Blog · Aquaculture PCR · 2026-10-13

Disease signs in whiteleg shrimp: 28 things a farmer sees, and the PCR that names the cause

Farmers see disease long before a laboratory sees a sample: white spots on the shell, a red tail, white strings on the feed tray, a shrunken hepatopancreas. The chart below collects 28 of these signs in Litopenaeus vannamei. A sign tells you where to look, not what you are looking at: several pathogens produce the same picture, and stress produces several of them too. This note maps each sign to the tests that tell the causes apart.

A reference chart circulated among shrimp farmers: 28 signs of disease in whiteleg shrimp, each with an arrow on the affected tissue, next to a healthy animal for comparison. Open the chart full size.

A sign is a reason to test, not a diagnosis

White spots on the carapace are the classic sign of white spot syndrome virus, and also of a bacterial infection and of calcium deposits in hard, high-alkalinity water. A red tail is the textbook sign of Taura syndrome, and also of a shrimp stressed by low oxygen. Mixed infections are common: a pond weakened by EHP is the pond where Vibrio takes hold.

The decision that follows depends on the cause, not the sign. White spot in a grow-out pond means preparing an emergency harvest within days; a bacterial shell infection means fixing the water and the bottom. So the sign chooses the test, and the test chooses the action.

The 28 signs and what to test for

Read across: the sign as it appears on the chart, the causes it is most often associated with, and the PCR kit in this catalogue that confirms or rules out each cause. Where a sign has no single cause, the table says so and points to the core panel.

Sign on the chart	Most often associated with	PCR to run
Healthy shrimp	Reference animal: transparent body, firm shell, full gut line	Routine screening: core panel AQ-48 (AHPND, EHP, WSSV, IHHNV)
White spots on carapace	White spot syndrome virus (WSSV); also bacterial white spot and mineral deposits in high-alkalinity water	WSSV: AQ-11 · WSSV + DIV1: AQ-22
Fluid filled cephalothorax	No single cause; part of the IHHNV runt deformity syndrome ('bubble head') and of systemic infections	Core panel AQ-48 (includes IHHNV)
Runt deformity syndrome	IHHNV, the classic cause of runt deformity syndrome; EHP also stunts growth and widens size variation	IHHNV: AQ-14 · EHP: AQ-01
Deformed abdominal segments	IHHNV (runt deformity syndrome); nutrition and handling damage look similar	IHHNV: AQ-14
Deformed tail	IHHNV: a deformed sixth abdominal segment in runt deformity syndrome, usually with a bent rostrum; also healed injury or bacterial tail necrosis	IHHNV: AQ-14 · Vibrio: AQ-27
Myonecrosis	Infectious myonecrosis virus (IMNV); covert mortality nodavirus (CMNV), Penaeus vannamei nodavirus and microsporidian infection look the same; stress causes a similar necrosis	IMNV: AQ-20 · CMNV + IMNV: AQ-24
Necrotic and reddened tissue	IMNV: white necrosis of the distal abdominal muscle and tail that turns red; CMNV looks similar; Vibrio invades the damaged tissue; acute Taura syndrome virus (TSV) reddens the whole body	CMNV + IMNV: AQ-24 · Vibrio: AQ-27 · TSV: AQ-08
Red tail	TSV in the acute phase, the original 'red tail disease'; also stress	TSV: AQ-08
Epithelial necrosis	Most typical of acute TSV: focal necrosis at the edges of the uropods and pleopods, with a red tail fan; bacterial shell necrosis looks similar	TSV: AQ-08 · Vibrio: AQ-27
Melanized cuticular lesions	TSV in the transition phase; bacterial shell disease	TSV: AQ-08 · Vibrio: AQ-27
Yellow colored shrimp	A yellow head (cephalothorax) can suggest yellow head virus (YHV) on Asian farms; whole-body yellowing is usually non-infectious, from feed pigments or water colour	YHV: AQ-09
Atrophy of hepatopancreas	AHPND (Vibrio carrying the pirAB toxin genes, also called EMS), mostly in the first 35 days after stocking; necrotising hepatopancreatitis (NHP bacterium), chronic, with a soft shell; hepatopancreatic parvovirus, mainly in other penaeid species. EHP slows growth but usually leaves the organ looking normal	AHPND: AQ-10 · NHP: AQ-51 · HPV: AQ-04 · EHP + AHPND: AQ-21
Loose shell	Loose shell syndrome: poor water quality and hepatopancreas disease, including necrotising hepatopancreatitis; no single agent	NHP: AQ-51 · EHP + AHPND: AQ-21 · Vibrio: AQ-27
Reddish pigmentation	Dying WSSV and TSV shrimp turn red; stress does the same	WSSV: AQ-11 · TSV: AQ-08
Blisters	No single cause	Core panel AQ-48
Body cramp	Muscle cramp: temperature shock, handling or mineral imbalance, not a pathogen	No PCR target: check temperature and minerals
White fecal matter	White faeces syndrome, associated with EHP and Vibrio; the worm-like bodies in the faeces are sloughed hepatopancreas tissue, not parasites	EHP + V. parahaemolyticus: AQ-30 · EHP: AQ-01
Brown gill	Gill fouling by organic matter and protozoa on a dirty pond bottom	Bottom and water management first; Vibrio AQ-27 if losses follow
Black gill	Melanised gill: Fusarium fungi, bacterial infection, or iron and organic deposits	Fusarium: AQ-06
Tail rot	Bacterial erosion, usually Vibrio, after injury	Vibrio: AQ-27 · V. harveyi + V. parahaemolyticus: AQ-28
Soldiers cap	No single cause	Core panel AQ-48
Opaque muscle	IMNV and CMNV; Penaeus vannamei nodavirus and microsporidian infection look the same; also stress and handling	CMNV + IMNV: AQ-24
Partial moulting	Moult problems from mineral imbalance or low alkalinity; infection makes them worse	No single PCR; core panel AQ-48 if losses rise
External fouling	Epibionts such as Zoothamnium, Epistylis and filamentous bacteria on a shell that is not moulting	No PCR target: water quality
Floating shrimp carcass	Non-specific: any dead shrimp floats once gas forms. Check dissolved oxygen and hydrogen sulphide first, then WSSV, and AHPND within about 35 days of stocking	Core panel AQ-48 (WSSV, AHPND) · then WSSV + DIV1: AQ-22
Snow white gills	No single cause	Core panel AQ-48
Continuous internal mortality	Steady losses on the pond bottom: covert mortality nodavirus (CMNV), chronic IMNV, necrotising hepatopancreatitis, EHP-weakened stock, Vibrio	CMNV + IMNV: AQ-24 · NHP: AQ-51 · EHP + AHPND: AQ-21

Which tissue to send for which test

Sample live, moribund animals from the pond edge rather than dead ones from the bottom: the tissue is fresher and the pathogen load is highest. To diagnose a sick pond, 10 to 20 moribund animals are enough. To screen healthy stock or certify post-larvae, test about 150 animals, which detects a 2 percent prevalence with 95 percent confidence, in several small pools rather than one.

Gill and pleopods (swimming legs) for WSSV, IHHNV and TSV; gill, lymphoid organ or haemolymph for YHV. Hepatopancreas for AHPND, necrotising hepatopancreatitis, EHP and hepatopancreatic parvovirus, plus faeces for EHP in broodstock, so the animal stays alive. Tail muscle for IMNV and CMNV. Whole post-larvae, ground together, for a batch test before stocking.

When the signs overlap

Most ponds show more than one sign at once, and the costliest pathogens often travel together. A multiplex kit answers several questions in one tube: the core panel AQ-48 covers AHPND, EHP, WSSV and IHHNV, four of the pathogens farms screen most often; duplex kits pair the causes that share a sign, such as CMNV with IMNV for white muscle, or EHP with Vibrio parahaemolyticus for white faeces.

The detection kits in the aquaculture line are lyophilised, and with the 24-test kits the compact analyser returns the result at the farm about 50 minutes after sampling. The time between seeing a sign and knowing its cause drops from days to an afternoon, which is the window in which the decision still saves the crop.

Written by the Medicare Vet product team from manufacturer data, WOAH guidance and published validation. Not a substitute for veterinary or laboratory advice in your market.

Products discussed

Catalogue items that apply to this note, each with its own page, specifications and quotation form. The full line is on the aquaculture pcr page.

Questions

Can shrimp disease be diagnosed from a photo?

No. A photo or a chart narrows the list, but several pathogens produce the same sign, mixed infections are common, and stress mimics several of them. The sign tells you which PCR to run; the PCR tells you what to do.

What causes white spots on shrimp?

White spot syndrome virus is the cause to rule out first, because an outbreak can empty a pond within a week. Bacterial white spot and calcium deposits in hard water look similar. A negative WSSV PCR on moribund animals points away from the virus and towards bacterial or mineral causes; if losses continue, resample and test again.

Which single test covers the most signs?

A multiplex panel. AQ-48 tests for AHPND, EHP, WSSV and IHHNV in one tube, four of the pathogens farms screen most often for stunting and mortality in whiteleg shrimp. Add TSV for red tail and IMNV with CMNV for white muscle.