The viruses

Coronaviruses (CoV), including SARS CoV, are single-stranded RNA viruses and belong to the family Coronaviridae.

Epidemiology

Route of spread

Coronaviruses are spread by the respiratory route.

Severe acute respiratory syndrome (SARS) is caused by SARS coronavirus (SARS CoV), which is spread by the respiratory route and through the ingestion of aerosolized faeces via contamination of the hands and environment. Close contact with a symptomatic person poses the highest risk of infection. In the 2003 outbreak, most cases occurred in hospital workers or family members in contact with cases.

Prevalence

Coronaviruses have a worldwide distribution and almost all adults in the UK have been infected by at least one type of coronavirus. Infection usually occurs in winter or spring and is associated with upper respiratory tract infection (a ‘cold’). The severity of illness is similar to that of rhinovirus infection, but less severe than infection with respiratory syncitial virus or influenza viruses. Symptoms are usually more severe in elderly persons. Reinfection is common.

SARS CoV caused a worldwide outbreak between March and July 2003, and there was a smaller outbreak, probably associated with laboratory-released SARS CoV, in 2004. There were over 8000 cases reported from 32 countries. There have been no more cases since then. The outbreak originated in Guandong Province in China and is thought to have been transmitted from civet cats (a variety of wild cat) to humans with subsequent human-to-human spread.

The viruses

Human T-cell leukaemia viruses 1 and 2 are retroviruses (like HIV) and belong to the family Retroviridae. However, they belong to the genus oncovirinae (onco = oncogenic), whereas HIV belongs to a separate genus of lentivirus (lenti = slow). Like HIV they possess a reverse transcriptase enzyme, which converts the viral RNA into DNA in the first step of the replication cycle. This pro-viral DNA is capable of integrating in the cellular DNA.

Epidemiology

Human T-cell leukaemia virus 1 was first isolated accidentally in 1979 from a human T-cell line, during experiments to stimulate cells so they could be maintained in cell culture for a longer period of time. The virus was quickly associated as the cause of adult T-cell leukaemia (ATL), which had been described in 1977, and because of a clustering of cases in southern Japan it was suspected to have an infectious aetiology. It was the first human retrovirus to be isolated (pre-dating the isolation of HIV). A few years later the second human retrovirus HTLV 2 was also isolated in the human T-cell line.

Human T-cell leukaemia viruses 1 and 2 are closely related, with some serological cross-reactivity between the two.

Route of spread

Both HTLV 1 and 2 are blood-borne viruses with essentially similar routes of spread as HIV. See Table 13.1.

There has been an explosion in international travel during the past two decades. Travel in the past was the domain of the rich, but due to the availability of cheap air travel and ‘package holidays’ it has come within the grasp of most people in the developed world. People are travelling far, and to parts of the world that were previously inaccessible to them. The desire to visit far-flung ‘exotic’ locations is insatiable. With this travel comes the danger of being exposed to infections outside one's routine experience. There is also a tendency to throw caution to the wind, not to take the usual precautions and to expose one's self to risks. One of the aims of a holiday, after all, is to relax and try new experiences; it is not surprising therefore that many travellers become ill with infections while on holiday or bring them back. Below are some common (and some not so common) clinical illnesses due to infections that are seen in returning travellers in the UK (See Table 45.1). The reader should consult the individual virus chapters for details of individual infections.

Gastroenteritis

Diarrhoea is by far the most common complaint in travellers. Most of the infections are due to bacteria. Noroviruses are important viral pathogens, especially in those who indulge in eating raw shellfish such as oysters and prawns.

The viruses

Orthopox and parapox viruses are double-stranded DNA viruses. They are the largest in size of all known viruses.

Introduction

Pox virus infections, with the exception of molluscum contagiosum, are very rare in the UK. Smallpox was eradicated from the world in 1977. The most commonly diagnosed infections in the UK are molluscum contagiosum, cowpox (most often acquired from cats) and orf (transmitted by sheep) and milker's node (acquired from cows). Other pox viruses, such as monkeypox, are endemic in a few tropical and sub-tropical countries, occasionally causing outbreaks in the Western world due to imported animals. All these viruses cause characteristic pustular skin lesions, which develop into large scabs that can leave permanent pock marks. These skin lesions and their distribution are different, facilitating clinical diagnosis. However, clinical diagnosis is not foolproof – with monkeypox, smallpox and chickenpox being mistaken for each other before smallpox eradication in Africa. Laboratory diagnosis used to be made by electron microscopy and via culture in embryonated eggs. Although diagnosis can still be made by electron microscopy, molecular methods, especially for pox viruses, are becoming the most commonly used.

History of viruses

The existence of viruses was first suspected in the nineteenth century when it was shown that filtered extract of infective material passed through filters small enough to stop all known bacteria could still be infectious, and hence the ‘virus’ (Latin for poisonous liquid) concept was first introduced. However, viral diseases such as smallpox and poliomyelitis had been known to affect mankind since many centuries before this.

Subsequent to the discovery of viruses, the next major step in elucidating their role in human disease was the invention of the electron microscope, followed by cell culture and now molecular diagnostic techniques to detect the presence of viruses in infected material. Many new viruses have been discovered in the past two to three decades, but it was the discovery of human immunodeficiency virus (HIV) (the virus responsible for acquired immunodeficiency syndrome (AIDS)) in 1983 and the explosion of the AIDS epidemic that brought clinical virology to the forefront as a significant specialty. Millions of dollars have been spent by pharmaceutical companies in discovering drugs to treat AIDS; a by-product has been that our understanding of virus replication and pathogenesis has improved substantially and this has resulted in new antiviral drugs becoming available to treat other viral infections.

The availability of rapid and sensitive molecular diagnostic techniques and effective antiviral drug therapy means that patients can now be treated in real time.

The virus

Hepatitis B virus (HBV) is a member of the Hepadnaviridae family of viruses, and has a double-stranded circular DNA and a DNA polymerase enzyme. It has two major proteins: hepatitis B surface antigen (HBs Ag), which is an outer protein expressed in excess when the virus replicates in the liver; and hepatitis B core antigen, an inner protein, which is expressed only within hepatocytes in the liver. A third protein, hepatitis B e antigen (HBe Ag), is also shed in the blood when the virus replicates, and its presence is associated with high infectivity.

Hepatitis D virus (HDV) is a defective RNA virus, which cannot replicate in humans in the absence of HBV. Patients can be co-infected with HBV and HDV, or HBV infected patients can be super-infected with HDV.

Epidemiology

Route of spread

The routes of transmission are

• parenteral (blood exposure)

• sexual

• vertical (from mother to baby).

Prevalence

Hepatitis B virus infection occurs worldwide with prevalence of infection varying between <2% to 15%, with 80% of the global population having a 60% lifetime risk of infection.

Incubation period

Infection can develop from 6 weeks to 6 months after exposure to the virus.

The virus

Hepatitis C virus is a single-stranded RNA virus belonging to the family Flaviviridae, to which flaviruses such as dengue and yellow fever viruses also belong. There is one serotype but at least 6 different genotypes (1 to 6). Some of the genotypes are further divided into subtypes. For example there are two subtypes to HCV genotypes 1 and 3 (e.g. 1a, 1b and 3a, 3b).

The genotypes are important because the treatment response depends upon the infecting genotype. Furthermore, genotypes and subtypes are important epidemiological tools as some are geographically limited in their distribution. In the UK most of the infections are due to genotype 1a, 1b, 2 and 3. In Egypt genotype 4 predominates.

Epidemiology

Route of spread

As for hepatitis B, exposure to infected blood and secretions contaminated with infected blood is the main route of transmission, through the following:

• Blood and blood product transfusion

1. A particular tragedy was the transmission of the virus to >90% of haemophiliacs through contaminated factor VIII prior to the introduction of screening of blood for HCV. An outbreak of HCV also occurred in Ireland related to a batch of contaminated immunoglobulin.

• Intravenous drug use

1. In the UK, intravenous substance use (drug use) accounts for most of the infected cases and up to 50% of all IVDUs have evidence of HCV infection. Sharing of contaminated equipment is the main cause.

• Iatrogenic (through medical treatment)

1. Reuse of needles, syringes and sharp instruments without proper sterilization for medical treatment in the developing countries has been responsible for the spread of the virus. Egypt has a high rate of HCV infection because of the reported reuse of needles during the national vaccination campaign to eliminate schistosomiasis (bilharzia), a parasitic infection.

2. […]

The virus

Parvovirus B19 is a small DNA virus, which belongs to the genera erythrovirus in the family Parvoviridae; it is the only known human parvovirus. Many other mammalian species including dogs have parvoviruses, but they don't cause infection in humans.

The virus replicates in the erythroid precursor cells, which it infects by attachment to one of the blood group antigens (P antigen) expressed at the surface of the cells which act as a receptor for the virus.

Epidemiology

Route of spread

The virus replicates initially in the respiratory mucosa and is spread by droplet (rather than aerosol) transmission by the respiratory route. Attack rate is about 50% in susceptible household contacts, but much lower in the community setting.

There is a short period of viraemia before a rash appears; therefore occasional transmissions by blood transfusion have been recorded where a donor has donated in the prodromal period.

Prevalence

Parvoviruses have worldwide prevalence. Parvovirus is a childhood infection with the prevalence of antibody rising with age; about 50% of young adults show evidence of previous infection.

Incubation period

Is about 12–18 days.

Infectious period

The highest infectivity period is in the prodromal phase, which is 2 days before the rash appears, but patients are not infectious after the rash appears.

At-risk groups

Pregnant women, immunocompromised patients and those with haemolytic anaemia.

The virus

Respiratory syncytial virus is a single-stranded RNA virus belonging to the family Paramyxoviridae.

Epidemiology

Route of spread

Respiratory syncytial virus is spread readily by direct contact with respiratory secretions, fomites and large droplets through the nose and eyes (but not the mouth). Nosocomial infections are common.

Prevalence

Respiratory syncytial virus has a worldwide distribution. In the developed world it occurs in epidemics in mid winter (November to February in the UK). Infection is common in young children; 70% are infected and 30% have clinical illness in their first year of life. Two per cent of infants have severe lower respiratory tract symptoms. All children are infected by 3 years of age, some having had more than one infection. Immunity is short lasting – just a few weeks or months. In families of pre-school age children as the primary case, 50% of family members will be infected. There are higher attack rates in nurseries and playschools.

Incubation period

3–6 days.

Infectious period

• Children are infectious for 9 days on average, but this can be much longer.

• Adults are infectious for about 2 days.

• Immunocompromised patients can be infectious for several weeks.

At-risk groups

Immunocompromised patients (e.g. those with severe combined immunodeficiency syndrome, bone-marrow transplant recipients, those on chemotherapy, HIV infected patients).

Detection of viruses in a patient's secretions or tissue provides direct evidence of current or ongoing infection (Table 48.1). This can be by:

• virus culture (also referred to as cell or tissue culture)

• electron microscopy – visualization of whole virus particles

• detection of viral antigens

• detection of viral genome (RNA or DNA) by molecular techniques.

This chapter will discuss the first three techniques; molecular diagnosis is discussed inChapter 49.

Virus or cell culture

Viruses, like bacteria, can be cultured in the laboratory. However, viruses are fastidious intracellular organisms and therefore living cells are required to grow viruses in the laboratory. Many cell lines have been developed to support the growth of different viruses. A single type of cell line is not adequate, as specific viruses need specific receptors on the cell surface to which they attach to gain entry into the cell and to initiate replication. The presence of specific cell receptors on the cell surface determines which viruses will be able to infect them, and this is called ‘viral cell tropism’. For this reason many cell lines have to be maintained in a diagnostic laboratory. Another problem in the laboratory is to maintain these living cells in culture long enough to allow sufficient virus growth.

A suspension of cells in growth medium (consists of a buffer plus calf serum to provide protein and amino acids, and antibiotics to prevent bacterial overgrowth) is put in glass or plastic tubes/flasks, the cells attach to the sides of the container and grow until they become confluent.

Infection control is a significant part of a clinical virologist's work. It is an important public health tool in the preventative measures to stop the spread of viral infections. To do this we must first understand how viruses spread and gain entry to infect susceptible hosts. Viruses may gain entry through mucous membranes or directly through blood. Skin, although a good barrier to infection, may also allow viral entry especially in the presence of breaks in the skin surface. Infections may then be localized to the site of entry or spread via the blood stream (viraemia) to distant sites and cause systemic infection. The route by which viruses enter the host to establish infection is dictated very much by viral cell tropism.

Viruses and their route of entry and spread

Respiratory route

There are a large number of viruses besides the respiratory viruses that enter the host via the respiratory route. Primary infection is established in the respiratory tract epithelium, and virus is also shed from the respiratory tract. Infection may remain localized to the respiratory tract or spread to other sites through viraemia and cause systemic infection (e.g. chickenpox, smallpox, measles, mumps, rubella and parvovirus B19 infections).

The infection is spread via small droplets, which are released in the environment while sneezing, coughing etc. These droplets containing the infectious virus may either be inhaled or be inoculated into respiratory mucous membrane via contaminated hands or fomites such as handkerchiefs.

The virus

Measles is an RNA virus belonging to the family Paramyxoviridae.

Epidemiology

Route of spread

Measles is highly infectious with a high secondary infection rate in contacts, especially household contacts. The infection is spread by the respiratory droplet route.

Prevalence

Measles has a worldwide prevalence with most infections occurring in childhood. In the Western world infection below the age of one year is unusual, due to protection offered by maternal antibody. In the developing world, however, due to poor acquisition of maternal antibody, measles under one year is common and has a high mortality rate because of secondary bacterial infection and poor nourishment. Measles was endemic in the UK with epidemics occurring every 2–3 years prior to the introduction of the childhood measles, mumps and rubella (MMR) vaccination programme in the mid 1980s. However, outbreak clusters have occurred recently because of the fall in the uptake of measles vaccination. Humans are the only host and the World Health Organization estimates that worldwide there are over a million childhood deaths due to measles each year, and has declared measles as one of the infections to be eradicated from the world.

Incubation period

10–15 days, an average of two weeks.

Infectious period

Prodromal period (2–3 days before the rash appears) to about 4 days after the rash appears.

At-risk groups

All susceptible individuals, but especially those who are immunocompromised or pregnant.

Cell growth, differentiation and death are controlled by genes. Mechanisms are needed for both stimulating and suppressing growth. Breakdown in the mechanism for control of cell growth leads to uncontrolled growth and malignancy. There are many ways in which cells may lose this genetic control, viral infections being one of those. Not all viruses are oncogenic (e.g. able to induce cancer). It is mainly, though not exclusively, the DNA viruses that have this potential. Human T-cell leukaemia virus types 1 and 2, and hepatitis C virus are examples of RNA viruses that are able to induce malignancy.

How do viruses cause cancer?

There are several mechanisms by which this may occur.

Some viruses, such as HTLV 1, possess a viral oncogene or v-onc gene. Integration of viral genome into the infected cell enables the v-onc gene to be activated. Products of this activated v-onc gene are able to transform the cell by affecting the function of cellular products normally responsible for cell growth. It is believed that v-onc genes have been acquired by viruses through capturing cellular gene material during the process of evolution.

Oncogenes are not unique to viruses, they also form part of the normal cellular genetic material. Cellular oncogenes are different in their structure to v-onc and are referred to as c-onc to differentiate them from viral oncogenes. The c-onc products are required for normal cell activities.

Mutation in the c-onc gene is an important mechanism for cell transformation.

Haemorrhagic fever viruses

Haemorrhagic fever viruses are viruses that cause outbreaks of severe or fatal infections with haemorrhagic symptoms, principally in the tropics. These infections are occasionally imported into the UK and other countries outside the tropics, usually causing disease in individual persons, but occasionally resulting in clusters of cases of those infections with person-to-person spread. Since there are several different viruses with different geographical distributions, animal vectors and symptoms, these details have been collated inTable 2.1 to aid differential diagnosis. Knowledge of the outbreaks occurring in different parts of the world and the recent travel history of returning travellers is very important for initial clinical diagnosis. Malaria should always be considered in the differential diagnosis. If haemorrhagic fever is suspected patients should be initially cared for in the highest security isolation rooms available, and immediately transferred to a specialist facility designed to care for cases with haemorrhagic fever once malaria is excluded. No special infection control precautions are required for hantavirus and dengue virus infections.

Although dengue fever is the most common of these viral infections to be imported into the UK, the haemorrhagic form of the disease is relatively rare.

Specimens for diagnosis

EDTA blood for virus culture, or polymerase chain reaction (PCR) and clotted blood for specific IgM antibody. In the UK all diagnostic tests are carried out, according to the Advisory Group on Dangerous Pathogens (ACDP) guidelines, in a category 4, high-security facility.