Viruses

This book is not great, but it’s also not bad – I ended up giving it three stars on goodreads, being much closer to 2 stars than 4. It’s a decent introduction to the field of virology, but not more than that. Below some quotes and links related to the book’s coverage.

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“[I]t was not until the invention of the electron microscope in 1939 that viruses were first visualized and their structure elucidated, showing them to be a unique class of microbes. Viruses are not cells but particles. They consist of a protein coat which surrounds and protects their genetic material, or, as the famous immunologist Sir Peter Medawar (1915–87) termed it, ‘a piece of bad news wrapped up in protein’. The whole structure is called a virion and the outer coat is called the capsid. Capsids come in various shapes and sizes, each characteristic of the virus family to which it belongs. They are built up of protein subunits called capsomeres and it is the arrangement of these around the central genetic material that determines the shape of the virion. For example, pox viruses are brick-shaped, herpes viruses are icosahedral (twenty-sided spheres), the rabies virus is bullet-shaped, and the tobacco mosaic virus is long and thin like a rod […]. Some viruses have an outer layer surrounding the capsid called an envelope. […] Most viruses are too small to be seen under a light microscope. In general, they are around 100 to 500 times smaller than bacteria, varying in size from 20 to 300 nanometres in diameter […] Inside the virus capsid is its genetic material, or genome, which is either RNA or DNA depending on the type of virus […] Viruses usually have between 4 and 200 genes […] Cells of free-living organisms, including bacteria, contain a variety of organelles essential for life such as ribosomes that manufacture proteins, mitochondria, or other structures that generate energy, and complex membranes for transporting molecules within the cell, and also across the cell wall. Viruses, not being cells, have none of these and are therefore inert until they infect a living cell. Then they hijack a cell’s organelles and use what they need, often killing the cell in the process. Thus viruses are obliged to obtain essential components from other living things to complete their life cycle and are therefore called obligate parasites.”

“Plant viruses either enter cells through a break in the cell wall or are injected by a sap-sucking insect vector like aphids. They then spread very efficiently from cell to cell via plasmodesmata, pores that transport molecules between cells. In contrast, animal viruses infect cells by binding to specific cell surface receptor molecules. […] Once a virus has bound to its cellular receptor, the capsid penetrates the cell and its genome (DNA or RNA) is released into the cell cytoplasm. The main ‘aim’ of a virus is to reproduce successfully, and to do this its genetic material must download the information it carries. Mostly, this will take place in the cell’s nucleus where the virus can access the molecules it needs to begin manufacturing its own proteins. Some large viruses, like pox viruses, carry genes for the enzymes they need to make their proteins and so are more self-sufficient and can complete the whole life cycle in the cytoplasm. Once inside a cell, DNA viruses simply masquerade as pieces of cellular DNA, and their genes are transcribed and translated using as much of the cell’s machinery as they require. […] Because viruses have a high mutation rate, significant evolutionary change, estimated at around 1 per cent per year for HIV, can be measured over a short timescale. […] RNA viruses have no proof-reading system so they have a higher mutation rate than DNA viruses. […] By constantly evolving, […] viruses appear to have honed their skills for spreading from one host to another to reach an amazing degree of sophistication. For instance, the common cold virus (rhinovirus), while infecting cells lining the nasal cavities, tickles nerve endings to cause sneezing. During these ‘explosions’, huge clouds of virus-carrying mucus droplets are forcefully ejected, then float in the air until inhaled by other susceptible hosts. Similarly, by wiping out sheets of cells lining the intestine, rotavirus prevents the absorption of fluids from the gut cavity. This causes severe diarrhea and vomiting that effectively extrudes the virus’s offspring back into the environment to reach new hosts. Other highly successful viruses hitch a ride from one host to another with insects. […] As a virus’s generation time is so much shorter than ours, the evolution of genetic resistance to a new human virus is painfully slow, and constantly leaves viruses with the advantage.”

“The phytoplankton is a group of organisms that uses solar energy and carbon dioxide to generate energy by photosynthesis. As a by-product of this reaction, they produce almost half of the world’s oxygen and are therefore of vital importance to the chemical stability of the planet. Phytoplankton forms the base of the whole marine food-web, being grazed upon by zooplankton and young marine animals which in turn fall prey to fish and higher marine carnivores. By infecting and killing plankton microbes, marine viruses control the dynamics of all these essential populations and their interactions. For example, the common and rather beautiful phytoplankton Emiliania huxleyi regularly undergoes blooms that turn the ocean surface an opaque blue over areas so vast that they can be detected from space by satellites. These blooms disappear as quickly as they arise, and this boom-and-bust cycle is orchestrated by the viruses in the community that specifically infect E. huxleyi. Because they can produce thousands of offspring from every infected cell, virus numbers amplify in a matter of hours and so act as a rapid-response team, killing most of the bloom microbes in just a few days. […] Overall, marine viruses kill an estimated 20-40 per cent of marine bacteria every day, and as the major killer of marine microbes, they profoundly affect the carbon cycle by the so-called ‘viral shunt‘.”

“By the end of 2015 WHO reported 36.7 million people living with HIV globally, 70 per cent of whom are in sub-Saharan Africa. Since the first identification of HIV-induced acquired immunodeficiency syndrome (AIDS) approximately 78 million people have been infected with HIV, causing around 35 million deaths […] Antiviral drugs are key in curtailing HIV spread and are being rolled out worldwide, with present coverage of around 46 per cent of those in need. […] The HIVs are most closely related to primate retroviruses called simian immunodeficiency viruses (SIVs) and it is now clear that these HIV-like viruses have jumped from primates to humans in central Africa on several occasions in the past giving rise to human infections with HIV-1 types M, N, O, and P as well as HIV-2. Yet only one of these viruses, HIV-1 type M, has succeeded in spreading globally. The ancestor of this virus has been traced to a subspecies of chimpanzees (Pan troglodytes troglodytes), among whom it can cause an AIDS-like disease. Since these animals are hunted for bush meat, it is most likely that human infection occurred by blood contamination during the killing and butchering process. This event probably took place in south-east Cameroon where chimpanzees carrying an SIV most closely related to HIV-1 type M live.”

“Flu viruses are paramyxoviruses with an RNA genome with eight genes that are segmented, meaning that instead of being a continuous RNA chain, each gene forms a separate strand. The H (haemaglutinin) and N (neuraminidase) genes are the most important in stimulating protective host immunity. There are sixteen different H and nine different N genes, all of which can be found in all combinations in bird flu viruses. Because these genes are separate RNA strands, on occasions they become mixed up, or recombined. So if two flu A viruses with different H and/or N genes infect a single cell, the offspring will carry varying combinations of genes from the two parent viruses. Most of these viruses will be unable to infect humans, but occasionally a new virus strain is produced that can jump directly to humans and cause a pandemic. […] The emergence of almost all recent novel flu viruses has been traced to China where they circulate freely among animals kept in cramped conditions in farms and live bird markets. […] once established in humans their spread has been much enhanced by travel, particularly air travel that can take a virus inside a traveller across the globe before they even realize they are infected. […] With over a billion people worldwide boarding international flights every year, novel viruses have an efficient mechanism for rapid spread.”

“Once an acute emerging virus such as a new strain of flu is successfully established in a population, it generally settles into a mode of cyclical epidemics during which many susceptible people are infected and become immune to further attack. When most are immune, the virus moves on, only returning when a new susceptible population has emerged, which generally consists of those born since the last epidemic. Before vaccination programmes became widespread, young children suffered from a series of well-recognized infectious diseases called the ‘childhood infections’. These included measles, mumps, rubella, and chickenpox, all caused by viruses […] following the introduction of vaccine programmes these have become a rarity, particularly in the developed world. […] Of the three viruses, measles is the most infectious and produces the severest disease. It killed millions of children each year before vaccination was introduced in the mid-20th century. Even today, this virus kills over 70,000 children annually in countries with low vaccine coverage. […] In developing countries, measles kills 1-5 per cent of those it infects”.

“Smallpox virus is in a class of its own as the world’s worst killer virus. It first infected humans at least 5,000 years ago and killed around 300 million in the 20th century alone. The virus killed up to 30 per cent of those it infected, scarring and blinding many of the survivors. […] Worldwide, eradication of smallpox was declared in 1980.”

“Viruses spread between hosts in many different ways, but those that cause acute epidemics generally utilize fast and efficient methods, such as the airborne or faecal-oral routes. […] Broadly speaking, virus infections are distinguished by the organs they affect, with airborne viruses mainly causing respiratory illnesses, […] and those transmitted by faecal-oral contamination causing intestinal upsets, with nausea, vomiting, and diarrhoea. There are literally thousands of viruses capable of causing human epidemics […] worldwide, acute respiratory infections, mostly viral, cause an estimated four million deaths a year in children under 5. […] Most people get two or three colds a year, suggesting that the immune system, which is so good at protecting us against a second attack of measles, mumps, or rubella, is defeated by the common cold virus. But this is not the case. In fact, there are so many viruses that cause the typical symptoms of blocked nose, headache, malaise, sore throat, sneezing, coughing, and sometimes fever, that even if we live for a hundred years, we will not experience them all. The common cold virus, or rhinovirus, alone has over one hundred different types, and there are many other viruses that infect the cells lining the nose and throat and cause similar symptoms, often with subtle variations. […] Viruses that target the gut are just as diverse as respiratory viruses […] Rotaviruses are a major cause of gastroenteritis globally, particularly targeting children under 5. The disease varies in severity […] rotaviruses cause over 600,000 infant deaths a year worldwide […] Noroviruses are the second most common cause of viral gastroenteritis after rotaviruses, producing a milder disease of shorter duration. These viruses account for around 23 million cases of gastroenteritis every year […] Many virus families such as rotaviruses that rely on faecal-oral transmission and cause gastroenteritis in humans produce the same symptoms in animals, resulting in great economic loss to the farming industry. […] over the centuries, Rinderpest virus, the cause of cattle plague, has probably been responsible for more loss and hardship than any other. […] Rinderpest is classically described by the three Ds: discharge, diarrhoea, and death, the latter being caused by fluid loss with rapid dehydration. The disease kills around 90 per cent of animals infected. Rinderpest used to be a major problem in Europe and Asia, and when it was introduced into Africa in the late 19th century it killed over 90 per cent of cattle, with devastating economic loss. The Global Rinderpest Eradication Programme was set up in the 1980s aiming to use the effective vaccine to rid the world of the virus by 2010. This was successful, and in October 2010 the disease was officially declared eradicated, the first animal disease and second infectious disease ever to be eliminated.”

“At present, 1.8 million virus-associated cancers are diagnosed worldwide annually. This accounts for 18 per cent of all cancers, but since these human tumour viruses were only identified fairly recently, it is probable that there are several more out there waiting to be discovered. […] Primary liver cancer is a major global health problem, being one of the ten most common cancers worldwide, with over 250,000 cases diagnosed every year and only 5 per cent of sufferers surviving five years. The tumour is more common in men than women and is most prevalent in sub-Saharan Africa and South East Asia where the incidence reaches over 30 per 100,000 population per year, compared to fewer than 5 per 100,000 in the USA and Europe. Up to 80 per cent of these tumours are caused by a hepatitis virus, the remainder being related to liver damage from toxic agents such as alcohol. […] hepatitis B and C viruses cause liver cancer. […] a large study carried out on 22,000 men in Taiwan in the 1990s showed that those persistently infected with HBV were over 200 times more likely than non-carriers to develop liver cancer, and that over half the deaths in this group were due to liver cancer or cirrhosis. […] A vaccine against HBV is available, and its use has already caused a decline in HBV-related liver cancer in Taiwan, where a vaccination programme was implemented in the 1980s”.

“Most persistent viruses have evolved to cause mild or even asymptomatic infections, since a life-threatening disease would not only be detrimental to the host but also deprive the virus of its home. Indeed, some viruses apparently cause no ill effects at all, and have been discovered only by chance. One example is TTV, a tiny DNA virus found in 1997 during the search for the cause of hepatitis and named after the initials (TT) of the patient from whom it was first isolated. We now know that TTV, and its relative TTV-like mini virus, represent a whole spectrum of similar viruses that are carried by almost all humans, non-human primates, and a variety of other vertebrates, but so far they have not been associated with any disease. With modern, highly sensitive molecular techniques for identifying non-pathogenic viruses, we can expect to find more of these silent passengers in the future. […] Historically, diagnosis and treatment of virus infections have lagged far behind those of bacterial diseases and are only now catching up. […] Diagnostic laboratories are still unable to find a culprit virus in many so-called ‘viral’ meningitis, encephalitis, and respiratory infections. This strongly suggests that there are many pathogenic viruses waiting to be discovered”.

“There is no doubt that although vaccines are expensive to prepare and test, they are the safest, easiest, and most cost-effective way of controlling infectious diseases worldwide.”

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Virology. Virus. RNA virus. DNA virus. Retrovirus. Reverse transcriptase. Integrase. Provirus.
Germ theory of disease.
Antonie van Leeuwenhoek. Louis Pasteur. Robert Koch. Adolf Mayer. Dmitri Ivanovsky. Martinus Beijerinck.
Tobacco mosaic virus.
Mimivirus.
Viral evolution – origins.
White spot syndrome.
Fibropapillomatosis.
Acyrthosiphon pisum.
Vibrio_cholerae#Genome (Vibrio cholerae are bacteria, but viruses play a very important role here regarding the toxin-producing genes – “Only cholera bacteria infected with the toxigenic phage are pathogenic to humans”).
Yellow fever.
Dengue fever.
CCR5.
Immune system. Cytokine. Interferon. Macrophage. Lymphocyte. Antigen. CD4⁺+ T cells. CD8+ T-cell. Antibody. Regulatory T cell. Autoimmunity.
Zoonoses.
Arbovirus. Coronavirus. SARS-CoV. MERS-CoV. Ebolavirus. Henipavirus. Influenza virus. H5N1. HPAI. H7N9. Foot-and-mouth disease. Monkeypox virus. Chikungunya virus. Schmallenberg virus. Zika virus. Rift valley fever. Bluetongue disease. Arthrogryposis. West Nile fever. Chickenpox. Polio. Bocavirus.
Sylvatic cycle.
Nosocomial infections.
Subacute sclerosing panencephalitis.
Herpesviridae. CMV. Herpes simplex virus. Epstein–Barr virus. Human herpesvirus 6. Human betaherpesvirus 7. Kaposi’s sarcoma-associated herpesvirus (KSHV). Varicella-zoster virus (VZV). Infectious mononucleosis. Hepatitis. Rous sarcoma virus. Human T-lymphotropic virus. Adult t cell leukemia. HPV. Cervical cancer.
Oncovirus. Myc.
Variolation. Edward Jenner. Mary Wortley Montagu. Benjamin Jesty. James Phipps. Joseph Meister. Jonas Salk. Albert Sabin.
Marek’s disease. Rabies. Post-exposure prophylaxis.
Vaccine.
Aciclovir. Oseltamivir.
PCR.