Architecture and biogenesis of plus-strand RNA virus replication factories

Table 1 Overview of plus-strand RNA viruses and induced replication factories

Invaginated vesicle/spherule type
Superfamily/order	Alphavirus like	Alphavirus like	Alphavirus like	Alphavirus like
Family	Togaviridae	Togaviridae	Togaviridae	Bromoviridae	Nodaviridae	Flaviviridae	Flaviviridae
Genus	Alphavirus	Alphavirus	Rubivirus	Bromovirus	Alphanodavirus	Flavivirus	Flavivirus
Species	SFV	SINV	RUBV	BMV	FHV	DENV	WNV
Genome	ss(+) RNA	ss(+) RNA	ss(+) RNA	tripartite ss(+) RNA	bipartite ss(+) RNA	ss(+) RNA	ss(+) RNA
Gene order	NS-S	NS-S	NS-S	NS-S	NS-S	S-NS	S-NS
Genome size (bases)	13000	12000	10000	8300	4500	10000	10000
Virion size (nm)	70	70	70	27	30	50	50
Envelope	Yes	Yes	Yes	No	No	Yes	Yes
Host	Mosquitoes, humans	Mosquitoes, humans	Humans	Plants, yeast	Insects	Mosquitoes, humans	Mosquitoes, mammals
Disease	Encephalitis	Sinbis fever	German measels	Plant disease	Unknown	Dengue fever	Mostly asymtomatic
Type of replication factories	Spherules at PM and CPVs	Spherules at PM and CPVs	Invaginations at CPVs	Spherules at the ER	Spherules at mitochondria	Invaginated vesicles at the ER	Invaginated vesicles at the ER
Diameter of invaginations (nm)	50	50	80-500	50-70	50	90	50-150
Primary membrane source	PM, endosomes	PM, endosomes	Endosomes	ER	Outer mitochondrial membrane	ER	ER
Proposed sites of replication	Inside spherules	Inside spherules	Inside invaginated vesicles	Inside spherules	Inside spherules	Inside invaginated vesicles	Inside invaginated vesicles
Double membrane vesicle type
Superfamily/order		Picornavirales	Picornavirales	Nidovirales	Nidovirales	Nidovirales
Family	Flaviviridae	Picornaviridae	Picornaviridae	Coronaviridae	Coronaviridae	Arteriviridae
Genus	Hepacivirus	Enterovirus	Enterovirus	Coronavirus	Coronavirus	Arterivirus
Species	HCV	PV	CVB3	SARS CoV	MHV	EAV
Genome	ss(+) RNA	ss(+) RNA	ss(+) RNA	ss(+) RNA	ss(+) RNA	ss(+) RNA
Gene order	S-NS	S-NS	S-NS	S-NS	S-NS	S-NS
Genome size (bases)	9600	8000	8000	30000	30000	13000
Virion size (nm)	50	30	30	80-160	80-160	40-60
Envelope	Yes	No	No	Yes	Yes	Yes
Host	Humans	Humans	Humans	Humans	Mice	Horses, donkeys
Disease	Hepatitis	Poliomyelitis	HFM disease	SARS	HMM illness	Haemorragic fever
Type of replication factories	DMVs	SMTs, DMVs	SMTs, DMVs	DMVs, VPs	DMVs	DMVs
Length/diameter of replication factories	150 nm	100-200 nm, 100-300 nm	650 nm, 150 nm	150 nm, 1-5 μm	200-350 nm	90 nm
Primary membrane source	ER	Golgi, ER	Golgi, ER	ER	ER	ER
Proposed sites of replication	Possible role of DMVs but largely unknown	On SMT/DMV outer membrane	On SMT/DMV outer membrane	Inside DMVs	Inside DMVs	Inside DMVs

NS: Genes encoding nonstructural proteins; S: Genes encoding structural proteins; ER: Endoplasmic reticulum; PM: Plasma membrane; HFM: Hand-foot-and mouth; SARS-CoV: Severe acute respiratory syndrome coronavirus; HMM: High mortality murine; DMVs: Double membrane vesicles; SMTs: Single membrane tubular vesicles; VPs: Vesicle packets; PV: Poliovirus; HCV: Hepatitis C virus; CVB3: Coxsackievirus B3; MHV: Mouse hepatitis virus; EAV: Equine arterivirus; CPV: Cytoplasmic vacuoles; RUBV: Rubella virus; SFV: Semliki Forrest virus; FHV: Flock-house virus; DENV: Dengue virus; WNV: West Nile virus; BMV: Brome mosaic virus; SINV: Sindbis virus.