DBT-NER-PROJECT ADVANCED ANIMAL DISEASE …neradslab.res.in/document/roadmap.pdf · SOP for use in...

DBT-NER-PROJECT

ADVANCED ANIMAL DISEASE DIAGNOSIS AND MANAGEMENT CONSORTIUM

Roadmap, 2014-16

After a threadbare discussion and interaction among the members, a consensus

was reached to prepare a road map with common minimum programme so that a visible

progress can be achieved. Identified areas are as follows:

1. Prioritization of livestock species to be covered in the first phase: Based on the

priority of the North Eastern Region, diagnostic facilities will be created in core labs with

the help of national laboratories for diseases of pigs, goats and ducks. Intensive

investigation on diseases affecting these species will be carried out in NE states during

the first two years. However, diagnostic activities on other animals will also continue at

the same time.

2. Infectious agents to be studied : Infectious agents affecting pigs, goats and ducks are

grouped as endemic and emerging/re-emerging.

Animal

species

Infectious

agent

Endemic Emerging/Re-

emerging

Pigs

Bacteria Salmonella, Pasteurella, Erysipelas,

Carbapenem resistant E Coli. Anthrax;

Clostridium, Brucella

Oedema disease,

Carbapenem

resistant E Coli.

Virus CSFV, PPV, RV, JEV, Rota, PRRS Circo virus, PEDV,

Swine Influenza,

Nipah virus, TGEV,

Swine Pox, TTV

Parasites Nematodes ( Ascaris, oesophagostomum,

stephanurus, gnathostoma, capillaria etc),

trematodes ( Fasciola, opisthorchis,

artyfechinostomum, gastrodiscoides), Larval

cestode ( Cysticercus cellulosae, hydatids) ,

Haemoprotozoa, coccidia

Goats

Bacteria Pasteurella, Clostridia, Listeria,

Mycobacterium paratuberculosis,

Mycoplasma, Anthrax, Brucella

Virus PPR, Orf, BTV,Goat pox, Para influenza, Nipah,Encephalities

causing virus

Parasites Trematodes (Fasciola, Amphistome,

Schistosomes), GI Nematodes (Haemonchus,

mecistocirrus, oesophagostomum,

bunostomum, cooperia), Cestodes (Moniezia,

stilesia, avitellina, Taenia & Echinococcus),

coccidian and haemoparasites (Babesia,

theileria, anaplasma).

Ducks

Bacteria Pasteurella, Salmonella, Botulism,

Mycotoxin

Virus DPV DV Hepatities, AI

Parasites Trematodes (Echinostoma, tracheophilus,

prosthogonimus), Nematodes ( Ascaridia,

heterakis, porocaecum, tetramers), Cestode

(Raillietina, Fibbriaria, hymenolepis),

coccidi and haemoparasite.

Each national partner and NE core lab will take responsibility to develop

diagnostics and confirm diseases prevalent in eight states. Action to be taken by the

respective centre as assigned below:

Action to be taken by NIVEDI :

Animal species Endemic & emerging/re-emerging infectious agents

Pigs

Bacteria Brucella, AMR

Virus CSFV, PRRS,TTV

Goats Bacteria Brucella, AMR, Mycoplasma

Action to be taken by NIHSAD:


Pigs Virus Nipah, Ebola, Influenza A virus, PRRS

Goats *Virus CCHF, NSD, RVF

Ducks Virus Influenza A virus

Action to be taken by NRCE/VTCC :


Pigs

Bacteria Salmonella, Pasteurella, Erysipelas

Virus RV, JEV, Swine Influenza,

Parasites Trypanosoma (rest of the component to be

taken up at Khanapara and NRCE will assist

for other parasites)

Goats

Virus Para influenza, Encephalities causing virus

Parasites Trypanosome (rest of the component to be

taken up at Khanapara and NRCE will assist

for other parasites)

Action to be taken by NRC on pigs:


Bacteria Salmonella, Pasteurella, Brucella

Pigs Virus CSFV, RV, Circo, Parvo virus

Action to be taken by Core Lab I :

Animal

species

Endemic & emerging/re-emerging infectious agents

Pigs

Bacteria Salmonella, Pasteurella, Brucella, Erysipelas, AMR, Anthrax;

clostridium ,Oedema disease

Virus CSFV, PPV, RV,PRRS, Swine Pox.

Parasites

, vector

Nematodes ( Ascaris, oesophagostomum, stephanurus,

gnathostoma,capillaria etc), trematodes ( Fasciola, opisthorchis,

artyfechinostomum, gastrodiscoides), Larval cestode ( Cysticercus

cellulosae, hydatids) , Haemoprotozoa, coccidian, vector

Goats Bacteria Brucella, AMR, Pasteurella, Clostridia, Listeria,

Mycobacterium paratuberculosis, Anthrax

Virus Orf

Parasites

, vector

Trematodes (Fasciola, Amphistome, Schistosomes ), GI Nematodes

(Haemonchus, mecistocirrus, oesophagostomum, bunostomum,

cooperia), Cestodes (Moniezia, stilesia, avitellina, Taenia &

Echinococcus), coccidian and haemoparasites (Babesia, theileria,

anaplasma). vector

Ducks

Bacteria Pasteurella, Salmonella, Botulism, Mycotoxin.

Virus DPV

Parasites Trematodes (Echinostoma, tracheophilus, prosthogonimus),

Nematodes ( Ascaridia, heterakis, porocaecum, tetramers), Cestode

(Raillietina, Fibbriaria, hymenolepis), coccidi and haemoparasite.

Action to be taken by Core Lab II :

Animal

species

Endemic & emerging/re-emerging infectious agents

Pigs

Bacteria Salmonella, Erysipelas, Brucella, AMR,

Virus CSFV, JEV,

Circo virus, PRRS

Parasites,

vector


gnathostoma,capillaria etc), trematodes ( Fasciola, opisthorchis,

artyfechinostomum, gastrodiscoides), Larval cestode ( Cysticercus

cellulosae, hydatids) , Haemoprotozoa, coccidian, vector

Goats Bacteria Brucella, AMR, Listeria

Virus Nipah

Parasites,

vector

Trematodes (Fasciola, Amphistome, Schistosomes ), GI Nematodes

(Haemonchus, mecistocirrus, oesophagostomum, bunostomum,

cooperia), Cestodes (Moniezia, stilesia, avitellina, Taenia &

Echinococcus), coccidian and haemoparasites (Babesia, theileria,

anaplasma), vector

Bacteria Pasteurella, Salmonella, Afla toxin

Ducks

Virus DPV


Nematodes ( Ascaridia, heterakis, porocaecum, tetramers), Cestode

(Raillietina, Fibbriaria, hymenolepis), coccidia and haemoparasite.

Action to be taken by Core Lab III :


Pigs

Bacteria Salmonella, Pasteurella, Brucella, AMR, E Coli.,

Oedema disease

Virus PRRS

Parasites,

vector


gnathostoma,capillaria etc), trematodes ( Fasciola,

opisthorchis, artyfechinostomum, gastrodiscoides), Larval

cestode ( Cysticercus cellulosae, hydatids) ,

Haemoprotozoa, coccidian, vector

Goats Bacteria Brucella, AMR, Pasteurella, Listeria, Mycobacterium

paratuberculosis

Parasites,

Vector

Trematodes (Fasciola, Amphistome, Schistosomes ), GI

Nematodes (Haemonchus, mecistocirrus, oesophagostomum,

bunostomum, cooperia), Cestodes (Moniezia, stilesia,

avitellina, Taenia & Echinococcus), coccidian and

haemoparasites (Babesia, theileria, anaplasma), vector

Ducks

Bacteria Pasteurella, Salmonella, Afla toxin


Nematodes ( Ascaridia, heterakis, porocaecum, tetramers),

Cestode (Raillietina, Fibbriaria, hymenolepis), coccidi and

haemoparasite.

*Goat diseases on PPR, BTV, Goat pox will be covered from 3rd

year onwards as there

are DBT funded ongoing projects on these agents.

3. Strengthening of Human Resource : The prime objective of the project is to develop

disease diagnostic competency in NER Labs through training human resources.

Accordingly certain topics are identified and decided to carry out training programmes at

national as well as at core lab levels within second year of the project as per tentative

time schedule indicated below:

Training

Module

Training Details Tentative

date

Action to be

taken by

Trainees

Passive

survey

Survey strategy, data entry, record

keeping

22-24

April, 2015

NE core Lab-

I/NIVEDI

Core lab

personnels,

Training carried out at National labs, necessary TA/DA for SAHD officers should be

arranged by the host institutes and at core labs fund should be arranged by core lab.

However, matter should be taken up at DBT level to obtain permission for payment of

TA & DA from Training & also allotment of more fund under head Training.

4. Development of Laboratory capability at Core Labs :

a. Protocols standardized/developed as per OIE guidelines and diagnostic kits/reagents/

positive control/negative control available at national labs as well as in other core labs

should be shared with NE core labs. Feed back of test results can be used as validation of

the tests. Such protocols can be finalised as common SOPs for use in the diagnosis of

Active

survey

Sampling strategy, collection of

samples, preservation &

dispatching

state Animal

Husbandry

personnels

TADs

samplings

Lab, sample handing, advanced

diagnosis of TADs

April, 2015

NIHSAD Core lab

personnels,

SAHD

personnels

Field

diagnosis

Basic Microbial, pathological,

parasitic methods – Gross

diagnosis, Microscopical,

Serodiagosis,

June, 2015

NE core Labs

I/II/III

state Animal

Husbandry

personnels

Advanced

diagnosis

Molecular diagnostic protocols

(OIE/Inhouse), Serodiagnosis,

isolation techniques

July, 2015

NIVEDI/

NIHSAD/NRC

E/VTCC/NRC

pigs

NE core

Labs/NIVEDI/

HSADL/NRC

E/VTCC/NRC

pigs

Disease

mapping

GIS application, analysis and

interpretation

May, 2015

NIVEDI/

NE core Labs/

NIVEDI

Core lab

personals,

state Animal

Husbandry

personals

Software

management

& Data

analysis

Data analysis, data interpretation

& presentation

Reposition Methods on reposition & storage,

Sample coding, record keeping,

preservation, dispatch.

August,

2015

NRCE/ VTCC

diseases in NE states. Necessary MTA should be completed by respective National

partners so as to dispatch kits/reagents to respective centres within 2 months.

Agents Type of SOPs/kits

available

Action to be taken by SOPs/kits provided to

PRRSV

PCR protocol NIHSAD, Core lab II,

NIVEDI

Core lab I & III

Indirect ELISA kits NISAD Core labs I,II,III

JEV PCR protocol NRCE, Core lab II Core lab I & III

HI protocol/kits NRCE Core labs I,II,III

AIV Ag –Ab kits NIHSAD Core labs I,II,III, Field

labs

NDV PCR protocol Core lab I Core labs II,III,

Field labs HI

protocol/reagents

DPV PCR protocol Core lab I Core lab II, III

i-ELISA protocol

RV PAGE, PCR

protocol

Core lab I, NRCE Core labs II,III

Isolation protocol Core lab I

Swine

pox

PCR protocol Core lab I Core labs II,III

Fowl pox PCR protocol Core lab I Core labs II,III

Swine

influenza

PCR protocol NRCE Core labs I,II,III

PPR,

BTV,

Goat Pox

PCR protocol NIVEDI Core labs I,II,III

AMR PCR protocol NIVEDI, Core lab III Core labs I,II

Brucella PCR protocol NIVEDI Core labs I,II,III,

Field labs Ab kits

Clostridia PCR protocol Core lab I Core labsII,III,

National lab Isolation protocol

Listeria PCR protocol Core lab II Core labs I, III

Isolation protocol

Trypenos

oma

PCR protocol NRCE Core labs I,II,III, Field

labs

ELISA protocol

Babesia,

Theileria

PCR protocol Core lab I Core labs II,III, National

lab

b. Common protocols used by Core lab I, II and NIVEDI for detection of CSFV by PCR

and Ag-Ab detection tests and isolation of the virus will be validated by ring tests.

Consensus protocols in the light of EU SOPs will be finalized and developed as common

SOP for use in diagnosis of CSFV in NE states. Action will be taken by Core lab I and

NIVEDI.

c. For development of SOPs to detect PPV, Circo virus, PEDV, TGEV, Nipah virus, TTV,

Duck hepatitis virus, Erysipelas, Oedema disease, cysticarcus, hydatid, coenurus, qPCR

for Theileria, Babesia, , Aflatoxin, Anthrax should be initiated by identified centres and

necessary clinical/tissue samples should be provided from field by core labs for

standardization of tests.

5. Development of Laboratory Capability at Field units :

a. A diagnostic laboratory manual will be prepared covering necessary formats,

protocols for preparation of various reagents, diagnosis of microbial, parasitic,

toxicological diseases and clinic-pathological, pathological investigations etc. Action

to be taken by scientists from NIVEDI, VTCC, Core labs I, II and III (2 months).

b. All 3 core labs should arrange training for field staffs for collection of disease data,

samples and despatch of samples to the core labs. Necessary reagents, plastic and

glass wares, preservation/transport media should be provided. To begin with

diagnostic activities quick and handy diagnostic kits/reagents should be arranged.

6. Formats to be prepared :

Type of formats Action to be taken (One month)

Passive survey format, outbreak survey, format

for Sero- survey, routine parasitic survey, check

list for collection of sample.

VTCC ; NIVEDI; core labs

Uniform sample code for tissue, sera, isolates

will be developed.


Guidelines & formats for reporting of

investigation results for

bacteria/Virus/serologcal/

parasitic/toxic/pathological investigations.

NRCE

Sample entry & sample registry formats NIVEDI;VTCC ; core labs

Disease data base/ Accessibility to NADRES. NIVEDI

Development of Website Core labs I, II and NIVEDI

Monthly report format from field unit NIVEDI

7. Sampling Strategy :

a. Initially for 6 months survey will be confined in and around field diagnostic units of

the respective state as there are no funds available in the 1st year for SAHDs.

Information on number of villages, type of species available, No of animal

herd/unit/bird unit, Av animals per herd/unit, Av. birds per unit will be collected and

intimated to NIVEDI through core Labs. Action to be taken by PIs of SAHD and

Core lab I (31st March 2015).

b. NIVEDI will identify the village and framed the sample number, frequency for sera

samples, clinical samples, faecal samples in routine survey as well as during

outbreak. Action to be taken by NIVEDI (April 2015).

c. Samples will be collected as stated below jointly by project staffs and Field lab

incharges. All consumables/ medicines/vaccines to be used in field dung collection of

samples should be arranged by core labs.

Animal/bird Type of sample No. of sample/state

Pig

Sera sample (3month-1 yr age group) 200 (50 /F. Lab)

Blood smears (Haemoprotozoa) 100 (25 / F. Lab)

Vector survey

Nasal swabs 100 (25 / F. Lab)

Faecal samples (herd/unit basis of young,

grower, adult)

400 (100 / F. Lab)

Organs in dead carcass As per the mortality/

outbreak

Goat



Vector survey

Nasal swabs 200 (50 / F. Lab)

Faecal samples (herd/unit basis of young,

grower, adult)

400 (100 / F. Lab)

Organs in dead carcass As per the mortality/

outbreak

Duck



Tracheal swabs 40 (10 / F. Lab)

Faecal droopings (unit basis of young,

grower, adult)

200 (50 / F. Lab)

Organs in dead carcass Dead/ ailing bird

d. The participation of NERDDL is crucial and agreement regarding sample sharing,

diagnostic protocol implementation and disease informatics need to be worked upon.

e. Samples collected in field will be dispatched to core labs through project staffs,

messenger from field, through courier service /overnight service. Expenditure will be

borne by respective core lab. Between core labs samples will be transported by

project staffs/courier service at every month. Samples from core labs to national labs

will be dispatched at every 3/6months by courier/messenger. Emergency samples will

be sent by messenger. All cost involve in dispatching samples to national labs should

be arranged by respective national lab. Official permission for interstate transport of

samples / dispatch to national lab will be arranged by PIs of SAHD and National labs.

f. A nodal liaison representative at the National Institute level needs to be finalised and

communicated to all implementing partners.

g. There should be communication of fortnightly reports regarding work progress under

this project to Core lab I in order to implement a real time monitoring and evaluate

progress achieved by the implementing partners.

1

ROAD MAP OF THE PROJECT FOR THE YEAR 2016-19 AND

ACTION TO BE TAKEN :

1. Prioritization of diseases:Based on the infrastructure available for disease diagnosis

in the North Eastern Regionthe diseases need to prioritized using retrospective

disease data of last 10 year for species –wise prevalent in the region.

2. Development of diagnostics:Based on met analysis, diagnostics need be

developedfor the diseases prevalent in the region for respective species with the

help of national partners.

3. Surveillance of Emerging/Re-emerging diseases:-Be undertaken in a holistic way

using proper sampling & diseases of regional importance.

4. Research/Actions to be undertaken by each institute:

Each national partner and NE core lab will take responsibility to develop diagnostics

and confirm diseases prevalent in eight states. Action to be taken by the respective

centre as assigned below:

a. NIVEDI, Bangaluru :

Molecular epidemiology & phylogenic analysis of various diseases including

risk & met analysis.

Development of fore-warning models with impact analysis of identified

diseases of national importance.

b. NIHSAD, Bhopal:

Human resource development & capacity building of officials of NER to

handle emerging /exotic diseases in the region..

Molecular genomics& diagnosis of trans-boundary/exotic diseases including

phylogenic analysis.

c. NRCE/VTCC, Hisar :

Molecular genomics& diagnosis of equine diseases except influenza virus

including phylogenic analysis & risk assessment.

Proper maintenance of isolates received from other units with cataloguing.

d. NRC on pigs, Guwahati

Development of infrastructure for proper conventional & molecular diagnosis

of pig bacterial diseases.

2

e. Core Lab I, II & III :

Development of infrastructure for proper conventional & molecular diagnosis

including molecular epidemiological studies on different livestock & poultry

diseases in the region with their prioritization

Development of competency & core competence in handling different

diseases of regional importance including emerging & exotic diseases,

Fore-warning disease modelling, risk assessment & impact analysis in

cooperation with NIVEDI,

5. Diagnostics or Vaccine development:-

It should be limited to one or two labs & in case any institution is developing

any diagnostic/vaccine need be validated in other labs & that institution

would be responsible for its commercialization.

SOP’s already developed need be standardized as per OIE/WHO norms &

guidelines.

Any new SOP developed by any institution need be validated & standardized

& Core Labs be involved in such procedures.

6. Strengthening of Human Resource:

Developdisease diagnostic competency in NER Labs through training human

resources in following training programmes.

Name of Training Name of Institution

imparting training

Name of Labs receingtrainig

Lab, sample handing, advanced diagnosis of TADs

NIHSAD Core lab &, SAHD personnel

Molecular diagnostic protocols (OIE/Inhouse), Serodiagnosis, isolation techniques

NIVEDI/ NIHSAD/NRCE/VTCC/NRC pigs

NE core Labs/NIVEDI/HSADL/NRCE/VTCC/NRC pigs

GIS application, analysis and interpretation

NIVEDI/ NE core Labs/ NIVEDI

Core lab personals, state Animal Husbandry personals

Data analysis, data interpretation & presentation

Methods on reposition & storage, Sample coding, record keeping, preservation, dispatch.

NRCE/ VTCC

3

6. Development of Laboratory Capability at Field units :

a. Point of care diagnostic developed by National Labs, Core Labs should made

available at field labs. Besides other conventional diagnostics tools and reagents

should be procured by respective core labs and distributed to field labs.

b. A diagnostic laboratory manual/protocols be made available on website.

c. Training for field staffs will continue.

d. Scientific staffs from respective core labs/ national labs visit field labs in

convenient intervals and perform diagnosis in the field labs along with field staff.

7. Formats to be prepared :

Type of formats Action to be taken

Passive survey format, outbreak survey, format for Sero-

survey, routine parasitic survey, check list for collection of

sample.


Uniform sample code for tissue, sera, isolates will be

developed.


Guidelines&formats forreporting of investigation results for

bacteria/Virus/serologcal/parasitic/toxic/pathological

investigations.

NRCE

Sample entry &sample registry formats NIVEDI;VTCC ; core labs

Disease data base/ Accessibility to NADRES. NIVEDI

Development of Website Core labs I, II and

NIVEDI

Monthly report format from field unit NIVEDI

These formats should be evaluated through an expert committee &cross

validations need be done to maintain uniformity and updating the same.

8. Sampling Strategy & Disease Risk Analysis:

a. Risk analysis and KAP formats should be prepared by NIVEDI in association with

Core Labs

b. Field study should be carried out as routine disease survey and outbreaks

investigation.

c. Villages surrounding to the Field labs should be identified . NIVEDI will identify

the village and framed the sample number, frequency for sera samples, clinical

samples, faecal samples in routine survey as well as during outbreak. Along with

routine survey data on Risk analysis and KAP will be collected.

4

d. Awareness & animal health camps should be organized in identified strategic

locations to understand farmers problems and collect samples. Awareness

through different media & distribution of leaflets in vernacular/Hindi language.

e. Samples will be collected as stated below jointly by project staffs and Field lab

incharges. All consumables/ medicines/vaccines to be used in field dung

collection of samples should be arranged by core labs.

9. Sharing of Samples & Data:Needs to be continued.

a. To compile disease map linkage should be established with ongoing disease

related projects under DBT, ICAR, DSTin NER to share samples/data.

b. The participation of NERDDL is crucial and agreement regarding sample sharing,

diagnostic protocol implementation and disease informatics need to be worked

upon.

c. Samples collected in field will be dispatched to core labs through project staffs,

messenger from field, through courier service /overnight service. Expenditure

will be borne by respective core lab. Between core labs samples will be

transported by project staffs/courier service at every month. Samples from core

labs to national labs will be dispatched at every 3/6months by

courier/messenger. Emergency samples will be sent by messenger. All cost

involve in dispatching samples to national labs should be arranged by respective

national lab. Official permission for interstate transport of samples / dispatch to

national lab will be arranged by PIs of SAHD and National labs.

10. Strengthening of National Repository.It should be continued & national repository

at VTCC need be strengthened by sharing the samples & it would not be proper to

develop another facility of same kinds due to involvement of huge manpower &

financial implications.

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