><TABLE class=rep_sub_table width="100%" border=0><TBODY><TR><TD class=rep_sub_item width="35%">Species</TD><TD class=rep_sub_item width="40%">Test</TD><TD class=rep_sub_item width="15%">Test date</TD><TD class=rep_sub_item width="10%">Result</TD></TR><TR vAlign=top><TD class=rep_sub_data>Birds</TD><TD class=rep_sub_data>agar-gel immunodiffusion (AGID)</TD><TD class=rep_sub_data>13/07/2007</TD><TD class=rep_sub_data>Negative</TD></TR></TBODY></TABLE></TD></TR><TR><TD class=rep_item width=200>Laboratory name and type</TD><TD class=rep_data width=*>National Veterinary Services Laboratory (NVSL) (National laboratory)</TD></TR><TR><TD class=rep_item width=200>Tests and results</TD><TD><TABLE class=rep_sub_table width="100%" border=0><TBODY><TR><TD class=rep_sub_item width="35%">Species</TD><TD class=rep_sub_item width="40%">Test</TD><TD class=rep_sub_item width="15%">Test date</TD><TD class=rep_sub_item width="10%">Result</TD></TR><TR vAlign=top><TD class=rep_sub_data>Birds</TD><TD class=rep_sub_data>haemagglutination inhibition test (HIT)</TD><TD class=rep_sub_data>07/07/2007</TD><TD class=rep_sub_data>Positive</TD></TR></TBODY></TABLE></TD></TR><TR><TD class=rep_item width=200>Laboratory name and type</TD><TD class=rep_data width=*>NVSL (National laboratory)</TD></TR><TR><TD class=rep_item width=200>Tests and results</TD><TD><TABLE class=rep_sub_table width="100%" border=0><TBODY><TR><TD class=rep_sub_item width="35%">Species</TD><TD class=rep_sub_item width="40%">Test</TD><TD class=rep_sub_item width="15%">Test date</TD><TD class=rep_sub_item width="10%">Result</TD></TR><TR vAlign=top><TD class=rep_sub_data>Birds</TD><TD class=rep_sub_data>agar-gel immunodiffusion (AGID)</TD><TD class=rep_sub_data>14/07/2007</TD><TD class=rep_sub_data>Negative</TD></TR><TR vAlign=top><TD class=rep_sub_data>Birds</TD><TD class=rep_sub_data>gene sequencing</TD><TD class=rep_sub_data>20/07/2007</TD><TD class=rep_sub_data>Positive</TD></TR><TR vAlign=top><TD class=rep_sub_data>Birds</TD><TD class=rep_sub_data>neuraminidase inhibition assay </TD><TD class=rep_sub_data>11/07/2007</TD><TD class=rep_sub_data>Positive</TD></TR><TR vAlign=top><TD class=rep_sub_data>Birds</TD><TD class=rep_sub_data>real-time reverse transcriptase/polymerase chain reaction (RRT-PCR)</TD><TD class=rep_sub_data>10/07/2007</TD><TD class=rep_sub_data>Negative</TD></TR><TR vAlign=top><TD class=rep_sub_data>Birds</TD><TD class=rep_sub_data>real-time reverse transcriptase/polymerase chain reaction (RRT-PCR)</TD><TD class=rep_sub_data>14/07/2007</TD><TD class=rep_sub_data>Positive</TD></TR><TR vAlign=top><TD class=rep_sub_data>Birds</TD><TD class=rep_sub_data>virus isolation</TD><TD class=rep_sub_data>19/07/2007</TD><TD class=rep_sub_data>Positive</TD></TR></TBODY></TABLE></TD></TR></TBODY></TABLE>
 
Re: US Reveals Genetic Information on its LP H5N1

Re: US Reveals Genetic Information on its LP H5N1

This was on a HEDDS email update I received today. I checked the table, and it shows "testing underway".

Aug 21, 2007: The LPAI H5N1 table has been updated with information on results from a
sample collected from a ruddy turnstone in Cape May, New Jersey on 5/10/2007.
 
Re: US Reveals Genetic Information on its LP H5N1

Re: US Reveals Genetic Information on its LP H5N1

yielddude said:
This was on a HEDDS email update I received today. I checked the table, and it shows "testing underway".

Aug 21, 2007: The LPAI H5N1 table has been updated with information on results from a
sample collected from a ruddy turnstone in Cape May, New Jersey on 5/10/2007.
Click to expand...
Tes, that sample seems to be trailing:

5/22/07 Kent
County, DE
Ruddy
turnstone Live birds USDA/DE Department of Natural Resources and
Environmental Control Yes Yes
Not related to HPAI
H5N1; Suspected
LPAI
No virus
isolated Not applicable
5/16/07 Sussex
County, DE
Ruddy
turnstone (#1) Live birds USDA/DE Department of Natural Resources and
Environmental Control Yes Yes
Not related to HPAI
H5N1; Suspected
LPAI
No virus
isolated Not applicable
5/16/07 Sussex
County, DE
Ruddy
turnstone (#2) Live birds USDA/DE Department of Natural Resources and
Environmental Control Yes Yes
Not related to HPAI
H5N1; Suspected
LPAI
No virus
isolated Not applicable
5/16/07 Sussex
County, DE
Ruddy
turnstone (#3) Live birds USDA/DE Department of Natural Resources and
Environmental Control Yes Yes
Not related to HPAI
H5N1; Suspected
LPAI
No virus
isolated Not applicable
5/11/07 Kent
County, DE
Ruddy
turnstone Live birds USDA/DE Department of Natural Resources and
Environmental Control Yes Yes
Not related to HPAI
H5N1; Suspected
LPAI
No virus
isolated Not applicable
5/10/07 Cape May
County, NJ
Ruddy
Turnstone Live birds Southeastern Cooperative Wildlife Disease Study Yes Yes
Not related to HPAI
H5N1; Suspected
LPAI
Testing​
Underway Testing Underway
 
Re: US Reveals Genetic Information on its LP H5N1

Re: US Reveals Genetic Information on its LP H5N1

yielddude said:
This was on a HEDDS email update I received today. I checked the table, and it shows "testing underway".

Aug 21, 2007: The LPAI H5N1 table has been updated with information on results from a
sample collected from a ruddy turnstone in Cape May, New Jersey on 5/10/2007.
Click to expand...

It is my understanding that the LPAI table discussed above only relates to wild bird detections. Therefore, if highly pathogenic H5N1 was detected in poultry flocks across seven states, this table would not reflect such an event. This is just another way for the USDA to communicate with its constituents.
 
Re: US Reveals Genetic Information on its LP H5N1

Re: US Reveals Genetic Information on its LP H5N1

For example:

"Information received on 10/08/2007 from Dr John Clifford, Deputy Administrator, Animal and Plant Health Inspection Service, United States Department of Agriculture, Washington, United States of America

Summary

Report type Follow-up report No. 1
Start date 25/06/2007
Date of confirmation of event 19/07/2007
Report date 10/08/2007
Date submitted to OIE 10/08/2007
Reason for notification Reoccurrence of a listed disease
Date of previous occurrence 03/04/2007
Manifestation of disease Sub-clinical infection
Causal agent Low pathogenic avian influenza virus
Serotype H7N9
Nature of diagnosis Laboratory (basic), Laboratory (advanced)
Report pertains to Entire country
Related reports Immediate notification (23/07/2007)
Follow-up report No. 1 (10/08/2007)

Outbreaks There are no new outbreaks in this report"

Didn't see this one in the table either, did you?
 
Re: US Reveals Genetic Information on its LP H5N1

Re: US Reveals Genetic Information on its LP H5N1

have they ever explained, _why_ they don't release the sequences ?
have they ever been asked about it ?
could it be disadvantageous for a reporter's/interviewer's career to
ask such questions in USA ?
 
Re: US Reveals Genetic Information on its LP H5N1

Re: US Reveals Genetic Information on its LP H5N1

gsgs said:
have they ever explained, _why_ they don't release the sequences ?
have they ever been asked about it ?
could it be disadvantageous for a reporter's/interviewer's career to
ask such questions in USA ?
Click to expand...
Canada has held their H5 sequences for TWO years now.
 
Re: US Reveals Genetic Information on its LP H5N1

Re: US Reveals Genetic Information on its LP H5N1

yielddude said:
Looks like a mallard from Kent, Maryland added to table ...

http://wildlifedisease.nbii.gov/ai/LPAI-Table.jsp
Click to expand...
My guess is that these samples have been sitting around for months and are just now being tested (or test results are now being analyzed), so efforts to further charaterized are months behind collection dates (and efforts to grow H5N1 will probably generate MORE negatives, as the foxes continue to guard the hen houses).

Most positives were in August in Canada in prior years.
 
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