Disease Informatics: Quality Aspects for Diseases Associated with Viruses

1. Disease Informatics: Quality Aspects for Diseases Associated with Viruses By Rajendra Prabhakar Deolankar

2. Prerequisite • Lecture no. 37971: Disease Informatics: How to handle diseases associated with viruses?, June 19, 2010 • Lecture no. 37141: Assessment of Holistic (Wholistic) Health and Fitness, Disease Informatics. February 17, 2010 • Lecture no. 36261: Disease Informatics: Living in the Toxic World, November 6, 2009 • Lecture no. 35791: Disease Informatics: The burden of disease, September 11, 2009 • Lecture no. 34141: Disease Informatics: Brush up the terms describing techniques and resources, February 19, 2009 • Lecture no. 34011: Disease Informatics: Terms and Jargon to begin with, February 1, 2009 • Lecture number -31981: Disease Informatics: ICD-11 at the doorstep, February 26, 2008 • Lecture number-30331: Disease Informatics: Phytates driving from the back-end to Influenza, Encephalitis, Hepatitis, Anemia at the front-end, July 10, 2007 • Lecture number-28921: Disease Informatics: Host factors simplified, February 07, 2007 • Lecture number-25381: DIG for Disease Informatics group; Part-II, November 07, 2006 • Lecture number-25371: DIG for Disease Informatics group; Part-I, November 07, 2006

3. Fundamental Quality Check:Definition of the Disease Earlier, we had a longitudinal view of “How to handle diseases associated with viruses” [Lecture no. 37971]. The purpose of defining diseases are to understand exactly what they are so that they can be prevented or reversed; public health strategies, by and large, depend on a disease defined on the basis of component cause while personal health strategies should consider sufficient causes and comprehensive disease definition. Let us now see some additional aspects of an exemplary chronic disease i.e. AIDS and one acute disease i.e. Acute Encephalitic Syndrome so as to understand the quality norms for virology laboratory

4. I. AIDS: SulfurAmino Acid Containing Defensin • Defensin is a family of potent antibiotics made within the body by neutrophils and macrophages • The defensins play important roles against invading microbes • They act against bacteria, fungi and viruses by binding to their membranes and increasing membrane permeability

5. Role of Defensin in Cervicovaginal Secretions • Mucosal surfaces of the cervix and vagina are portals for heterosexual transmission of HIV and, therefore, play a fundamental role in the pathogenesis of primary infection • Cationic antimicrobial polypeptides, including defensins, are the principal effector molecules of mucosal innate immunity against microbes and viruses such as HIV • Do you think that Good quality definition of AIDS should take cognizance of the protective principles?

6. Biomarker Defensin; Continued… • In cervicovaginal secretions, antimicrobial polypeptides constitute the majority of the intrinsic anti-HIV activity, synergism between cationic polypeptides is complex, and full anti-HIV activity involves the complete complement of cationic polypeptides • Periods in which cationic antimicrobial polypeptide expression is reduced (back-end for HIV infection) are likely associated with increased susceptibility to HIV infection. Hormones and bacterial infections can regulate the expression of defensin

7. Bacterial Vaginosis and HIV Connection • Bacterial vaginosis (back-end for HIV infection in some cases) was consistently associated with an increased risk of HIV infection • High bacterial vaginosis prevalence may result in a high number of HIV infections being attributable to bacterial vaginosis (BV) indicating prevention of BV as also a potential public health strategy for prevention of AIDS. • The power of strategy for prevention and treatment of disease depends upon quality of definition of the disease

8. Glutathione • Glutathione (GSH) is a tripeptide (cysteine, glutamic acid, glycine); Glutathione deficiency results in early aging and in the loss of coordination, balance, tremors, and mental disorders. • Orally supplemented glutathione is not assimilated. Cysteine (sulfur amino acid) supplementation improves glutathione level. Cystine gives two molecules of cysteine. Cystine as well as cysteine can enter cell; glutathione cannot. • Cysteine can be synthesized from methionine. Intestinal flora converts inorganic sulfur to the sulfur compounds that can be assimilated.

9. HIV and Glutathione • “Glutathione (GSH) deficiency” is common (front-end mediator of HIV progression) in HIV-infected individuals and is associated with impaired T cell function and impaired survival; it must be prevented. N-acetylcysteine (NAC), a cysteine prodrug, replenishes glutathione in HIV infection. However, repeated use of NAC further induces oxidative stress [PMID: 17612979]. Should quality definition of AIDS progression take cognizance of GSH deficiency? • Gandhaka rasayana (sulfur preparation) has been used on AIDS patients successfully by several doctors, however, reports of systematic studies are lacking.

10. Malnutrition in AIDS • Malnutrition leads to immunodeficiency. Immunodeficiency makes the host susceptible to opportunistic infections. Simple multivitamin / mineral supplement can prolong survival in HIV/AIDS • Depletion of cysteine (sulfur amino acid) causing drop in glutathione (sulfur containing antioxidant) is a common observation in several AIDS cases • Dietary Selenium strongly influences inflammation and immune responses

11. Continued… • Furthermore catabolism of tryptophan also occurs in AIDS • This is associated with intracellular niacin deficiency • All these compose sufficient cause in some cases and can lead to the front end event of loss of lean mass typically revealed as wasting syndrome, or pellagra or kwashiorkor like disease

12. Oxidative Stress-induced Niacin Sink (OSINS) Existing evidence supports the hypothesis that the nutrient-related metabolic abnormalities in HIV infection regarding antioxidants, selenium, sulfur, tryptophan and niacin are interrelated. This has been described as "oxidative stress-induced niacin sink" (OSINS) model. The OSINS model can be used to guide the design of nutraceutical regimens for AIDS patients

13. Continued… • Rectification of malnutrition can be achieved by correcting the balance of nutrients and/or reversing the disease process • Host specific treatment on the basis of Ayurved could be a strategy to reverse the disease as well as certain host specific foods and supplements (nutrigenomics) could cater for supply of functional principles and nutrients • A good quality definition of the disease should provide scope for such treatments

14. Calophyllum Anti-HIV Calophyllum: Coumarin is a compound that smells like vanilla; and xanthone is a cholesterol lowering compound commonly extracted from kokum. Coumarins and Xanthones extracted from a tree Calophyllum (Known as Undi in Marathi language) inhibit HIV reverse transcriptase and HIV replication

15. Continued… Mollusk eating Calophyllum: HIV reverse transcriptase inhibitors have been isolated from acetone extract of the giant African snail, Achatina fulica . These snails had been eating Calophyllum

16. Lectins in Mollusk • Lectins are natural compounds found in various foods. These bind to specific sugar moieties expressed on human cell surface • The lectin from a Roman snail Helix pomatia recognizes terminal sugar (alpha N-acetylgalactosamine) as a part of glycoprotein residues expressed on the cancer cells. The expression of the lectin binding glycoproteins by cancer cells has some value as a marker of metastatic competence and prognosis of cancer in a range of common human adenocarcinomas, including those of breast, stomach, ovary, oesophagus, colorectum, thyroid and prostate

17. Recovery From AIDS; A Case • An AIDS case that could be ranked as stage 4 by WHO criteria was reversed to stage 1 after eating regularly the fresh water river snail Pila virens. This was observed by a senior clinician, Dr. Sharad Joshi, JKRP, Pune, India • It is a research question whether the benefits are due to coumarins, xanthones and lectins or something beyond these. Ayurveda text recommends the mollusk as food therapy in disease resembling AIDS. • How would you react to this information? • Would you recommend compilation of such observations? Why?

18. Nonprogressors • AIDS is CD4+ T cell count below 200 per µL of blood or 14% of all lymphocytes in HIV+ve individuals or in terms of clinical conditions the progression described in 4 stages depending on severity. HIV+ve case could be with or without AIDS • AIDS case is a progressor when it is with AIDS (stage-2 onwards). When it is without AIDS (stage-1) it is nonprogressor • HIV+ve individuals showing no AIDS more than a decade without antiretroviral medications are called as long-term nonprogressors; abbreviated as LTNP

19. Elite Controllers • Elite controllers are HIV-positive people whose immune systems for long periods of time have been able to keep the virus at undetectable levels without using antiretroviral drugs • These patients maintain viral loads below the limit of detection of commercial assays for many years and generally do not show any clinical signs of disease progression • The mechanisms responsible for this remarkable control may lead to the design of effective therapy

20. Viremic Controllers • Viremic controllers are HIV-positive people whose immune systems have kept the virus at barely detectable levels without antiretrovirals • What could happen if these controllers are treated with combination therapy including HIV protease inhibitors?

21. Lypodystrophy Combination therapy including HIV protease inhibitors (PIs) is associated with a lipodystrophy syndrome characterized by selective loss of subcutaneous fat from the face and extremities and, in some patients, accumulation of fat around the neck, dorsocervical region, abdomen, and trunk

22. Causation of Lypodystrophy The pathogenesis is multifactorial, with contributions from other antiretroviral medications, patient-related factors, and HIV itself. Switching to a less toxic highly active antiretroviral therapy, regimen has shown partial effectiveness for the management of fat atrophy and lipid abnormalities

23. Associations With Lypodystrophy Cardiac involvement includes coronary artery disease, dilated cardiomyopathy, pericardial effusion, pulmonary hypertension, and ill effects of highly active antiretroviral therapy in the form of lipodystrophy, lipoatrophy, and dyslipidemia

24. Anthropometry The increased rate of change in waist/hip ratio in HIV-infected men receiving HAART compared with HIV-seronegative men is attributable to slower increases in hip circumference rather than an increased rate of change in waist circumference. These findings underscore the importance of body fat composition changes in the peripheral compartment relative to the central compartment among HIV-infected men receiving HAART

25. II. Childhood Brain Disease Outbreaks in India • High case-fatality • Recurrent, annual, seasonal • Vague clinical descriptions • Floating numerator errors in outbreak investigations • Being reported in India for more than 4 to 5 decades, yet to be controlled successfully

26. Virus Hypotheses • Seroconverted denominator is very big, disease-case numerator is extremely small. Earlier outbreaks were mostly attributed to Japanese Encephalitis virus, now attributed to one or other type of virus. Several viruses have been associated with the disease • Virus denial hypotheses: Cassia occidentalis poisoning [PMID’s: 18515940, 17704552 and 17684305]

27. Complex Cause Hypotheses  • Virus-aspirin-malathione- neem-deficiency of intracellular protein UNC93B- low 1,25-dihydroxyvitamin D3 as moderator- low estrogen- low DHEA- low melatonin etc some of them working together to cause said brain disease [10750089, 10750088, 1818875, 2593049, 3440601, 6348317, 6407704, 6618571, 16973841, 17056528, 10696912, 9605130, 17261778, 16099910, 17286740 ]  • Sufficient causes are not worked out and regarding virus as a sufficient cause is a dogma

28. Probable Non-viral Component Causes of AES • What are the orthologs of Acute Encephalitic Syndrome (AES) in India? • How far: Human microbiome offers protection to AES? Endocrine anomalies (seasonal or genetical) contribute to AES? Nutrient metabolites regulate the genes associated with AES? Opioid peptides derived from food proteins like gluten exorphins, beta-casomorphins etc play role in sensitive individuals? Host specific treatments in Ayurveda are helpful?

29. Editorial in Indian Pediatrics Pinpoints Ignorance Title: Investigation of Outbreaks in India. How good are we at it? [PMID: 14581729] • Often associations have been interpreted as causality • This has lead to professional disagreement on the etiology • Vaguely, CNS related outbreaks in the community have been labeled as Japanese Encephalitis • Viral diagnosis is taken for granted until proven otherwise • Wrong concepts are common like invasion of virus in CSF is necessary to cause CNS symptoms

30. Editorial Also Pinpoints Mismanagement in Planning • Investigations lack: Evidence from control samples, a systematic approach, Analytical studies and Cooperation between clinical and public health communities  • Investigations are not well coordinated, shows discrepancy between clinic and laboratory when a new disease emerges • Rivalry for credit sharing, conflicting roles and inefficient use of NGOs

31. Quality Check: Are Top Men Dedicated Epidemiologists? • How to promote problem based learning? • How to develop a problem solving approach? • How to promote public funded labs to work on non-profitable diseases? • How to provide simple feasible solutions? • Quality protocols should check that the persons having “no answers” to these questions should not lead or assess or victimize the persons who “have answers”

32. Epidemiology is a Problem-Solving Discipline • The editorial makes it clear by now that outbreak investigation is handled by top men having dogmatic views • Strategy planning for outbreak investigation is not only to know all the components but also to know how they work together; information is the crux • Those who claim themselves to be epidemiologists without having systems approach are pseudoepidemiologists • Professional epidemiologist applies Information Science in defining the diseases with least error, identifies most of the targets to combat a cluster of diseases (Disease Causal Chain) and designs a holistic solution (Health strategy) to the problem

33. Quality Check:Field and Diseases as Bases • Is the problem of childhood brain disease in India not solved because nobody knows who is accountable for solving the problem? Right To Information (RTI) and Legal action for “not having the right strategy” are poorly exploited? • Are National funds spent on executives rather than the work? Are donor funds conditional and go to rich super-specialty labs rather than for problem solving NGO organization? Are committees appointed by a biased view? • Are workers trained for “the purpose” in the school for Problem Based Learning? and are they diverted to the field where problem exists?

34. Disease Informatics Group to Take Quality Decisions • Whether the Disease Informatics Group (DIG) exists is the main query to be put by the quality auditor • What are the standard norms for DIG? Is it possible for an NGO to form DIG? Is there provision for participation of NGO with Government? • Is DIG dominated by vested interest? • Is DIG oriented for solving the disease problem? • Funds invested are wasted if problem is not solved

35. Quality Check: Involvement of Statisticians • All the members of Disease Informatics Group (DIG) need to be well trained in statistics • It is felt that DIG needs to have at least 15 to 20% professional statisticians • Statistician should not be dominated, should be given credit for their work and should be involved early

36. Media is Often Blamed for Creating Panic Leading to Wrong Focus • Panic α Diversion of attention of masses from sufficient causes • Sufficient cause is by and large an unknown word; why? • Say 1 case results in disease out of 500 cases exposed to virus; then Why only the one got the disease? Which factors other than virus protected other 499? • Why panic-preventing data is often censored by higher authorities? Should media get obligations from profit makers? There is no training course for media people on disease reporting

37. Quality of Diagnostic Virology The quality program includes Internal Quality Control (IQC), Internal Quality Assessment (IQA) and External Quality Assessment (EQA) Such program exists in GCLP (Good Clinical Laboratory Practice) labs Lab having no quality program can potentially mix-up the clinical specimens received from medical establishment and specialists, epidemiologists during outbreak of diseases or samples obtained during clinical trials

38. Some More Probable Errors Labs may also send results on wrong address A data entry error could also occur at specimen reception Virologists not having clinical qualification tend to interpret results in a wrong manner Hence, samples should be sent to GCLP / GLP (Good Laboratory Practice) certified labs only

39. Staffs is the Key for Quality The quality and education of staff is the foremost requirement for making reagents with good quality, maintaining quality of apparatus, getting good quality clinical specimens, maintaining quality of sampling and aliquots, understanding the suitability of the techniques in use

40. Training Courses… Good quality scientific report can be obtained from well qualified technicians, trained in health research (Statistics of Bioassay, Training in Experimental Designing), Diagnostic Virology, building Professional Charts and Diagrams, and Database using Software for Project Management, Infrastructure Maintenance and Management, Store and Inventory Management, Document and Record Management, Bio-resource Conservation and Banking, GLP, GCP (Good Clinical Practice) and GCLP

41. Impact of Low Quality Diagnosis Laboratory diagnosis has to be accurate and unchallengeable Papers published even in good journals are based on data generated from non-GCLP labs Unfortunately, National labs in most of the developing countries providing viral diagnosis are yet to be GLP or GCLP certified by accreditation body Quality auditors need to see whether real solutions to the viral diseases had been researched upon; we have seen that the answer is “no” for AIDS and childhood brain disease outbreaks in India

42. Dispatch of Clinical Sample GCLP certified laboratories expect clinical specimen to be proper, properly collected, properly labeled and properly packed It is customary to publish the Standard Operating Procedure (SOP) for collecting the clinical specimen by the diagnostic labs and also send those to clinical establishments before the samples are collected Several specimens are rejected by diagnostic lab as found abused during transportation

43. Doctor’s Requirement Doctor may prefer to send specimens to different labs to know more about different component causes of the disease Whether to send documentation of details of a patient and provisional diagnosis along with the specimen is a matter of policy Doctor should be clear about what he wants from virology lab; viral load, viral antigen detection by PCR, IgM titre, IgG titre, or antigen titre through ELISA

44. Serum Specimen for IgM IgM antibody is involved in primary response Their presences in high titre in serum indicate recent infection Its presence in a neonate's serum indicates intrauterine infection (e.g. congenital rubella) It is responsible for the agglutination of red blood cells

45. Serum Specimen for IgG IgG antibody is involved in the secondary immune response Diagnosis is based on difference in titre of acute and convalescent serum Serological diagnosis is usually retrospective as paired acute and convalescent sera are required Arboviruses and other acute infections are diagnosed serologically Serological diagnosis of Mumps can be easily made by Complement Fixation Test or by ELISA

46. Other Specimen IgG is present in high concentration in colostrums IgA antibody is found in mucous secretions (tears, saliva, colostrums, genito-urinary tract, gastrointestinal tract, prostate and respiratory epithelium). It is also present in small amounts in blood Stool samples, CSF and tissue biopsies are rarely used

47. Continued… Enteroviruses like polio, coxsackie B and echoviruses can be easily identified and cultured from faecal and throat swab specimens during the acute phase of the illness RSV, influenza A and B, parainfluenza 1-3, non-enteric adenoviruses and rhinoviruses can often be identified / isolated from sputum and nasal aspirate Throat and nasopharyngeal swabs is not a good specimen but usually collected because of convenience Mumps virus can be isolated from saliva and urine specimens

48. Labs Examining the Specimen The diagnostic lab detects virus, viral antigen or viral antibodies This is usually done by performing qualitative, quantitative or both types of assays These services are sometimes free as the labs may isolate virus from clinical specimen and bank it for further commercial development or research without the permission of patients or their doctors

49. In the Event of Disease Outbreak Public health preparedness is the management of knowledge, information, time and organization to check the spread of disease and minimize the morbidity and mortality and not designed for individuals or families A good family doctor or well trained health worker does not totally depend on the services provided by Public Health Preparedness but additionally provides individual and family strategies to fight the disease

50. Divya Aushadhi (Panacea): One complete solution to several diseases is a better strategy than having several incomplete solutions to one disease. Thank you