Infectious diseases Infectious diseases are all caused by pathogenic microorganisms/infective agents such as bacteria, viruses, fungi or parasites.

s. Some infectious diseases can be passed from person to person. The diseases can be spread, directly or indirectly, from one person to another. Some, however, are transmitted via bites from insects or animals. Others are acquired by ingesting contaminated food or water or other exposures in the environment. Zoonotic diseases are infectious diseases of animals that can cause disease when transmitted to humans. Infectious diseases can be caused by: Bacteria. These one-cell organisms are responsible for such illnesses as strep throat, urinary tract infections and tuberculosis. Viruses. Even smaller than bacteria, viruses are the cause of a multitude of diseases ranging from the common cold to AIDS. Fungi. Many skin diseases, such as ringworm or athlete's foot, are caused by fungi. Other types of fungi can infect your lungs or nervous system. Parasites. Malaria is caused by a tiny parasite that is transmitted by a mosquito bite. Other parasites may be transmitted to humans from animal feces. General Laboratory tests Many infectious diseases have similar signs and symptoms. Samples of your body fluids can sometimes reveal evidence of the particular microbe that's causing your illness. This helps doctor tailor treatment more precisely. Nucleic acid testing has had a tremendous impact on the practice of infectious diseases. These tests are used in a variety of ways, including diagnosis of pathogens that do not grow using conventional methods or grow very slowly, monitoring response to therapy, assessing risk of disease development, and determining disease prognosis. Blood tests, Urine tests, Throat swabs, Spinal tap (lumbar puncture), Imaging scans, X-rays, Computerized tomography (CT), Magnetic resonance imaging (MRI), Biopsies. For example, a biopsy of lung tissue can be checked for a variety of fungi that cause a specific type of pneumonia. 1. Bacterial Infections: Bacterial diseases include any type of illness or disease caused by bacteria. Pathogenic bacteria can enter the body through a variety of means, including inhalation into the nose and lungs, ingestion in food or through sexual contact. Once bacteria enter the body, a healthy immune system will recognize the bacteria as foreign invaders and try to kill or stop the bacteria from reproducing. However, even in a healthy person with a healthy immune system, the body is not always able to stop the bacteria from multiplying and spreading. As the harmful bacteria reproduce, many emit toxins which damage the cells of the body, resulting in symptoms of a bacterial disease.

Examples:

A. Chlamydia trachomatis B. Neisseria gonnorhoeae C. Mycibacterium tuberculosis A. Chlamydia trachomatis Chlamydia, is a sexually transmitted disease (STD), which is caused by the bacteria Chlamydia trachomatis and can be cured. C. trachomatis is a Gram-negative bacteria, therefore its cell wall components retain the counter-stain saffarin and appear pink under a light microscope. C. trachomatis is an obligate intracellular pathogen (i.e. the bacterium lives within human cells) and can cause numerous disease states in both men and women. Both sexes can display urethritis, proctitis (rectal disease and bleeding), trachoma, and infertility. The bacterium can cause prostatitis and epididymitis in men. In women, cervicitis, pelvic inflammatory disease (PID), ectopic pregnancy, and acute or chronic pelvic pain are frequent complications. C. trachomatis is also an important neonatal pathogen, where it can lead to infections of the eye (trachoma) and pulmonary complications. Diagnostic Tests The traditional methods for the diagnosis of CT infections include cell culture, immunofluorescent antigen detection, enzyme immunoassay, and more recently nonamplified nucleic acid detection. These traditional methods have been replaced in many laboratories with amplified nucleic acid tests because of their greater sensitivity in detecting CT from genital specimens. Detection of the bacterium can be accomplished using both non-culture and culture tests. Non-culture tests include the following: Classic diagnostics: Immunofluorescence using polyclonal antisera had been used since the 1960s for the detection of chlamydial antigen, both in cell culture and in clinical material. i. Fluorescent Monoclonal Antibody Test: detects either the major outer membrane protein or the lipolysaccharide (LPS). A direct fluorescent antibody kit using a monoclonal antibody produced to recognise the major outer membrane of all 15 serotypes of Chlamydia trachomatis. The antibody is conjugated with fluoroscein and stains Chlamydia trachomatis elementary bodies and reticulate bodies. ii. Enzyme immunoassay: detects a colored product converted by an enzyme linked to an antibody. This quick test finds substances (chlamydia antigens) that trigger the immune system to fight chlamydia infection. iii. DNA probes: uses DNA complementary to specific ribosomal RNA sequences iv. Rapid Chlamydia tests: uses antibodies against the LPS v. Leukocyte esterase tests: Leukocyte esterase (LE) is a urine test for the presence of white blood cells and other abnormalities associated with infection. White blood cells in the urine usually indicate a urinary tract infection. The leukocyte esterase (LE) test detects esterase, an enzyme released by white blood cells. Positive test results are clinically significant.

The combination of the LE test with the urinary nitrite test provides an excellent screen for establishing the presence of a urinary tract infection (UTI). A urine sample that tests positive for both nitrite and leukocyte esterase should be cultured for pathogenic bacteria. It has been proposed that the reagent strip for leukocyte esterase designed for the testing of urine (Combur test UX) could be a useful tool for diagnosing [spontaneous bacterial peritonitis] SBP." Chlamydia culture. A culture is a special cup that allows the chlamydia bacteria to grow. This test is more expensive, and the results take longer (5 to 7 days) than the other tests. The culture must be done in a lab. The chlamydia culture test may be done when child sexual abuse is suspected or when treatment for infection has not worked. Culture tests identify intracytoplasmic inclusions in cells stained with monoclonal fluorescent antibodies. The cells are subsequently amplified on cyclohexamide-treated McCoy cells (a mouse cell line easily infected with the bacterium). Unlike non-culture tests, culture tests are 100% specific. Disadvantages are that it requires 3-7 days to obtain results, is technically difficult, requires special transport media, and is subject to contamination. Similarly, sample collection, if delayed more than 48 hours, requires storage at -70 C. Because Chlamydia is normally found in association with the normal flora, samples must be treated with gentamycin to kill other microorganisms. Dead microorganisms or effect of the gentamycin on chlamydia may bias results.

vi.

vii.

Nucleic acid amplification tests (NAAT). These tests find the genetic material (DNA) of chlamydia bacteria. These tests are the most sensitive tests available. They are very accurate and are very unlikely to have falsepositive test results. A polymerase chain reaction (PCR) test is an example of a nucleic acid amplification test. This test can also be done on a urine sample. All nucleic acid-based chlamydial diagnostic assays depend on hybridization. In direct hybridisation probe tests, signal is generated without any intermediary target amplification. A number of commercial products using nucleic acid amplification technology are now available. These tests amplify either a) the target nucleic acid, DNA or RNA ; or b) the probe after it has annealed to target nucleic acid. Such tests are generally more sensitive than liquid or solid phase hybridization tests which do not embody an amplification process and are considerably more sensitive than culture or antigen detection methods. The major target for amplification based tests against C. trachomatis are generally multiple-copy gene products, such as the cryptic chlamydial plasmid or ribosomal RNA. Starting with a multiple copy gene offers a clear starting advantage with respect to sensitivity. Initial nucleic acid amplification based tests were based on the detection of chlamydial DNA in clinical samples. a. The well known polymerase chain reaction, e.g. the Roche Amplicor PCR, uses selected primers, nucleotide triphosphates and taq polymerase to amplify

chlamydial DNA sequences, which are captured by hybridization on oligonucleotide-coated microplates. The Roche Amplicor PCR was the first commercial nucleic acid amplification test to be made available for the diagnosis of human chlamydial infections. viii. The ligase chain reaction, commercialised as the Abbott LCx also detects chlamydial DNA and is based on the ligation of chlamydia-specific oligonucleotide probes which serve as a copy of the original target sequence and which are adjacent to each other. The ligase chain reaction (LCR) is a method of DNA amplification. While the betterknown PCR carries out the amplification by polymerizing nucleotides, LCR instead amplifies the nucleic acid used as the probe. For each of the two DNA strands, two partial probes are ligated to form the actual one; thus, LCR uses two enzymes: a DNA polymerase and a DNA ligase. Each cycle results in a doubling of the target nucleic acid molecule. A key advantage of LCR is greater specificity as compared to PCR. It has been widely used for the detection of single base mutations, as in genetic diseases.[ LCR and PCR may be used to detect gonorrhea and chlamydia, and may be performed on first-catch urine samples, providing easy collection and a large yield of organisms. Endogenous inhibitors limit the sensitivity, but if this effect could be eliminated, LCR and PCR would have clinical advantages over any other methods of diagnosing gonorrhea and chlamydia.
B. Neisseria gonorrhoeae Neisseria gonorrhoeae is the causative agent of the sexually-transmitted disease (STD)

gonorrhea, and is second only to chlamydia infection in the number of cases reported. Neisseria are Gram-negative diplococci. Pili on the surface of the bacteria bind to CD46, an abundant human complement C3b/C4b-binding cell surface glycoprotein. This allows the bacteria to enter host cells, where they can survive and grow. Diagnosis of gonorrhea is thus commonly performed by vizualization of Gram-negative diplococci within leukocytes (white blood cells). CT and GC can cause a variety of Clinical infections.
(Note: Diagnostic tests are the same as for CT please refer above)

C. Mycobacterium tuberculosis Mycobacterium tuberculosis (MTB) is a pathogenic bacterial species in the genus Mycobacterium and the causative agent of most cases of tuberculosis. The physiology of M. tuberculosis is highly aerobic and requires high levels of oxygen. Primarily a pathogen of the mammalian respiratory system, MTB infects the lungs, causing tuberculosis. M. tuberculosis requires oxygen to grow. It does not retain any bacteriological stain due to high lipid content in its wall, and thus is neither Gram positive nor Gram negative; hence Ziehl-Neelsen staining, or acid-fast staining, is used.

While Mycobacteria do not seem to fit the Gram-positive category from an empirical standpoint (i.e., they do not retain the crystal violet stain), they are classified as acid-fast Grampositive bacteria due to their lack of an outer cell membrane. M. tuberculosis divides every 1520 hours, which is extremely slow compared to other bacteria, which tend to have division times measured in minutes (Escherichia coli (E. coli) can divide roughly every 20 minutes). It is a small bacillus that can withstand weak disinfectants and can survive in a dry state for weeks. Its unusual cell wall, rich in lipids (e.g., mycolic acid), is likely responsible for this resistance and is a key virulence factor. When in the lungs, M. tuberculosis is taken up by alveolar macrophages, but they are unable to digest the bacterium. Its cell wall prevents the fusion of the phagosome with a lysosome. Specifically, M. tuberculosis blocks the bridging molecule, early endosomal autoantigen 1 (EEA1); however, this blockade does not prevent fusion of vesicles filled with nutrients. Mycobacterium tuberculosis (MTb) causes a wide range of clinical infections, including pulmonary disease, miliary tuberculosis, meningitis, pleurisy/pericarditis/peritonitis, gastrointestinal disease, genitourinary disease, and lymphadenitis. Consequently, the bacteria multiply unchecked within the macrophage. The bacteria also carried the UreC gene, which prevents acidification of the phagosome. The bacteria also evade macrophage-killing by neutralizing reactive nitrogen intermediates. The ability to construct M. tuberculosis mutants and test individual gene products for specific functions has significantly advanced our understanding of the pathogenesis and virulence factors of M. tuberculosis. Many secreted and exported proteins are known to be important in pathogenesis. The MTD test utilizes Transcription-Mediated Amplification (TMA) and the Hybridization Protection Assay (HPA2) to qualitatively detect M. tuberculosis complex ribosomal ribonucleic acid (rRNA). The MTD test will detect rRNA from both cultivable and non-cultivable organisms. Organisms The MTD test is a two-part test in which amplification and detection take place in a single tube. Initially, nucleic acids are released from mycobacterial cells by sonication. Heat is used to denature the nucleic acids and disrupt the secondary structure of the rRNA. The Gen-Probe TMA method, using a constant 42 C temperature, then amplifies a specific mycobacterial rRNA target by transcription of DNA intermediates, resulting in multiple copies of mycobacterial RNA amplicon. M. tuberculosis complex-specific sequences are then detected in the RNA amplicon using the Gen-Probe HPA method. The Mycobacterium Tuberculosis Hybridization Reagent contains a single-stranded DNA probe with a chemiluminescent label. This probe is complementary to M. tuberculosis complex-specific sequences. When stable RNA:DNA hybrids are formed between the probe and the specific sequences, hybridized probe is selected and measured in a GENPROBE 50 LEADER luminometer. D. Enteroviruses

Enteroviruses are members of the picornavirus family, a large and diverse group of small RNA viruses characterized by a single positive-strand genomic RNA. All enteroviruses contain a genome of approximately 7,500 bases and are known to have a high mutation rate due to low-fidelity replication and frequent recombination. After infection of the host cell, the genome is translated in a cap-independent manner into a single polyprotein, which is subsequently processed by virus-encoded proteases into the structural capsid proteins and the nonstructural proteins, which are mainly involved in the replication of the virus. Virus that enters the body through the gastrointestinal tract and thrives there, often moving on to attack the nervous system. The polioviruses are enteroviruses. Enteroviruses are small viruses that are made of ribonucleic acid (RNA) and protein. In addition to the three different polioviruses, there are 61 non-polio enteroviruses that can cause disease in humans: 29 Coxsackieviruses (23 Coxsackie A viruses and 6 Coxsackie B viruses), 28 echoviruses, and 4 other enteroviruses. They are responsible for a myriad of clinical syndromes, including hand-foot-and-mouth (HFM) disease, herpangina, myocarditis, aseptic meningitis, and pleurodynia. Patients with enterovirus infections may present with symptoms as benign as an uncomplicated summer cold or as threatening as encephalitis, myocarditis, or neonatal sepsis Pathophysiology The enterovirus enters the human host through the GI or respiratory tract. The cell surfaces of the GI tract serve as viral receptors, and initial replication begins in the local lymphatic GI tissue. The virus seeds into the bloodstream, causing a minor viremia on the third day of infection. The virus then invades organ systems, causing a second viremic episode on days 3-7. This second viremic episode is consistent with the biphasic prodromal illness. The infection can progress to CNS involvement during the major viremic phase or at a later time. Antibody production in response to enteroviral infections occurs within the first 7-10 days. Males and females are equally affected. Males are more likely to be symptomatic. Laboratory Studies The diagnosis of enteroviral infection is most often based on the clinician's assessment of the patient in conjunction with seasonal outbreaks, known exposure risks, geographic locations, and age groups. Ancillary laboratory test results aid the physician in supportive care of the patient and eliminate other potentially harmful and treatable bacterial illnesses. Diagnostic testing plays a role in enteroviral infections. As newer methods have demonstrated increased sensitivities, determining viral etiologies of aseptic meningitis and neonatal sepsis has resulted in improved patient care. Cell culture, serology, and polymerase chain reaction (PCR) laboratory testing can diagnostically isolate enteroviral infections. Enteroviruses are found in stool, the pharynx, blood, and cerebral spinal fluid (CSF). Blood cultures and serology are of questionable use because the viral levels may be undetectable by the time symptoms have appeared. Pharyngeal viral levels remain present from 2 days to 2 weeks after the infection. Stool isolation of enteroviruses is not specific to acute infections because viral stool shedding persists for as long as 3 months after the infection. Historically, the criterion standard of isolation has been cell cultures; however, clinical evidence is proving PCR tests to be both more sensitive and more efficient. Tissue cultures take approximately 3-8 days to grow the enterovirus, and the identification of the subtype requires

even more time. Overall, low cell culture sensitivity rates of 65-75% have been repeatedly demonstrated in enteroviral meningitis. Another method, serologic testing, uses multiple titers to identify a pattern of rising antibody levels over a 2-week to 4-week period. A single level of enteroviral antibodies can be present in a healthy patient; therefore, monitoring the serology to identify a 4-fold increase in levels is needed. Identifying the specific subtype and monitoring the antibody levels is labor intensive. Furthermore, waiting for periods of 2-4 weeks for tissue results is not useful in improving patient care. o In contrast, the reverse transcriptase PCR testing is designed to detect a common genetic area in the enteroviral subtypes. The results are available in 24 hours, making detection more sensitive (95%), more specific (97%), and more time efficient. o Recent studies have demonstrated the efficacy and increased sensitivity of using the PCR technique to isolate CSF enterovirus. o PCR testing may also play a pivotal role in identifying epidemiological outbreaks of infections. o In 1997, Ahmed et al demonstrated 100% sensitivity and 90% specificity using PCR CSF assays in conjunction with viral cultures to detect enteroviral meningitis in infants younger than 3 months.8 Poliomyelitis can be isolated from stool, nasopharyngeal mucosa, and CSF. Stool specimens have the greatest yield for polio. Antibody serology titers demonstrate a 4-fold rise and must be acquired at early onset of illness. If positive, samples must be sent to the CDC. Ancillary laboratory tests may also be helpful in treating patients. CBC count results vary, demonstrating a WBC count within the reference range or demonstrating a mild elevation of WBCs with neutrophilia or leukocytosis. A basic chemistry panel is only useful in patients with extreme lethargy or dehydration and is used to eliminate possible diagnosis of electrolyte imbalances. Erythrocyte sedimentation rate is a nonspecific test, and the results should be elevated in any inflammatory process, including enteroviral infections. Urinalysis is a part of the sepsis workup in neonates and young children to eliminate bacterial infections. Also, blood and urine cultures should be obtained. Measure cardiac enzymes. Imaging Studies Chest radiographs should be obtained as part of the neonatal sepsis workup and in cases of pleurodynia. Radiographic findings are normal in patients with pleurodynia. Obtain echocardiographs. Other Tests Obtain ECG in suspected cases of pericarditis. The ECG results can be normal, can be nonspecific, or can have changes common to all causes of pericarditis. Procedures Lumbar puncture is the most important test in meningitis. Send CSF for cell count with differential, protein, glucose, Gram stain, and bacterial cultures. Send extra fluid for PCR testing and viral cell cultures. o CSF fluid demonstrates aseptic meningitis in patients with polio and nonpolio virus.

Often, the WBC count is less than 500/mL, with an initial 2 days of polymorphonuclear cell predominance that is replaced by mononuclear cells. The protein level can be within the reference range or mildly elevated (80-100 mg/100 mL). The glucose level is within the reference range.
o

E. Human papillomaviruses A human papillomavirus (HPV) is a member of the papillomavirus family of viruses that is capable of infecting humans. Like all papillomaviruses, HPVs establish productive infections only in the stratified epithelium of the skin or mucous membranes. Human papillomaviruses (HPVs) produce epithelial tumors of the skin and mucous membranes. There are more than 100 types of HPV. The current classification system, which is based on similarities in their genomic sequences, generally correlates with the 3 categories used to describe HPV clinically: anogenital and/or mucosal, nongenital cutaneous, and epidermodysplasia verruciformis (EV). Human papillomaviruses (HPV) are common viruses that can cause warts. Most are harmless, but about 30 types put you at risk for cancer. These types affect the genitals and you get them through sexual contact with an infected partner. They are classified as either low-risk or high-risk. Low-risk HPV can cause genital warts. High-risk HPV can lead to cancers of the cervix, vulva, vagina, and anus in women. In men, it can lead to cancers of the anus and penis. Pathophysiology Papillomaviruses are highly species specific and do not infect other species, even under laboratory conditions. Humans are the only known reservoir for HPV. Papillomaviruses are nonenveloped viruses of icosahedral symmetry with 72 capsomeres that surround a genome containing double-stranded circular DNA with approximately 8000 base pairs. Papillomaviruses are thought to have 2 modes of replication. One is stable replication of the episomal genome in basal cells; the other is runaway, or vegetative, replication in more differentiated cells to generate progeny virus. Although all cells of a lesion contain the viral genome, the expression of viral genes is tightly linked to the state of cellular differentiation. Most viral genes are not activated until the infected keratinocyte leaves the basal layer. Production of virus particles can occur only in highly differentiated keratinocytes; therefore, virus production occurs only at the epithelial surface where the cells are ultimately sloughed into the environment. HPV lesions are thought to arise from the proliferation of infected basal keratinocytes. Infection typically occurs when basal cells in the host are exposed to infectious virus through a disturbed epithelial barrier as would occur during sexual intercourse or after minor skin abrasions. HPV infections have not been shown to be cytolytic; rather, viral particles are released as a result of degeneration of desquamating cells. The HPV virus can survive for many months and at low temperatures without a host; therefore, an individual with plantar warts can spread the virus by walking barefoot. The HPV genome exists as a circular episomal DNA separate from the host cell nucleus in benign or low-risk HPV lesions, such as those typically associated with HPV types 6

and 11. The genomes of high-risk HPV types 16 and 18 are typically integrated into the host cell DNA in malignant lesions. Integration of the viral genome into the host cell genome is considered a hallmark of malignant transformation. HPV proteins E6 and E7 of high-risk serotypes have been shown to inactivate the host's tumor suppressor proteins p53 and Rb, thereby resulting in unregulated host cell proliferation and malignant transformation.

Tests: DNA test for HPV could result in the elimination or reduction of use of the Pap smear, the gold standard for cervical cancer detection in the United States. With the Pap smear, cells from the cervix are collected by a clinician and sent to a laboratory where they are examined for cellular abnormalities. In contrast, the DNA screening test also uses cervical cells but results are read by a machine and not as prone to subjective assessment. Histologic Findings Virus multiplication is confined to the host cell nucleus. Consequently, infected cells exhibit a high degree of nuclear atypia. Koilocytosis describes a combination of perinuclear clearing with a pyknotic or shrunken nucleus and is a characteristic feature of productive papillomavirus infection. Other cytologic markers of HPV infection include acanthosis, dyskeratosis, and multinucleation. Other Tests Various methods are available, including detection of HPV DNA by signal amplification and PCR. Currently the only available FDA-cleared test for the detection and classification of HPV DNA is the Hybrid Capture 2 (HC2) test (Digene Corporation, Gaithersburg, Md.). The test relies on signal amplification technology and probe hybridization. The test uses two separate pools of RNA probes: one for detecting high-risk HPV DNA and another for low-risk HPV DNA. The high-risk pool contains RNA probes specific for HPV types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, and 68, and the low-risk pool of RNA probes detects HPV types 6, 11, 42, 43, and 44. The test results are reported as high-risk or low-risk HPV DNA detected. There is no identification of the specific high-risk type or low-risk type. PCR-based assays for the detection and typing of HPV are used in research laboratories; however, PCR-based methods are in commercial development for use in the clinical laboratory. The recommended specimen types for HPV DNA testing include cervical swabs, liquidbased cytology specimens, and cervical biopsy specimens. The HYBRID CAPTURE2 HPV (HC2) test manufactured by Digene is a microtitration plate hybridization test intended for detection of low-risk (LR) and high-risk (HR) types of human papillomaviruses (HPV) in cervical swab specimens. The test is able to detect 5 LR HPV types (6, 11, 42, 43 and 44) and 13 HR HPV types (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59 and 68). Specimens potentially containing HPV DNA hybridize in solution with several specific RNA probes. Resulting RNA/DNA hybrid molecules are fixed to RNA/DNA hybrid specific antibodies on the surface of the microtitration plate wells. The specific antibodies subsequently react with monoclonal antibodies to RNA/DNA hybrid molecules conjugated to alkaline phosphatase to be detected by a chemoluminiscent substrate. Light produced as a result of the substrate split is measured by a luminometer and expressed in relative light units (RLU), the RLU value allows for

semiquantitative determination of viral DNA quantity in the specimen. The method also uses signal amplification and thus the determination sensitivity becomes comparable with that provided by PCR methods. The presence of some HPV DNA types can be detected with a sensitivity of 1pg viral DNA/ml of specimen. The indispensable part of the test is Digene Cervical SamplersTM with Digene Specimen Transport MediumTM. The HC2 test can also be used for specimens collected into sampling tubes Cytyc PreservCyt thanks to the HC Sample Conversion Kit. Several new approaches to HPV testing are under investigation that may provide more insight into identifying those women at highest risk of progressing to cervical cancer. These include assessing if there is prognostic value in determining HPV viral load and evaluating expression of HPV E6 and E7 mRNA as a marker for viral persistence and disease progression. F. HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 HIV infects primarily vital cells in the human immune system such as helper T cells (to be specific, CD4+ T cells), macrophages, and dendritic cells. HIV infection leads to low levels of CD4+ T cells through three main mechanisms: First, direct viral killing of infected cells; second, increased rates of apoptosis in infected cells; and third, killing of infected CD4+ T cells by CD8 cytotoxic lymphocytes that recognize infected cells. When CD4+ T cell numbers decline below a critical level, cell-mediated immunity is lost, and the body becomes progressively more susceptible to opportunistic infections. HIV-1, the causative agent of the acquired immunodeficiency syndrome (AIDS), is an RNA virus belonging to the genus lentivirus of the family Retroviridae. The replication of the virus is complex and involves reverse transcription of the RNA genome into a double-stranded DNA molecule, with subsequent integration into the host genome. The reverse transcriptase enzyme does not have proofreading capabilities, leading to the marked genetic diversity of HIV-1. There are two distinct genetic groups: the major (M) and outlier (O) groups. Viruses in the M group are further divided into 8 subtypes or clades, designated A through H, based on the sequence diversity within the HIV-1 gag and env genes. Group M virus is found worldwide, with clade B predominating in Europe and North America. Complex replication cycles and genetic diversity are two factors that influence the design and interpretation of HIV-1 molecular assays. How does HIV live in humans? HIV uses human cells, mainly white blood cells, as host cells to in which to replicate and thrive. The white blood cells that HIV uses as host cells are called CD4 T-lymphocytes, which are commonly called "CD4 cells" or "T-cells" for short. The numbers of these cells are what are referred to when someone discusses a "CD4 count," or a "T-cell count." CD4 cells are used to fight infection and are a key element of the immune system. In the process of replication, HIV kills CD4 cells. By replicating and killing CD4 cells, HIV degrades the immune system and renders the patient more susceptible to infections that would otherwise be easily fought off. An adult with a healthy immune system generally has a CD4 cell count of from 600 to 12001 What is AIDS?

A person is diagnosed with AIDS, or acquired immunodeficiency syndrome, according to the U.S. Centers for Disease Control and Prevention (CDC), when they have tested positive for HIV and have one or both of the following conditions: A CD4 cell count (or T-cell count) of below 200 per cubic millimeter of blood One or more AIDS-related illnesses. These illnesses are sometimes referred to as opportunistic infections since they develop due to the weakened immune system. Standard Types Of HIV Tests? The main tests used for detecting HIV infection are blood tests: Enzyme immunoassay (EIA) This test is widely used by just about all HIV testing programs. It is highly accurate but no test is 100 percent accurate. Accuracy depends on following proper procedures as well as the person's stage of infection. That is why all HIV testing programs use more than one test to confirm the presence of HIV. Enzyme-linked immunosorbent assay (ELISA) Western blot test, which is used to confirm the EIA/ELISA screening tests In all of these tests, a small amount of blood is drawn from the arm and taken to the lab to be tested. The EIA and ELISA tests take from one to two weeks to complete, depending on where the test is performed. These tests check for the presence of antibodies to HIV; they do not check for the virus itself. In addition to the standard blood tests for HIV, other tests are available: Rapid HIV test Home test kit Oral test Viral test Urine-based test Rapid HIV Test A rapid test for detecting antibodies to HIV was first approved in the U.S. in 1996. This test produces very quick results, usually in 10 minutes, much faster that the standard HIV tests (EIA and ELISA) that are not available for one to two weeks. The rapid HIV test is an ELISA test. But instead of being analyzed in large batches along with other individual tests, the rapid test is analyzed alone. Home Test Kit Consumer-controlled test kits (popularly known as "home test kits") were first licensed in 1997. Home Access Express HIV-1 Test System manufactured by Home Access Health Corporation is approved by the U.S. Food and Drug Administration (FDA). The approved Home Access test kit can be found at most local drug stores. The testing procedure involves pricking your finger with a special device, placing drops of blood on a specially treated card, then mailing the card in to be tested at a licensed laboratory. Customers are given an identification number to use when phoning for the test results. Callers may speak to a counselor before taking the test, while waiting for the test result, and after getting the result. Oral Test Oral tests can be performed in a doctor's office or clinic. To use an oral HIV test, the inside of the mouth is gently scraped and the saliva is tested for the presence of HIV antibodies.

The result is as accurate as the blood tests because the saliva is tested using an EIA test and then a Western blot test if necessary. It's important to remember that saliva is not a medium through which the HIV virus is transmitted. Semen, vaginal fluids, and blood are the main body fluids by which the HIV virus is transmitted. Urine-Based Tests A urine-based test is also available for screening in a doctor's office or clinic. However, it is somewhat less accurate than the blood or saliva-based tests. Like other tests, positive results must be confirmed with the Western blot test. A physician must order these tests, and the results are reported to the physician's office. Viral Test Other tests that measure HIV in the blood directly are available: A p24 antigen test measures a specific protein of the virus in the blood. An RNA viral load test measures the quantity of viral RNA in the blood. This test is often used to measure the effectiveness of drugs used to treat HIV infected people. CD4-T cell count: The CD4 T-cell count is not an HIV test, but rather a procedure where the number of CD4 T-cells in the blood is determined. A CD4 count does not check for the presence of HIV. It is used to monitor immune system function in HIV-positive people. Declining CD4 T-cell counts are considered to be a marker of progression of HIV infection. Nucleic acid based tests (NAT) Nucleic-acid-based tests amplify and detect one or more of several target sequences located in specific HIV genes, such as HIV-I GAG, HIV-II GAG, HIV-env, or the HIVpol. In the RT-PCR test, viral RNA is extracted from the patient's plasma and is treated with reverse transcriptase (RT) to convert the viral RNA into cDNA. The polymerase chain reaction (PCR) process is then applied, using two primers unique to the virus's genome. After PCR amplification is complete, the resulting DNA products are hybridized to specific oligonucleotides bound to the vessel wall, and are then made visible with a probe bound to an enzyme. The amount of virus in the sample can be quantified with sufficient accuracy to detect three-fold changes. In the Quantiplex bDNA or branched DNA test, plasma is centrifugated to concentrate the virus, which is then opened to release its RNA. Special oligonucleotides are added which bind to viral RNA and to certain oligonucleotides bound to the wall of the vessel. In this way, viral RNA is fastened to the wall. Then new oligonucleotides are added which bind at several locations to this RNA; and other oligonucelotides which bind at several locations to those oligonucleotides. This is done to amplify the signal. Finally, oligonucleotides that bind to the last set of oligonucleotides and that are bound to an enzyme are added; the enzyme action causes a color reaction which allows quantification of the viral RNA in the original sample. Monitoring the effects of antiretroviral therapy by serial measurements of plasma HIV-1 RNA with this test has been validated for patients with viral loads greater than 25,000 copies per milliliter.

Need To Know: Polymerase chain reaction (PCR) is a new blood test that looks for HIV genetic information. It has very limited availability. It is expensive and labor intensive but the advantage is that the test can detect the virus even in someone who is newly infected. The FDA has indicated that the development and implementation of tests for HIV genetic material such as PCR is warranted.

G. HEPATITIS C VIRUS HCV, an RNA virus, is a major cause of chronic liver disease. Hepatitis C is an infectious disease affecting the liver, caused by the hepatitis C virus (HCV). The infection is often asymptomatic, but once established, chronic infection can progress to scarring of the liver (fibrosis), and advanced scarring (cirrhosis) which is generally apparent after many years. In some cases, those with cirrhosis will go on to develop liver failure or other complications of cirrhosis, including liver cancer or life threatening esophageal varices and gastric varices. The hepatitis C virus is spread by blood-to-blood contact. Most people have few, if any symptoms after the initial infection, yet the virus persists in the liver in about 85% of those infected. Persistent infection can be treated with medication, peginterferon and ribavirin being the standard-of-care therapy. Fifty-one percent are cured overall. Those who develop cirrhosis or liver cancer may require a liver transplant, and the virus universally recurs after transplantation. An estimated 270-300 million people worldwide are infected with hepatitis C. The development of molecular testing for HCV infection has been a major advance in the clinical care of infected individuals, because the virus cannot be grown in a culture. Summary of tests that can be carried out for any of the above mentioned Viral Infections A. DIRECT HYBRIDIZATION Hybridization Protection Assay Gen-Probe Hybrid Capture Digene bDNA Bayer In situ hybridization B. NUCLEIC ACID AMPLIFICATION 1. PCR based Real-time PCR Roche Diagnostics 2. Non-PCR based Nucleic acid sequence-based amplification (NASBA) bioMericux Transcription-mediated amplification (TMA) Gen-Probe

B.

Standard displacement amplification (SDA) Becton Dickinson Ligase chain reaction (LCR) Abbott Signal-mediated amplification of RNA (SMART) POST-AMPLIFICATION ANALYSIS Bead-based flow cytometric assays Luminex Sequencing Applied Biosystems Microarray 2. Parasitic Diseases A parasitic disease is an infectious disease caused or transmitted by a parasite. Many parasites do not cause diseases. Parasitic diseases can affect practically all living organisms, including plants and mammals. The study of parasitic diseases is called parasitology. The three main types of organisms causing these conditions are protozoa (causing protozoan infection), helminths (helminthiasis), and ectoparasites. Protozoa and helminths are usually endoparasites (usually living inside the body of the host), while ectoparasites usually live on the surface of the host. Occasionally the definition of "parasitic disease" is restricted to diseases due to endoparasites. Mammals can get parasites from contaminated food or water, bug bites, or sexual contact. Ingestion of contaminated water can produce Giardia infections. Parasites normally enter the body through the skin or mouth. Close contact with pets can lead to parasite infestation as dogs and cats are host to many parasites. Approximately 240 diseases may be spread from animals to humans through parasites. Other risks that can lead people to get parasites are walking barefeet, inadequate disposal of faeces, lack of hygiene, close contact with someone who carries specific parasites, eating undercooked or exotic foods. Parasite infections are even worse when people have a high carbohydrate diet, low in protein, and high in alkaline. Symptoms of parasites may not always be obvious. Actually, such symptoms may mimic anemia or a hormone deficiency. Some of the symptoms caused by several worm infestation can include itching affecting the anus or the vaginal area, abdominal pain, weight loss, increased appetite, bowel obstructions, diarrhea and vomiting eventually leading to dehydration, sleeping problems, worms present in the vomit or stools, anemia, aching muscles or joints, general malaise, allergies, fatigue, nervousness. The effects caused by parasitic diseases range from mild discomfort to death. The nematode parasites Necator americanus and Ancylostoma duodenale cause human hookworm infection which leads to anaemia and protein malnutrition. This infection affects approximately 740 million people in the developing countries, including children and adults, of the tropics specifically in poor rural areas located in sub-Saharan Africa, Latin America, South-East Asia and China. Chronic hookworm in children leads to impaired physical and intellectual development, school performance and attendance are reduced. Pregnant women affected by a hookworm infection can also develop anemia which results in negative outcomes both for the mother and the infant. Some of them are: low

birth weight, impaired milk production, as well as increased risk of death for the mother and the baby. Examples of parasitic diseases A. Amebiasis Amebiasis is a disease caused by a one-celled parasite called Entamoeba histolytica. An intestinal infection caused by a parasitic amebic organism. It is usually associated with poor sanitation. {Check for the articles on parasitic diseases: Disease, symptoms, diagnostic tests}