ssDNA viruses

Question 1

Baltimore classification of ssDNA viruses

Answer 1

•ssDNAviruses belong to Class II group of viruses according to the Baltimore classification of viruses

Question 2

Taxonomy of ssDNA viruses

Answer 2

• The parvoviruses belonging to the family Parvoviridaeforms an important group.
• The family derived its name from their small size which was translated in latin.
• Thus, Latin word for small = ParvusParvoviruses
• Parvoviruses ranks amongst the smallest viruses having a diameter of between 18-26 nm

Question 3

Classification of Parvoviridae

Answer 3

•The family Parvoviridaecan be grouped into two subfamilies:

1.Parvovirinae: parvoviruses infecting vertebrates.

• One genus: Dependovirus: Possesses a defective genome (satellite virus) and can only replicate in host cells co-infected with a second virus (helper virus).
• Other parvovirus that do not require a helper virus are referred to as autonomousviruses.

2. Densovirinae: parvoviruses infecting invertebrates

Question 4

Dependoviruses(a genus from the family parvoviridae)

Identificaton

Answer 4

Identification: Dependoviruswas first observed under the electron microscope as a contaminant of an adenovirus preparation.

• The virus was observed as a defective virus which was dependent on a second or helper virus (the adenovirus) for replication.
• The identified virus was first referred to as an adeno-associated virus.
• Other dependoviruseswith different serotypes have since been observed to be associated with other adenoviruses in infected humans and other animal species.
• Dependovirusesare widespread based on PCR and other molecular evidences

Question 5

helper viruses of the dependovirus

Answer 5

• Dependovirusesmay depend on other helper virus apart from the adenovirus.
• The herpesvirusesmay serves as helper viruses.
• Under certain conditions, some dependovirusesmay replicate by themselves without a helper virus

Question 6

Uses of dependoviruse

Answer 6

• Vectors for protein synthesis: They play important role as vectors in protein production.
• Vectors for gene therapy: Serve as vectors for introducing specific genes into cell cultures for mass production of the protein encoded by the gene(s).
• Thus, they are been considered for use as vectors for introducing specific genes in human cells for the treatment of genetic diseases and cancer therapy.
• Note: Dependovirusesare ideal candidate as vectors for gene therapy because they are notknown to cause human diseases when compared to other virus vectors such as the retroviruses

Question 7

Autonomous Parvoviruses

Answer 7

•Are parvoviruses that do not require a helper virus to replicate their genome. All other genera under the family Parvoviridaeexcept the dependovirusesare autonomous.

Question 8

Autonomous Parvoviruses

ErythrovirusB19

Answer 8

1. ErythrovirusB19: In 1975, an unknown virus was observed to infect red blood cell precursors and was named B19.

• B19 virus can be transmitted mainly through infected respiratory droplets, putting up to 50% of household members at risk. Also, blood-borne transmission has been reported.
• Many B19infections are without signs or symptoms while some could result in disease conditions such as:

I. Fifth disease (erythema infectiosum): infected children develop ‘’slapped cheek’’ or (reddish rash) appearance.

II. Acute arthritis

III. Aplastic anaemiain persons with chronic hemolytic anaemia

IV. Hydropsfetalis(infection may be transmitted from a pregnant woman to fetus which may lead to the death of the fetus

Question 9

Autonomous Parvoviruses

Human bocavirus(genus-Bocavirus):

Answer 9

Human bocavirus(genus-Bocavirus):

was discovered in 2005 through the molecular screening of nasopharnygealaspirates from children with lower respiratory tract disease

.•The virus is speculated to be spread through respiratory secretions. However, it can also be found in blood and stool (diarrhea) from infected persons

Question 10

Autonomous Parvoviruses

Subfamily Densovirinae(genus-Iteravirus)

Answer 10

Subfamily Densovirinae(genus-Iteravirus):

can cause the formation of dense inclusions in the nucleus of infected insect cells. Some members of the group can cause disease in the silk worm (Bombyxmori), which can lead to economic loss to the silk industry

Question 11

Structure of Parvovirus virion

Answer 11

•Parvoviruses are small sized virionswith simple structure made up ssDNA, surrounded by an icosahedral-shaped capsid

Question 12

Parvovirus capsid

Answer 12

• The capsid is constructed from 60 protein molecules.
• However, the capsid structure of the parvoviruses is majorly made up of one protein species and there may be minute amount of one and three other protein species depending on the virus.
• The virionproteins are numbered according to size, with VP1 the largest and the smallest proteins are the shorter versions of VP1

Question 13

Parvovirus capsid

VP1

Answer 13

• VP1 phospholipase domain: Inside VP1 lies a phospholipase domain that plays a role in aiding penetrationof the virionthrough the endosome membrane during cell entry.
• The shape of the virionis roughly spherical, with surface protrusions and canyons.
• Each of the vertices of the icosahedron-shaped capsid has a protrusion with a pore at the center

Question 14

Parvovirus genom

Answer 14

• The genome of parvoviruses is made up of linear ssDNA, having size range of 4-6 kb.
• The 5’ end of the gene is covalently linked with a protein molecule;
• This protein, depending on the virus is known either as a ‘’Rep’’ (due to its role in replication) or NS1 (formerly known as non-structural).
• The ‘’Rep’’ protein is linked with a short DNA sequence and both are found on the surface of the virion.

Question 15

Secondary structures on the genome of parvoviruses

Answer 15

•Parvoviruses possess a number of short complementary sequences at each end of the DNA that can base pair to form secondary structure

Question 16

Figure 4: Base pairing at the termini of parvovirus DNA

Answer 16

1. Inverted Terminal Repeats (ITR): Some genome have sequences at their ends (ITRs), where the sequence of one end is complementary to, and in opposite orientation to the sequence at the other end.The two ends of the sequence are complementary indicating similarity in structure.
2. Unique terminal sequences: Other parvoviruses have unique sequences (secondary structures) at the ends of each DNA sequence

Question 17

Secondary structures on the genome of parvoviruses

ITR

Answer 17

• Parvoviruses with internal terminal repeats (ITR) and unique terminals do not generate and package equal number of (+) and (-) strands of DNA during replication;
• Those with ITR generate equal number of (+) and (-) DNA strands while viruses with unique termini do not.
• Thus, the percentages of virionscontaining (+) DNA and (-) DNA differs among the parvoviruses.
• In a (-) DNA virion, the genes for structural proteins are towards the 5’ end while those for non-structural proteins are towards the 3’ en

Question 18

Replication in parvoviruses

numbered steps

Answer 18

Replication in parvoviruses

• Attachment •Entry
• Transcription
• Translation•Genome replication
• Assembly
• Exit

Question 19

Replication in Parvoviruse

Answer 19

• The genome of parvoviruses are small sized from which the family name was derived.
• Small-sized genome implies that the parvoviruses do not encode all the needed proteins.
• Thus, some of the required proteins are derived from the host cell or from another virus.
• Important enzymes in DNA replication such as polymerase are derived from the nucleus of host cell during cell DNA synthesis.
• Parvoviruses exploit this period of cell DNA synthesis to replicate virus DNA.
• Thus, virus DNA can only be replicated when the infected cell is in its S phase (DNA synthesis) in the cell cycle.
• This is in contrast to the large DNA viruses that encode their proteins for DNA synthesis in their genome and can to replicate at any phase in the cell cycl

Question 20

Attachment of Parvoviruses to host cells

Answer 20

• The virionsof parvoviruses attached to suitable host cells via the cell receptors and co-receptors on the plasma membrane.
• For instance the B19 virus which infect red blood cell precursors uses blood group P antigen as its receptorand α5β1integrin as its co-receptor.
• Thereafter, The ‘’Rep’’ protein is lost from the 5’ end of the genome prior to entry of the virioninto the cell.

Question 21

Entry of Parvoviruses into host cell

Entry of cell to nuclues

Answer 21

• Parvovirus entry into host cells is mediated by clathrin-mediated endocytosis.
• The phospholipid domain of VP1fuses with the endosome membrane which facilitates virionentry through the cell membrane into the cytoplasm.
• Transport to the nucleus: cell invading virionsassociates with microtubulesto arrive at a nuclear pore to gain entry into the nucleus.
• Reason: the virionrequires cell enzymes that are present in the nucleus for replication of its DN

Question 22

Entry of Parvoviruses into host cell

entering the nucleus

Answer 22

• Virionentering the Nucleus: Nuclear localization signals have been found to be associated with the VP1 protein of some parvoviruses and a possibility of the capsid linking with the nuclear pore is likely.
• Releasing of viriongenome in the nucleus: Although, parvoviruses are small enough to fit in the nucleus (18-26 nm in diameter), it is still unclear if the virus enters the nucleus with its capsid before releasing it or releases it at the nuclear pore before entry into the nucleus

Question 23

Parvovirus conversion of ssDNA to dsDNA

Answer 23

•Parvoviruses must convert its ssDNAinto dsDNAusing cell DNA polymerase.

Figure 7: Summary of ssRNAviruses:Base pairing result in the ends of the gene been double stranded.

The 3’ end of the -OH group acts as a primer to which the enzyme binds

Question 24

Transcription and translation in parvovirus

Answer 24

Cell RNA polymerase II:

It plays important role in the transcription of virus genes into mRNA.

•Splicing events occurring in the primary transcript(s) results in two groups of mRNAs with varying sizes (small and large).

1. The smaller mRNAs encode the structural proteins.
2. The larger mRNAs encodes the non-structural proteins which are phosphorylatedand are important in various ways as follows:
   a. control of gene expression
   b. DNA replication and packagin

Question 25

DNA replication and virionassembly among parvoviruses

Answer 25

• Parvoviruses are largely dependent on the DNA replicating machinery of the host cells, though some replicating activities are done by the virus Rep/non structural proteins.
• Rolling-hairpin replication (RHR)

Question 26

•Rolling-hairpin replication (RHR)

Answer 26

• Rolling-hairpin replication (RHR): Is a mechanism by which parvoviruses replicate their genome (a unidirectional, strand displacement form of DNA replication in which DNA replication progresses in a continuous manner back and forth).
• RHR involves a leading strand mechanism and differentiates parvoviruses from other DNA viruses which replicates by leading and lagging strand synthesis.
• Structural proteins synthesized from small mRNAs forms the procapsid.
• Each procapsidis filled with a copy of the viral genome; either (+) DNA or (-) DNA as appropriate.
• Entry of progeny virus genome into the procapsidcould possibly be through one of the twelve pores at the vertices at the surface.•Matured virionsleave infected cell through cell lysisor exocytosis

Question 27

What kind of genomes do most ssDNA viruses have

Answer 27

circular genomes in contrast to the parvoviruses which possess a linear genome