Virology
Virology is the scientific discipline concerned with the study of the biology of viruses and viral diseases, including the distribution, biochemistry, physiology, molecular biology, ecology, evolution and clinical aspects of viruses. Even today, virus isolation in cell culture is still considered the gold standard against which other assays must be compared. Still, the most obvious method
of virus detection and identification is direct visualization of the agent. The morphology of most viruses is sufficiently characteristic to identify the image as a virus and to assign an unknown virus to the appropriate family. Furthermore, certain non-cultivable viruses can be detectable by electron microscopy. The culture of animal cells typically involves the use of a culture medium containing salts, glucose, vitamins, amino acids, antimicrobial drugs, buffers, and, typically, blood serum, which provides a source of necessary cellular growth factors. For certain cell-lines, defined serum-free media have been developed, which contain specific growth factors without requiring the addition of blood serum into the medium. Serological tests are used to show the presence or absence of antibodies to a specific virus. The presence of certain antibodies indicates exposure to the agent, which may be due to a current clinical condition or as a result of an earlier unrelated infection. Some tests that can be used to identify viral antibodies include hemagglutination, complement fixation tests, radioimmunoassays, immunofluorescence, enzyme-linked immunosorbent assay (ELISA), radioimmune precipitation, and Western blot assays. Molecular techniques such as polymerase chain reaction (PCR) are also widely used for both the detection of an active virus as well as to determine whether any antibodies against the virus are present. Some of the different applications of PCR tests can be found in diagnostic clinical virology, as well as for research purposes. The use of such nucleic acid-centered technology offers substantial advances in the detection of viruses and can be further enhanced with the incorporation of certain nucleic acid hybridization techniques. It will be some time before a substantial fraction of the human population is immunized to prevent COVID-19. In the meantime, widespread use of face masks can have an impact on disease, a conclusion suggested by results of a trial carried out in Bangladesh. WHO would not recommend the use of face masks until June 2020 for two reasons: there was no evidence for their effectiveness from controlled trials, and the idea that wearing them would encourage behaviors, such as failing to physically distance, leading to more transmission. Both have been tested in the Bangladeshi trial. The face mask trial was carried out in rural Bangladesh from November 2020 to April 2021. It enrolled 342,183 adults in 600 villages and consisted of control groups (no mask wearing) and groups that wore either a surgical mask or a cloth mask. Mask wearing was 13.3% in control villages and 42.3% in treatment villages. The primary outcome was symptom seroprevalence, determined by assaying blood samples from those who reported symptoms. Wearing masks reduced symptomatic seroprevalence in treatment villages (0.68%) compared with control villages (0.76%). The reduction in seroprevalence by mask wearing was 11% overall, and 23% among those between the ages of 50 and 60, and 35% among those over 60 years of age. This reduction corresponds to 1,514 fewer people reporting symptoms, and 105 fewer seropositive. It is not clear why a greater reduction in COVID-19 cases were observed in the elderly. A higher percentage of them might have worn masks, or they might be more susceptible to infections that can be stopped by masks. Surgical masks had a clear impact on development of COVID-19, while the effects seen with cloth masks did not reach statistical significance. These results do not imply that mask wearing prevents only 10% of COVID-19 cases or deaths. It is likely that near-universal masking could have an even greater impact. Equally important were the findings that masking increased, rather than decreased, physical distancing: in control villages, 24.1% of observed individuals were physically distanced, compared with 29.2% in treatment villages. An explanation for this result is that wearing a mask may convince people to take the pandemic more seriously. Also interesting was the observation that in-person reinforcement was the best way to encourage people to wear masks. This reinforcement includes stopping people in public places and reminding them to wear masks. Public messaging, such as text messages, had no effect. This information is important for policy makers who feel that public messaging can be effective. Finally, there was little reduction in mask-wearing in the 10 weeks after the study ended. After this time mask wearing dropped but was still 10 percentage points higher in treatment regions. There is still no real cure for HIV infection. Only two people have been intentionally and successfully cleared of the virus thus far – the Berlin patient and the London patient. However, both subjects needed dangerous stem cell transplants to replenish their blood stem cells that had been destroyed during chemotherapy regimens needed to treat their HIV-induced blood cancers. In their transplants, doctors used bone marrow cells from a donor who was homozygous for a mutation in the gene encoding the HIV co-receptor CCR5 (CCR5 Δ32/Δ32), because this genotype confers resistance to HIV-1 infection. Such a transplant strategy cannot be realistically applied to most HIV patients. Recently, a thirty-year-old female resident of Esperanza, Argentina, was declared to be cured of HIV-1 without receiving long-term treatment. The “Esperanza patient” is actually the second individual known to have cleared the infection naturally. The first person, known as the “San Francisco patient,” is a 67-year-old woman who appears to have cleared the virus in the absence of treatment after living with HIV for 28 years. Standard HIV treatment involves a combination of drugs known as antiretroviral therapy (ART), which is very effective at reducing the viral load in the blood of infected individuals and preventing transmission to others. However, ART does not eliminate all infected cells, allowing the persistence of a small pool of cells collectively known as the HIV reservoir. If ART is interrupted or terminated, the virus will begin replicating again within a couple of weeks because of this reservoir. The reservoir cells are capable of clonally expanding, and surprisingly, not all offspring of a clone exhibit identical levels of viral expression. Developing effective strategies to identify and eliminate such pools of cells is a prevailing challenge in the HIV field. Even the small group of HIV-infected individuals known as “elite controllers” who are able to maintain suppressed viral levels without ART retain a low frequency of intact integrated HIV DNA copies known as proviruses in their peripheral T helper cells. The Esperanza patient was determined to be an elite controller because she had a very low viral load and no clinical or laboratory signs of HIV-1-associated disease for the entire eight years following her diagnosis, despite receiving no ART during that time. She only underwent ART when she became pregnant, but discontinued treatment after giving birth. To determine whether she had a persistent HIV-1 reservoir, the authors of a recent publication collected blood samples and placental tissue from the patient. They then isolated ~1.2 billion peripheral blood cells and ~0.5 million placental cells from the samples and subjected the cells to amplification and sequencing using primers and probes specific for HIV-1 in a technique that detects single, near full-length HIV-1 proviral genomes. The authors only detected seven proviral HIV-1 DNA species in the blood cells and none in the placenta. However, each of the seven HIV-1 DNA species was defective: one near-full-length sequence contained mutations that were lethal for the virus, and the other six sequences each contained large deletions. Three of these six sequences with deletions were completely identical to each other, suggesting that they were products of clonal expansion. These results distinguished the patient from other elite controllers, indicating that even though she had been infected with HIV-1 at some point and viral replication had occurred in the past, all viral DNA resulting from recent replication cycles was damaged. The patient’s peripheral blood cells were also used to isolate 150 million T helper cells, which are the primary target of HIV-1. When the authors analyzed these T cells for the presence of replication-competent HIV-1 particles, they did not detect a single virion, a feature that further distinguished the Esperanza patient from other elite controllers, whose blood typically contains up to 50 replication-competent virions per milliliter. The entry of HIV-1 into cells requires the presence of two cell surface proteins: the receptor CD4, and one of two co-receptors, either CXCR4 or CCR5. Individuals with a CCR5 Δ32/Δ32 genotype, which signifies a mutation in both copies of the gene encoding CCR5, are resistant to HIV-1 infection. Analysis of T helper cells isolated from the Esperanza patient revealed that they fully expressed both wild-type versions of CCR5 and CXCR4 co-receptors, and when tested in vitro, these cells were able to support HIV-1 infection and replication. This observation suggests that the patient was not resistant to infection. However, her serum did not contain the entire antibody profile usually found in HIV-1-positive patients, implying that even though she became infected and replicated virus, she never developed a full HIV-1-specific antibody response. The complete elimination of all virus-carrying cells in the context of HIV infection is termed a “sterilizing cure,” and the mechanism responsible for this exceedingly rare phenomenon is unclear. The human immune proteins APOBEC3G and APOBEC3F are known to induce destructive nucleotide changes in the HIV genome, and the authors hypothesize that the lethal mutations found in the near full-length HIV-1 proviral sequence were likely induced by these immune proteins. However, it is unclear why the overall number of proviral species was so low. Whether or not the Esperanza patient will remain permanently free of HIV is currently unclear. The authors are careful to note that “absence of evidence for intact HIV-1 proviruses in large numbers of cells is not evidence of absence of intact HIV-1 proviruses.” Nevertheless, this study suggests that a sterilizing cure of HIV-1 infection is possible, even if it is rare. The authors hope that additional data collected from the San Francisco and Esperanza patients will provide further insight into the mechanism responsible for a sterilizing cure, which might lead to treatments that cause the immune system to mimic the responses observed in these two patients.
