Guide to Clinical and Diagnostic Virology

Reeti Khare

• Publisher: ASM Press
• Year: 2019
• ISBN:
  9781683672920
• Edition: 1
• Topic: Medicina
• Subtopic: Microbiologia medica e parassitologia

The explosion in clinical testing has been especially rapid in virology, where emerging viruses and growing numbers of viral infections are driving advances. The Guide to Clinical and Diagnostic Virology offers a digestible view of the breadth and depth of information related to clinical virology, providing a practical, working knowledge of the wide array of viruses that cause human disease.

Introductory chapters cover the basics of clinical virology and laboratory diagnosis of infections, including virus structure, life cycle, transmission, taxonomy, specimen types and handling, and a comparison of assays used for detection. Detailed sections on important topics include

• Viral pathogens and their clinical presentations
• Diagnostic assays and techniques, including culture-based, immunological, and molecular
• Prevention and management of viral infections, with guidance on biosafety, vaccines, and antiviral therapies
• The regulatory environment for laboratory testing, including regulatory requirements and assay performance and interpretation

Critical concepts are carefully curated and concisely summarized and presented with detailed illustrations that aid comprehension, along with important highlights and helpful hints. These features, plus question sections that reinforce significant ideas and key concepts, make this an invaluable text for anyone looking for an accessible route through clinical and diagnostic virology. Laboratory technologists, medical students, infectious disease and microbiology fellows, pathology residents, researchers, and everyone involved with viruses in the clinical setting will find the Guide to Clinical and Diagnostic Virology an excellent text as well as companion to clinical virology references.

SECTION II

VIRAL PATHOGENS AND CLINICAL PRESENTATION

CHAPTER 3

RESPIRATORY VIRUSES

I. OVERVIEW. Many viruses can cause respiratory symptoms, from mild cough and cold to severe lower respiratory tract infections.

1. Background: Most respiratory infections are caused by RNA viruses. Most of them are also enveloped (Box 3.1).

Most respiratory viruses contain RNA genomes.

Box 3.1. Common and/or important respiratory viruses

2. Transmission: Respiratory viruses are highly contagious and are transmitted primarily by respiratory secretions. Some individuals shed viruses asymptomatically for a prolonged period and others (e.g., children) shed large amounts of virus. Common modes of transmission include the following.

• Inhalation of respiratory droplets (e.g., cough or sneeze)
• Direct contact with respiratory secretions
• Contact with contaminated objects (fomites). Viruses can survive for days to weeks on environmental surfaces, especially hard, nonporous surfaces like metal and plastic (2).
• Many respiratory viruses have a distinct pattern of seasonality (Fig. 3.1). Seasonality is affected by various factors, such as the amount of close contact, temperature, humidity, and precipitation. For example, seasonal influenza outbreaks in temperate climates occur in the winter months, likely because people spend more time indoors (e.g., transmission via close contact). However, in tropical climates, influenza can occur all year-round, or during the rainy season (3).

Figure 3.1. Seasonality of respiratory viruses in temperate regions.

3. Clinical presentation: Respiratory viruses can cause overlapping clinical symptoms. Disease ranges from mild to severe upper and lower respiratory tract symptoms such as nasal discharge, cough, cold, fever, croup, bronchiolitis, pneumonia, and acute respiratory distress syndrome (4)

• Viruses have different incubation periods before time to onset of symptoms (Fig. 3.2).

Figure 3.2. Respiratory viruses have different incubation periods (time before symptom onset). Colored squares represent the range; dark orange shows the most frequent incubation period.

• The duration of symptoms for most respiratory viruses is typically 7 to 14 days.
• Immunosuppressed patients (e.g., transplant recipients) or patients with underlying pulmonary disorders (e.g., individuals with chronic obstructive pulmonary disease or asthma) have a high risk of prolonged infection, serious respiratory disease, and persistent shedding.

Croup (laryngotracheobronchitis) exhibits a characteristic inspiratory stridor, or “seal bark cough.”

4. Diagnostic testing: In cases where there are underlying risk factors or very severe infection, broad “syndromic” testing can be done to identify multiple pathogens that can cause overlapping symptoms, or narrow testing can be done for agents that are treatable (such as bacterial infection or infection with influenza virus or respiratory syncytial virus [RSV]).

• No testing: Most uncomplicated respiratory infections are self-limited and testing is not necessary.
• Nucleic acid amplification tests (NAATs): a commonly used method because it provides rapid results. Some newer PCR assays can be used to detect multiple respiratory pathogens simultaneously.
• Culture: can detect several respiratory pathogens simultaneously, but it is labor-intensive and has a long turnaround time. This makes diagnosis of acute infections difficult. Shell vials are also labor-intensive but have a shorter turnaround time.
• Antigen tests: Rapid antigen detection tests and direct fluorescence antigen (DFA) testing have relatively low sensitivity but are sometimes used to rapidly screen for some respiratory pathogens.
• Serology: not typically used. Respiratory viruses cause acute illness and antibodies form only after ~1 to 2 weeks. Also, these viruses are common in the population, so it is difficult to differentiate between current and past exposures.
• Speci...