Section 2
USFWS/AFS-FHS Standard Procedures for
Aquatic Animal Health Inspections
Chapter 1 Introduction
1.1 INTRODUCTION
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Chapter 2 Sampling
2.1 SAMPLING INTRODUCTION
2.2 SAMPLING
2.3 REAGENTS, MEDIA, AND MEDIA PREPARATION
2.4 GLOSSARY
2.5 REFERENCES
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Chapter 3 Bacteriology
3.1 BACTERIOLOGY INTRODUCTION
3.2 AEROMONAS SALMONICIDA (FURUNCULOSIS)
3.3 YERSINIA RUCKERI (ENTERIC REDMOUTH DISEASE, ERM)
3.4 EDWARDSIELLA ICTALURI (ENTERIC SEPTICEMIA OF CATFISH, ESC)
3.5 RENIBACTERIUM SALMONINARUM (BACTERIAL KIDNEY DISEASE, BKD)
3.6 PISCIRICKETTSIA SALMONIS
3.7 REAGENTS, MEDIA, AND MEDIA PREPARATION
3.8 BACTERIAL IDENTIFICATION TECHNIQUES
3.9 GLOSSARY
3.10 REFERENCES
3.A1 Laboratory Reference Flow Chart Appendix 1
3.A2 Profiles Obtained with API-20E for Known Fish Pathogens
3.A3.A Worksheet A – PCR Sample Data/Log Sheet
3.A3.B Worksheet B – Initial Amplification of Nucleic Acid by PCR for the Confirmation of R. salmoninarum
3.A3.C Worksheet C – Nested Amplification of Nucleic Acid by PCR for the Confirmation of R. salmoninarum
3.A3.D Worksheet D – Initial Amplification of Nucleic Acid by PCR for the Confirmation of P. salmonis
3.A3.E Worksheet E – Nested Amplification of Nucleic Acid by PCR for the Confirmation of P. salmonis
3.A3.F Worksheet F – Direct Amplification of Nucleic Acid by PCR for the Confirmation of P. salmonis
3.A3.G Worksheet G – Photodocumentation of the PCR Product Gel
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Chapter 4 Virology
4.1 VIROLOGY INTRODUCTION
4.2 SELECTION OF APPROPRIATE CELL LINES
4.3 CELL CULTURE
4.4 SAMPLE PROCESSING PROCEDURES
4.5 SCREENING METHOD FOR VIRAL ISOLATION
4.6 IDENTIFICATION OF VIRUSES
4.7 SERUM NEUTRALIZATION
4.8 INDIRECT FLUORESCENT ANTIBODY (IFAT) PROCEDURE
4.9 REAGENTS AND MEDIA
4.10 GLOSSARY
4.11 REFERENCES
4.A1.A Worksheet A – PCR Sample Data/Log Sheet
4.A1.B Worksheet B – Amplification of Nucleic Acid by PCR for the Confirmation of Viral Fish Pathogens
4.A1.B.1 Worksheet B.1 – Infectious Hematopoietic Necrosis Virus (IHNV)
4.A1.B.2 Worksheet B.2 – Infectious Pancreatic Necrosis Virus (IPNV)
4.A1.B.3 Worksheet B.3 – Infectious Salmon Anemia Virus (ISAV)
4.A1.B.4 Worksheet B.4 – Largemouth Bass Virus (LMBV)
4.A1.B.5 Worksheet B.5 – Oncorhynchus masou Virus (OMV)
4.A1.B.6 Worksheet B.6 – Spring Viremia of Carp Virus (SVCV)
4.A1.B.7 Worksheet B.7 – Viral Hemorrhagic Septicemia Virus (VHSV)
4.A1.C Worksheet C – Photodocumentation of the PCR Product Gel
4.A2 Cell Enumeration
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Chapter 5 Parasitology
5.1 PARASITOLOGY INTRODUCTION
5.2 MYXOBOLUS CEREBRALIS (WHIRLING DISEASE) Updated 2014
5.3 CERATOMYXA SHASTA (CERATOMYXOSIS)
5.4 TETRACAPSULA BRYOSALMONAE (PROLIFERATIVE KIDNEY DISEASE)
5.5 BOTHRIOCEPHALUS ACHEILOGNATHI (BOTHRIOCEPHALOSIS, ASIAN TAPEWORM)
5.6 MEDIA AND REAGENTS
5.7 GLOSSARY
5.8 REFERENCES
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Chapter 6 Polymerase Chain Reaction
6.1 POLYMERASE CHAIN REACTION (PCR) INTRODUCTION
6.2 PCR – QUALITY ASSURANCE/QUALITY CONTROL
6.3 PCR PROTOCOLS
6.4 REAGENTS
6.5 ANALYSIS OF EXTRACTED DNA USING AN UV SPECTROPHOTOMETER
6.6 TABLE OF PCR PROTOCOLS
6.7 REFERENCES
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Section 2 Appendices
APPENDIX 1 THE COMMITTEE
A1.1 Format of the Handbook
A1.2 Handbook Revision and Oversight Committee
A1.3 Process for Amending the Handbook
APPENDIX 2 HANDBOOK COMMITTEES
A2.1 2000 – 2002 Handbook Development Committee
A2.2 2002 – 2003 Handbook Development Committee
A2.3 2003 – 2004 Handbook Development Committee
A2.4 2004 – 2005 Handbook Development Committee
A2.5 2006 – 2007 Handbook Development Committee
A2.6 2008 – 2010 Handbook Development Committee
A2.7 2011 – 2012 Handbook Development Committee
A2.8 2013 – 2014 Handbook Development Committee
APPENDIX 3 POSITION STATEMENTS
A3.1 Position Statements Introduction
A3.2 Sampling Position Statements
A3.3 Bacteriology Position Statements
A3.4 Virology Position Statements
A 3.5 Parasitology Position Statements
A3.6 Polymerase Chain Reaction Position Satement
A3.7 The Handbook and Oversight Committee Position Statements