MICROBIOLOGY II WEEK 2 (05/04/2021) MORAL, JRC

CLASSIFICATION OF VIRUSES AND

LABORATORY DIAGNOSIS
● Names of viruses may be derived from:
○ Viral characteristics (type of genome, structure,
size, etc)
○ Disease associated
○ Tissue location during infection
○ Geographical location where they were first
identified

Names of virus families & genera derived from place names

Place name Family/genus name

Bunyamwera (Uganda) Family Bunyaviridae

Ebola (river in Zaire) Genus Ebolavirus

Hantaan (river in Genus Hantavirus

South Korea)

Hendra (Australia) and Nipah Genus Henipavirus

(Malaysia)

Norwalk (United Genus Norovirus

States)

○ Based on vectors
■ Arbovirus - informal name used to refer to
any viruses that are transmitted by
arthropod vectors.
● Dengue virus and Yellow Fever
virus – transmitted by Aedes
mosquitoes
● West Nile Virus and Japanese
Baltimore’s classification
Encephalitis virus – transmitted by |
Culex mosquitoes ● Classified viruses into 7 groups based on the type of
● Examples: genome and the way in which the genome is transcribed
○ Picornavirus – pico (small); rna (ribonucleic acid) and replicated
○ Togavirus – toga (Greek word for mantle/ cloak)– ● Suggested by David Baltimore, American Virologist
referring to the membrane envelope surrounding ○ Received a nobel prize in physiology and
the virus medicine
○ Retrovirus- retro (reverse) – refers to the virus’ ● Co-discovered reverse transcriptase
directed synthesis of DNA from RNA template by
RT Class I-Double Stranded DNA viruses
○ Poxviruses – named after the disease “smallpox” ● Enters the host’s nucleus before it begins to replicate.
caused by a member of the family (Variola virus) ● It makes use of the host’s polymerases to replicate its
○ Adenovirus- named after their site of infection- genome and is therefore highly dependent on the host cell
adenoids cycle.
○ Reovirus – named after their site of infection – ● mRNA transcription is the same way as with cellular (host)
respiratory, enteric, “orphan” virus (REO) DNA
■ Called as orphan since they are not
associated with known diseases

International Committee on Taxonomy of

Viruses (ICTV)
● A virology division of the International Union of
Microbiological Societies
● Determined viral taxonomy
● Viral taxonomy is divided into categories:
○ Six orders (name ending in -virales)
○ 87 families (ending in –viridae)
○ 19 subfamilies (ending in -virinae)
Class II-Single Stranded DNA viruses
○ 384 genera (ending in –virus)
● Convert their single stranded DNA genome to double
○ 2290 species
stranded DNA intermediate before transcription to mRNA
can occur

Classification based on genome, type of capsid,

and whether the virion is naked or enveloped
MICROBIOLOGY II WEEK 2 (05/04/2021)
Class III-Double Stranded RNA viruses
● The negative strand of dsRNA is transcribed into mRNA
by the viral RNA-dependent RNA polymerase
Class IV-Single Stranded positive sense RNA viruses
● Single stranded positive polarity –it means that the
genomic RNA can serve directly as mRNA
○ No transcription required
● In the process of copying the genomic RNA, intermediate
dsRNA are formed ➔ more pos strand
● From these dsRNA intermediates, full length strands of
negative polarity RNA are formed and are used to
synthesize more single positive polarity RNA strands.
Class V-Single Stranded negative sense RNA viruses
● Single stranded negative polarity –it means that the
sequence is complementary to the mRNA
● As with group 4, intermediated dsRNA are formed to make
copies of the genome and produce mRNA
● Negative strand is converted directly to mRNA
● Full length RNA positive strands are formed and serve as
template for the production of negative stranded genome
Class VI-Single Stranded positive sense RNA viruses
with
reverse transcriptase
● RNA is converted to DNA by reverse transcriptase and
then the viral DNA is integrated into the host genome for
subsequent transcription and translation using the enzyme
integrase
Class VII-dsDNA reverse transcriptase virus
● Viruses have dsDNA genomes with RT and make ssRNA
intermediates by that act as mRNA, but are also
converted back into dsDNA genome by reverse
transcriptase, necessary for genome replication.
MORAL, JRC
Classification Examples
I: dsDNA Adenoviruses, Herpesviruses, Poxviruses
II: ssDNA Parvoviruses
III: dsRNA Reovirus
IV: +sense, ssRNA Picornavirus and Togavirus
V: -sense, ssRNA Orthomyxoviruses, Rhabdoviruses
VI: ssRNA-RT Retrovirus
VII: dsDNA-RT Hepadnaviruses
Laboratory Diagnosis |
Specimen Collection and Processing
● Almost 60% of all infectious cases seen by a physician are
due to viral infections
● Quality of patient specimens and their transport to the
laboratory is important.
Considerations for Specimen Collection
● Clinical signs and symptoms
● Basic understanding of viral pathogenesis
○ Viral shedding is greatest during the early
stage of infection even before symptoms
○ Sensitivity of viral culture decreases rapidly 3
days after the onset of acute symptoms
● Specimens collected must be able to isolate a wide range
of viral agents with similar syndromes.
● Specimens for viral isolation through tissue culture –
must be isolated from the affected site
● Must be collected aseptically
● Can be sterile or non-sterile (anatomical sites)
● Aspirated specimen - Preferred
● Swabs are acceptable – easier to use for collection
○ Must be made of Dacron or Rayon
○ Calcium alginate swabs – Not recommended
■ Inhibit the replication of some viruses
■ IInterfere with NAT
● Tissue samples – must be kept moist
○ Must not be placed in viral transport media
unless the media is designed for virus
preservation
● Virus transport media (VTM)
○ Should be unbreakable and can withstand
freezing and thawing
MICROBIOLOGY II WEEK 2 (05/04/2021) MORAL, JRC
○ Consists of:
Source Specimen Processing Cells for
Buffered isotonic solution Protect less stable viruses detection of
Protein (albumin) common
Gelatin viruses
Serum
Blood Anti- coagulated Separate leukocytes PMK, HDF,
Antibacterial agents Inhibit contamination blood HEp-2
Antifungal agents
CSF 1 mL CSF Inoculate directly

Specimens collected WITH Specimens that should be Stool or Pea-sized aliquot Place in 2 mL of VTM
viral transport collected WITHOUT viral transport rectal of feces vortex. Centrifuge at
swab 1000× g for 15 min and
Respiratory specimens Blood, bone marrow, CSF, use supernatant fluid for
Swabbed samples amniotic fluid, urine, Pericardial inoculum
Tissue fluid, and pleural fluid
Genital, Vesicle fluid or Emulsify in viral HDF
skin scraping transport medium
● Must be processed immediately (between 12-24 hours
after collection) Miscel- Swab, fluids Emulsify in viral PMK, HDF,
○ RSV difficult to recover after a few hours of laneous transport medium HEp-2
collection ➔ ASAP Fluid, inoculate directly
● If not immediately processed:
○ Stored at 4°C Respi Nasopharyngeal Dilute with viral
○ Should not be frozen unless a significant delay Tract secretions, transport medium
throat swab, RT
of >4 days of processing is anticipated
washings,
■ Frozen at -70°C sputum
○ Should never be stored at -20°C
■ facilitates formation of ice crystals that Tissue Tissue in sterile Mince with sterile
disrupts the hosts cells resulting in container scalpel and scissors
loss of viral viability and gently grind.
○ Repeated thawing and freezing must be avoided Prepare 20%
– may result in loss of viral viability suspension in VTM.
Centrifuge at 1000× g
● Specimens received in the laboratory should be
for 15 min and
accompanied with: use supernatant fluid for
○ Label (patient identification and demographics) inoculum
○ Request form having the following information:
■ Source of the specimen Urine Midstream Clear: Inoculate directly. HDF, HEp-2 (if
■ Clinical history of viruses suspected specimen Turbid: Centrifuge at adenovirus
■ Date and time of specimen collection 1000× g for 15 min and suspected)
use supernatant fluid for
inocula

Methods in Diagnostic Virology

Direct Detection
● Bright field Microscopy
● Direct Immunofluorescence Assay (DFA)
● Enzyme Immunoassay (EIA)
● Nucleic Acid-Based Detection
Virus isolation
● Virus culture
● Hemagglutination for Influenza that do not produce CPE
● Centrifugation enhanced Shell vial culture

Serologic assays
● Diagnosis of infections caused by non culturable agents
● Detects IgM or IgG antibodies
● Determination of immune status
● Monitoring of patients who are immunosuppressed
● Epidemiologic or prevalence studies