HIV Microbiology PDF

Dr. Marwa A. Meheissen HUMAN IMMUNODEFICIENCY VIRUS: MICROBIOLOGICAL OVERVIEW ILOs By the end of this lecture, students will be able to: 1. Recognize the structure and the replication cycle of HIV. 2. Describe the course and pathogenesis of HIV infection. 3. Interpret the l...

Dr. Marwa A. Meheissen HUMAN IMMUNODEFICIENCY VIRUS: MICROBIOLOGICAL OVERVIEW ILOs By the end of this lecture, students will be able to: 1. Recognize the structure and the replication cycle of HIV. 2. Describe the course and pathogenesis of HIV infection. 3. Interpret the laboratory HIV testing methods. 4. Select the appropriate antiretroviral treatment regimen according to patients’ condition. Classification of Retroviruses Classification of retroviruses is complicated by an older classification scheme based upon the ultrastructural appearance of the virion. Other classification schemes are based upon horizontal versus vertical transmission of individual retroviruses, or their ability to transform infected cells (oncogenic retroviruses). Currently, the most widely accepted taxonomic classification of retroviruses is based upon their genomic sequence; viruses are thereby grouped by evolutionary relatedness. HIV belongs to genus Lentivirus in the Retroviridae family. There are two types that are pathogenic for humans: HIV-1, which is most common; and HIV-2, which is found mainly in West Africa and appears to be less virulent. Figure 1. Classification of Retroviruses Epidemiology of HIV Globally, approximately 39.0 million people were living with HIV (PLHIV) at the end of 2022. 1.5 million children living with HIV (0–14 years old). In 2022, 630 000 people died from HIV-related causes globally. Since 2010, HIV-related deaths have been reduced by 51%, from 1.3 million. 84 000 children died from HIV-related causes in 2022. HIV continues to be a major global public health issue, claiming 40.4 million lives so far. The WHO African region remains most severely affected, with nearly 1 in every 25 adults (3.6%) living with HIV and accounting for more than two-thirds of the people living with HIV worldwide. The Middle East is from the lower regions in the world. Page 1 of 14  Dr. Marwa A. Meheissen Structure of HIV virion HIV is a spherical, with cylindrical core, enveloped RNA virus. The RNA is single-stranded, linear, positive-sense, diploid. HIV genome contains three structural genes in the order of gag–pol–env genes. The gag (group-specific antigen) gene encodes the structural proteins (matrix, capsid, nucleocapsid) of the virus. The pol (polymerase) gene encodes the protease, reverse transcriptase, and the integrase. The env (envelope) gene encodes the two membrane glycoproteins found in the viral envelope, SU gp120 and TM gp41. Up to six additional genes regulate viral expression and are important in disease pathogenesis, encode proteins that serve regulatory or accessory roles during the infection. Figure 2. HIV structure HIV receptors HIV uses as a receptor the CD4 molecule, which is expressed on macrophages and T lymphocytes. A second coreceptor in addition to CD4 is necessary for HIV-1 to gain entry to cells. The second receptor is required for fusion of the virus with the cell membrane. The virus first binds to CD4 and then to the coreceptor. These interactions cause conformational changes in the viral envelope, activating the gp41 fusion peptide and triggering membrane fusion. Chemokine receptors serve as HIV-1 second receptors. CCR5 is the predominant coreceptor for macrophage-tropic strains of HIV-1, whereas CXCR4, is the coreceptor for lymphocyte-tropic strains of HIV-1. Individuals who possess homozygous deletions in CCR5 or produce mutant forms of the protein may be protected from infection by HIV-1; heterozygous mutations in the CCR5 gene promoter appear to delay disease progression. The requirement for a coreceptor for HIV fusion with cells provided new targets for anti- viral therapeutic strategies, with the first HIV entry inhibitor. Figure 3. HIV receptors Page 2 of 14  Dr. Marwa A. Meheissen HIV Replication cycle The replication cycle of HIV is initiated with the binding of the envelope glycorpotein, gp 120, to a cell surface molecule, CD4. Following binding, penetration takes place by direct fusion of the virion envelope with the host cell membrane. Uncoating takes place and the HIV RNA is released into the cytoplasm. Reverse transcriptase present in the virion makes a DNA copy of the RNA genome. This copy is then double stranded using the DNA polymerase activity of the reverse transcriptase and moves to nucleus to be integrated into the host chromosomal DNA where it becomes a provirus. The integrase enzyme catalyzes the integration of the linear DNA into host DNA. The virus is then replicated from the integrated provirus DNA copy i.e the proviral DNA is template for viral RNA. The “provirus” becomes an integral part of the cell i.e., it will be duplicated together with the cells’ own genes every time the cell divides. Thus, infection is permanent. The provirus inside the infected cell may exist in one of the three states: 1- Latency (no viral expression). 2- Low level chronicity (expression of virus particles takes place sporadically). 3- Full blown expression (production of virus and lysis of the cell). Viral genomic and/or mRNAs are formed. HIV mRNA is subsequently translated into proteins. The HIV proteins, enzymes and genomic RNA assemble at the host cell plasma membrane to form the viral core. The HIV core acquires its envelope as it buds through the host cell membrane. Protease is required for production of infectious virus. Figure 4. Replication cycle of HIV. HIV reservoir Humans are the only reservoirs of HIV. In the human body, the reservoirs of HIV can be viewed as cellular and tissue reservoirs. The most important cellular reservoirs are all the subsets of memory CD4+ T cells, macrophages, brain microglia, and astrocytes, while the main tissue reservoir is the gut-associated lymphoid tissue which constitutes the largest reservoir of CD4+ T cells in the body. Immune response to HIV Early control of HIV infection is achieved by innate immunity. Soon after infection, dendritic cells respond through recognition of viral products (viral RNA) by pattern recognition receptors (TLR 7 and 8) and releasing antiviral cytokines, INF-α and TNF-α, which inhibit viral Page 3 of 14  Dr. Marwa A. Meheissen replication and promote activation of immune response. Several other innate immune cells respond to HIV infection by releasing antiviral cytokines. These cells include phagocytes (monocytes, macrophages,), cytolytic cells (NK cells that destroy the pathogen or pathogen- infected cells). However, HIV has found ways to interfere with the components of innate immunity and the infection proceeds. The professional APCs, dendritic cells, make the transition from innate to adaptive immunity by presenting antigens to T-lymphocytes. HIV-specific CD8+ CTLs (cytotoxic T-lymphocytes) are generated that control plasma viremia by killing HIV-infected cells. CD8+ T-lymphocytes produce INF-γ that creates an antiviral state and chemokines that bind to CCR5 and reduce the ability of HIV to infect other uninfected cells. However, the emergence of CTL escape mutants, because of mutations generated due to continued viral replication, are unable to sustain suppression of viral replication. The B lymphocytes respond to HIV antigens by making neutralizing antibodies after the decline in the level of viremia. These neutralizing antibodies neutralize cell-free virions. However, the levels of neutralizing activity are low; many anti-envelope antibodies are nonneutralizing. It is believed that the dense glycosylation may inhibit binding of neutralizing antibody to the envelope protein. The envelope glycoprotein shows great sequence variability. This natural variation may allow the evolution of successive populations of resistant virus that escape recognition by existing neutralizing antibodies. The CD4+ T-lymphocytes that make cytokines (especially IL-2) to help B lymphocytes and both CD4+ and CD8+ T-lymphocytes are impaired because CD4+ T-lymphocytes are infected and killed by HIV. In early infection, memory CD4+ T-lymphocytes are depleted; however, both memory and naïve CD4+ T-lymphocytes are depleted as the infection progresses. Despite a robust immune response, the immune system fails to eliminate HIV from infected individuals. Several reasons could be attributed, including cell-to-cell spread of the virus that avoids recognition by the neutralizing antibodies; high mutation rates resulting in antigenic variation causing CTL and antibody escape variants; interference with cytokine production; suppression of MHC I and II; integration of proviral DNA into the host chromosome; establishment of persistent infection; and diminished ability of T-lymphocyte precursor to generate mature CD4+ and CD8+ T-lymphocytes. The immune system is unable to keep up with the pace of mutating virus, resulting in impaired T- and B-lymphocyte functions and immune deficiency. It is not clear which host responses are important in providing protection against HIV infection or development of disease. A problem confronting AIDS vaccine research is that the correlates of protective immunity are not known, including the relative importance of humoral and cell- mediated immune responses. Figure 5. The Immune response to HIV Page 4 of 14  Dr. Marwa A. Meheissen Transmission of HIV High titers of HIV are found in two body fluids—blood and semen. HIV is transmitted during (1) sexual contact (including genital–oral sex), (2) through parenteral exposure to contaminated blood or blood products, (3) Injection users of illicit drugs are commonly infected through the use of contaminated needles. Injection drug use accounts for a substantial proportion of new AIDS cases, (4) and from mother to child during the perinatal period. The presence of other sexually transmitted diseases, such as syphilis, gonorrhea, or herpes simplex type 2, increases the risk of sexual HIV transmission as much as a 100-fold because the inflammation and sores facilitate the transfer of HIV across mucosal barriers. Asymptomatic virus-positive individuals can transmit the virus. Mother-to-infant transmission rates vary from 13% to 40% in untreated women. Infants can become infected in utero, during the birth process, or through breastfeeding. In the absence of breastfeeding, about 30% of infections occur in utero and 70% during delivery. Data indicate that from one-third to one-half of perinatal HIV infections in Africa are due to breastfeeding. Transmission during breast- feeding usually occurs early (by 6 months). High maternal viral loads are a risk factor for transmission. Health care workers have been infected by HIV following a needlestick with contaminated blood. (estimated risk of transmission 50 copies/mL at any stage, then this should be an indication for urgent action: The patient should receive counselling and interventions should be implemented to improve adherence. A repeat measurement of VL should then be done in 2–3 months. Virological criteria for treatment success Treatment success is defined as a decline in VL to < 50 copies/mL within 6 months of commencing ART, and sustained thereafter. Virological criteria for treatment failure Treatment failure is defined as a confirmed VL > 50 copies/mL on two consecutive measurements taken 2–3 months apart: The decision to alter ART should therefore be based on the results of repeat testing after 2–3 months, following intensive adherence counselling. Although previous guidelines used a threshold of 1000 copies/mL to define virological failure, there is now good evidence that a VL > 50 copies/mL is robustly associated with subsequent virological failure. Sustained viral replication, even at these low levels, can lead to the accumulation of resistance mutations. N.B. If CD4+ count does not rise despite viral suppression, the ART regimen does not need to be altered. Page 14 of 14