HIV-1 in plasma represents the viral quasispecies replicating in the patient at any given time. Studies of HIV-1 viral RNA from plasma or other body fluids therefore reflect the virus present in real time. To obtain near full-length genomic sequences derived from virion RNA it is first necessary to ...

The presence of cellular proteins outside and inside retroviruses can indicate the roles they play in viral biology. However, experiments examining retroviruses can be complicated by the contamination of even highly purified virion preparations with nonviral particles (either ...

Studies of HIV-1 replication kinetics and fitness require an accurate determination of the level of infectious HIV-1 present in virus stocks. The standard technique for measuring the level of replication-competent infectious virus in culture supernatants or patient samples is the t ...

Imaging studies have benefited from the development of a novel technique for non-destructive labeling of proteins within living cells, based on the use of a reagent called FlAsH-EDT2, a bisarsenical derivative of fluorescein capable of binding with high affinity and specificity to a tetr ...

A discerning feature of the retrovirus lifecycle is the covalent integration of the viral reverse transcript into a chromosome within the infected cell. Integration is required for productive infection and therefore defines the viral integrase protein of human immunodeficiency ...

Virus assembly constitutes a key phase of the HIV-1 replication cycle. The assembly process is initiated by the synthesis of the Gag precursor protein, Pr55Gag, in the cytosol of the infected cell. After its synthesis, Pr55Gag is rapidly transported in most cell types to the plasma membrane (PM) wh ...

For many years it has been known that viral capsid proteins are capable of self-assembly, but increasing evidence over the past decade indicates that in cells HIV-1 capsid assembly occurs via a complex but transient series of steps requiring multiple viral–host interactions. To better unde ...

Avian influenza (AI) viruses have been isolated from a wide diversity of free-living avian species representing several orders. Isolations are most frequently reported from aquatic birds in the Orders Anseriformes and Charadriiformes, which are believed to be the reservoirs for all AI ...

Immunohistochemical methods are commonly used for studying the pathogenesis of the avian influenza (AI) virus by allowing the identification of sites of replication of the virus in infected tissues and the correlation with the histopathological changes observed. In this chapter, t ...

Reverse genetics is the creation of a virus from a full-length cDNA copy of the viral genome, referred to as an infectious clone, and is the most powerful genetic tool in modern virology. The generation of influenza A viruses by reverse genetics has lagged mainly due to the inherent technical difficul ...

The measurement of avian cellular immunity is critical to understanding the role and regulation of avian lymphocytes following avian influenza (AI) virus infection. Although the ability to measure avian T cell responses has steadily increased over the last few years, few studies have ex ...

Functional and molecular techniques have both been employed to measure the production of cytokines following influenza infection. Historically, the use of functional or antibody-based techniques was employed in mammalian immunology. In avian immunology, only a few commercial ...

The avian influenza (AI) virus is type A influenza isolated from and adapted to an avian host. Type A influenza belongs to the orthomyxovirdae virus family, is enveloped, and is pleiomorphic with a size ranging from 80–120 nm (reviewed in ). Type A influenza strains are classified by the serological su ...

The efficient extraction and purification of viral RNA are critical for downstream molecular applications, whether it is the sensitive and specific detection of virus in clinical samples, virus gene cloning and expression, or quantification of the avian influenza (AI) virus by molecu ...

Successful detection of the avian influenza (AI) virus, viral antigen, nucleic acid, or antibody is dependent upon the collection of the appropriate sample type, the quality of the sample, and the proper storage and handling of the sample. The diagnostic tests to be performed should be consider ...

Real-time RT-PCR (rRT-PCR) is a relatively new technology that has been used for avian influenza (AI) virus detection since the early 2000s for routine surveillance, during outbreaks, and for research. Some of the advantages of rRT-PCR are high sensitivity, high specificity, rapid time-to- ...

Serological methods, gene sequencing, and RT-PCR-based methods have all been used for the identification of influenza virus hemagglutinin (HA) subtypes. Compared to serological methods and gene sequencing, RT-PCR is fast, sensitive, and relatively inexpensive. However, since RT ...

The avian influenza (AI) virus is usually isolated and propagated by inoculating either swab or tissue samples from infected birds into the chorioallantoic sac of embryonating chicken eggs. This is the accepted method, but occasionally an isolation may only be successful when inoculat ...

The hemagglutination (HA) assay is a tool used to screen cell culture or amnioallantoic fluid harvested from embryonating chicken eggs for hemagglutinating agents, such as type A influenza. The HA assay is not an identification assay, as other agents also have hemagglutinating properti ...

The hemagglutination-inhibition (HI) assay is a classical laboratory procedure for the classification or subtyping of hemagglutinating viruses. For the avian influenza (AI) virus, the HI assay is used to identify the hemagglutinin (H) subtype of an unknown AI virus isolate or the HA subty ...