Detection and identification of non-polio enteroviruses

Details Detection and identification of non-polio enteroviruses Detection and identification of non-polio enteroviruses

1999-07-09

2001-01-02

Jones, W. Gary (Department: 1655)

Chemistry: molecular biology and microbiology

Measuring or testing process involving enzymes or...

Involving virus or bacteriophage

C435S005000, C435S091200, C435S235100, C536S024330, C536S024310, C536S024320

Utility Patent

active

06168917

ABSTRACT:

BACKGROUND OF THE INVENTION
A. Field of the Invention
The invention relates to the detection and classification of pathogenic viruses. In particular, the invention provides diagnostic assays for the detection and classification of enterovirus nucleic acids in biological and other samples.
B. Related Art
Enteroviruses are a heterogeneous group of pathogens responsible for a broad spectrum of human and nonhuman diseases. Enteroviruses belong to a large genus within the family Picornaviridae; other genera within this family include rhinoviruses, hepatoviruses, cardioviruses, and aphthoviruses. The enterovirus genus encompasses polio viruses, coxsackie A viruses (CAV), coxsackie B viruses (CBV), echoviruses, and enteroviruses 68-71, as well as a number of uncharacterized enteroviruses isolated from humans and other primates. (For a review of taxonomy of Picornaviridae see,
VIRUS TAXONOMY: CLASSIFICATION AND NOMENCLATURE OF VIRUSES
Murphy et al., eds. Springer Verlag, 1995).
1. Biological properties of enteroviruses
Like other picornaviruses, enteroviral virions comprise an icosahedral capsid, about 30 nm in diameter, with no envelope, enclosing a core comprising infectious, single-stranded genomic sense RNA, about 7-8.5 kb in size. Enteroviruses are distinguished from other members of the picornaviridae by their stability in acid and their fecal-oral route of passage and transmission. Virus entry into cells is believed to involve specific cellular receptors.
Virion proteins include multiple copies of four capsid proteins (P1 gene products IA, IB, IC, ID such as poliovirus VP4, VP2, VP3, VP1, respectively. A small protein, VPg (Mr about 24×10
3
), is linked covalently to the 5′ terminus of the genomic RNA.
The viral genome consists of a ssRNA with a 5′ untranslated sequence of variable length followed by an ORF encoding the polyprotein precursor (Mr 240-250×10
3
) to the structural proteins (P1) and the predominantly nonstructural proteins (P2, P3), followed by a short non-coding sequence and a poly (A) tract of variable length.
FIG. 1
depicts a generalized enteroviral genome. The filled circle at the 5′ end is the genome-linked protein VPg (also referred to as the 3B gene product), followed by, the 5′ non-translated region (line). The open boxes depict a long open reading frame encoding a polyprotein that is split to yield the individual proteins mentioned above, followed by the 3′ non-translated region (line) and a poly (A) track (angled line). The eventual cleavage products of the polyprotein are indicated by vertical lines in the boxes, the nomenclature of the polypeptides follows an L:4:3:4 scheme corresponding to the genes (numbers) encoded in the L, P1, P2, P3 regions (Rueckert and Wimmer, 1984). The P1 region encodes the structural proteins 1A, 1B, 1C and 1D, usually referred to as VP4, VP2, VP3, and VP1, respectively. VP0, not shown here, is an intermediate precursor for VP4 and VP2. In all viruses, 3C is a protease, in enteroviruses and rhinoviruses 2A is a protease, while in all viruses 3D is considered to be a component of the RNA replicase.
The serotype designations (in parenthesis) of a number of enteroviruses and their genomic sequence accession numbers [in brackets] are:
bovine enterovirus 1
(BEV-1)
[D00214]
bovine enterovirus 2
(BEV-2)
human coxsackievirus A1 to 22
(CAV-1 to 22)
[D00538]
human coxsackievirus A24
(CAV-24)
human coxsackievirus B I to 6
(CBV-1 to 6)
[M33854]
human echovirus 1 to 7
(EV-1 to 7)
human echovirus 9
(EV-9)
human echovirus 11 to 27
(EV-11 to 27)
human echovirus 29 to 33
(EV-29 to 33)
human enterovirus 68 to 71
(HEV68 to 71)
human poliovirus 1
(HPV-1)
[V01150]
human poliovirus 2
(HPV-2)
human poliovirus 3
(HPV-3)
porcine enterovirus 1 to 11
(PEV-1 to 11)
simian enterovirus 1 to 18
(SEV-1 to 18)
Vilyuisk virus
Sequence identities for different enteroviruses, or between enteroviruses and rhinoviruses are more than 50% over the genome as a whole. Strains within a species often have more than 75% sequence identity over the genome as a whole. Viruses grouped by biological criteria, e.g., the polioviruses, or Coxsackie B viruses, are generally closely related in terms of overall nucleotide sequence identity over the genome as a whole. Different enteroviral serotypes are classified by cross-protection neutralization of infectivity, complement-fixation, specific ELISA using a capture format, or immunodiffusion. Some species can be identified by hemagglutination.
The following is a partial listing of reported correlations between enteroviral species and diseases (Morens, et al.,
Textbook of Human Virology,
pp. 427-497, 2nd ed., Mosby-Year Book, St. Louis (1991); Grandien, et al.,
Diagnostic Procedures for Viral, Rickettsial and Chlamydial Infections,
pp. 513-569, 6th ed. American Public Health Association, Washington, D.C. (1989)):
Poliovirus
PV1
PM
AFP
AM
C*
URI*
PV2
PM
AFP
AM
C*
URI*
PV3
PM
AFP
AM
C*
URI*
Coxsackievirus A
CA01
AM*
ABP*
Ena*
CA02
AFP*
AM*
Enc*
Ena
Ex*
CA03
AM*
Ena*
CA04
AFP*
AM*
Enc*
NND*
C*
Ena
HFM*
Ex*
PI*
CA05
AM*
Enc*
Ena
HFM*
Ex*
CA06
AM*
Enc*
Ena
P1*
CA07
AFP*
AM*
Ena*
LRI*
CA08
AFP*
AM*
Ena
CA09
AFP*
AM
Enc
NND*
ABP*
Ena*
Ex*
P1*
LRI*
Cr
CA09var
HFM*
CA10
AFP*
AM*
Ena
HFM*
P1*
URI
CA11
AM*
CA12
CA13
CA14
AM*
C*
CA15
CA16
AFP*
AM*
NND*
C*
Ena
HFM
EX*
CA17
AM*
CA18
AM*
CA19
Guillain-Barr{acute over (e)}
CA20
Hep
CA21
URI
CA22
AM*
Ena*
GI
CA24
AM*
URI
CA24var
AHC
CB1
AM
AFP*
Enc*
NND
M
ABP
Ena*
Ex*
P1
URI*
LRI*
CB2
AM
AFP
Enc*
NND
M
ABP
Ena*
Ex*
P1
URI
CB3
AM
P1
AFP
Enc*
NND
M
ABP
Ena*
Ex*
P1
URI*
CB4
AM
AFP
Enc*
NND
M
ABP
Ena*
Ex*
P1
URI*
LRI*
CB5
AM
M
AFP
Enc
NND
M
ABP
Ena*
HFM*
Ex*
P1
Cr
CB6
AFP*
AM*
P1
Echovirus
E01
AFP*
AM*
NND*
ABP*
Ex*
P1*
URI
E02
AFP*
AM*
Enc*
NND*
Ex*
E03
AM
AFP
Enc*
NND*
Ena*
Ex*
URI*
E04
AM
AFP
Enc*
NND*
C*
Ex*
URI*
E05
AM*
NND*
Ex*
E06
AM
AFP
Enc*
NND*
C*
Ena*
Ex*
P1*
URI*
E06′
E06″
AM
E07
AM
AFP*
Enc*
NND*
C*
URI*
E08
ABP*
E09
AM
AFP
Enc
NND
C*
ABP*
Ena*
Ex
LRI*
E11
AM
AFP
Enc*
NND
Ex*
P1*
URI*
Cr
E11′
AM
E12
E13
AFP*
E14
AM*
Enc*
NND
Ex*
E15
NND*
E16
AFP*
AM*
NND*
Ena*
BE
Ex*
E17
NND*
Ena*
E18
AFP*
Enc
NND
Ex*
GI
E19
AM*
AFP*
Enc*
NND
C*
ABP*
Ex*
P1*
URI*
GI
E20
AFP*
C*
URI*
E21
NND*
E22
AM*
NND
URI*
GI
E23
GI
E24
AM*
E25
Enc*
Ex*
URI*
E26
E27
AM*
E29
E30
AFP*
AM*
Ena*
E31
AM*
NND*
E32
AM
E33
AM*
E34
GI
Other enteroviruses
EV68
LRI*
EV69
EV70
AHC
EV71
Pa
AM
HFM*
ABP-acute benign pericarditis, AFP-acute flaccid paralysis, AHC-acute hemorrhagic conjunctivitis, AM-aseptic meningitis, BE-Boston exanthema, C-carditis, Cr-croup, Enc-encephalitis, Ena-enanthema, Ex-exanthema other than BE or HFM, GI-gastrointestinal disease, Hep-hepatitus, HFM-hand-foot-and-mouth disease, LRI-lower respiratory infection, M-myocarditis, NND-neonatal disease, Pe-pericarditis, Pl-pleurodynia, PM-poliomyelitis, Ra-rash, RD-respiratory disease,
# UF-undifferentiated fever; URI-upper respiratory infection;
*infrequent association.
Other possible associations: nonspecific febrile illness; fatigue syndrome; gastrointestinal disease; hepatitis; diabetes mellitus; pancreatitis; urinary tract infection; arthritis; hemolytic uremic syndrome; orchitis; et al.
Polioviruses (which exist as at least three serotypes) are the most clinically significant of the enteroviruses worldwide, causing paralytic disease in children in developing countries.
Non-polioenteroviruses (NPEV) are also responsible for large numbers of symptomatic and asymptomatic infections each year. Data suggests that there are between 10-15 million illnesses due to NPEV infections each year in the United States (Strikes et al., 1986). NPEVs are responsible for 30,000-50,000 hospitalizations each year for aseptic meningitis, myocarditis, encephalitis, acute hemorrhagic conjunctivitis, nonspecific febrile illnesses, and upper respiratory tract infections (Melnick,
Biologicals
21:305-309 (1993)). Certain forms of insulin-dependent diabetes mellitus, affecting an estimated 1 million individua

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