Chapter 4.3

Molecular Epidemiology of Astroviruses

P. Khamrin^*

N. Maneekarn^*

H. Ushijima^**
^* Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
^** Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan

Abstract

Astroviruses are members of the large and growing family Astroviridae. The viruses can infect both humans and a wide variety of mammals and avian species, including lambs, sheep, calves, pigs, dogs, cats, deer, mice, minks, bats, cheetahs, sea lions, dolphins, rats, rabbits, chickens, ducks, turkeys, and pigeons. In humans, astroviruses cause acute gastroenteritis and mainly affect children under 2 years old with general prevalence rates of up to 10%. Using advanced diagnostic assays, recent epidemiological studies have highlighted the impact of astrovirus-associated gastroenteritis, with additional novel astroviruses MLB and VA being discovered in human stool samples. Continued surveillance studies and the molecular characterization of the viral genome will permit the identification of new strains and potential zoonotic transmission of astroviruses in different host species.

Keywords

molecular epidemiology

astrovirus

MLB

diarrhea

animal astroviruses

1. Introduction

Astroviruses are enteric viruses associated with acute gastroenteritis in humans and a number of animal species (Mendez and Arias, 2013). Since the first human astrovirus was discovered using electron microscope in 1975, extensive epidemiological studies on astrovirus infection and disease have been carried out and these viruses are considered to be among the most common viral agents that causes gastroenteritis in young children worldwide (Appleton and Higgins, 1975; Bosch et al., 2014; De Benedictis et al., 2011; Madeley and Cosgrove, 1975). Soon after the first description in humans, astrovirus infections have been reported from a wide variety of mammals and avian species, including lambs, sheep, calves, pigs, dogs, cats, deer, mice, minks, bats, cheetahs, sea lions, dolphins, rats, rabbits, chickens, ducks, turkeys, and pigeons (Bosch et al., 2014; De Benedictis et al., 2011; Madeley and Cosgrove, 1975). The chronology of astrovirus discoveries is shown in Table 4.3.1.

Table 4.3.1

Chronology of Astrovirus Discoveries From Human and Animal Species

Host	Year of detection	Disease associated	References
Human (Classic HAstV)	1975	Gastroenteritis in children	Madeley and Cosgrove (1975)
Ovine	1977	Diarrhea in lambs	Snodgrass and Gray (1977)
Bovine	1978	Diarrhea in calves, asymptomatic	Woode and Bridger (1978)
Chicken	1979	Interstitial nephritis in young chicks, enteritis	Yamaguchi et al. (1979)
Turkey	1980	Poultry enteritis and mortality	McNulty et al. (1980)
Pig	1980	Diarrhea in piglets, asymptomatic	Bridger (1980)
Dog	1980	Diarrhea in pups, asymptomatic	Williams (1980)
Cat	1981	Pyrexia and mild diarrhea, asymptomatic	Hoshino et al. (1981)
Red deer	1981	Diarrhea	Tzipori et al. (1981)
Duck	1984	Acute hepatitis	Gough et al. (1984)
Mouse	1985	Diarrhea, asymptomatic	Kjeldsberg and Hem (1985)
Mink	2002	Preweaning diarrhea, shaking mink syndrome	Englund et al. (2002)
Guinea fowl	2005	Enteritis	Cattoli et al. (2005)
Insectivorous bat	2008	—	Chu et al. (2008)
Human (MLB1)	2008	Acute diarrhea	Finkbeiner et al. (2008)
Human (VA1)	2009	Gastroenteritis	Finkbeiner et al. (2009b)
Cheetah	2009	Lethargy and anorexia, watery diarrhea	Atkins et al. (2009)
California sea lion	2010	Diarrhea (pups), asymptomatic (adults)	Rivera et al. (2010)
Steller sea lion	2010	Asymptomatic	Rivera et al. (2010)
Bottlenose dolphin	2010	Asymptomatic	Rivera et al. (2010)
Brown rat	2010	—	Chu et al. (2010)
Roe deer	2010	Diarrhea	Smits et al. (2010)
Rabbit	2011	Rabbit enteritis	Martella et al. (2011b)
Feral pigeon	2011	—	Kofstad and Jonassen (2011)
Wood pigeon	2011	—	Kofstad and Jonassen (2011)
Shorebird	2014	Asymptomatic	Honkavuori et al. (2014)

Astroviruses belong to the family Astroviridae, which are small, nonenveloped, single-stranded, positive-sense RNA viruses. The genomes range from 6.1 to 7.9 kb in size and contain three open reading frames (ORFs). The ORF1a and ORF1b encode nonstructural proteins, whereas ORF2 encodes the capsid protein precursor (Mendez and Arias, 2013) (see Chapter 4.1). Although astroviruses have been known to be major causative agents for gastroenteritis in humans worldwide, there is relatively little information on their association with gastroenteritis diseases in other animal species. Surveillance investigations conducted previously in several countries worldwide indicated that human astroviruses are involved in 2–30% of diarrhea in children (De Benedictis et al., 2011).

2. Classification

Astroviruses have been found to be morphologically unique and typically appear as a star-like structures by electron microscopy, with the icosahedral capsid particles measuring approximately 28–30 nm in diameter (Appleton and Higgins, 1975; Madeley and Cosgrove, 1975). The term “astron” (greek) refers to the appearance of the icosahedral capsid which is similar to a star shape. The Astroviridae family contains several important human and animal pathogens and is further differentiated into two genera: Mamastrovirus (MAstV) and Avastrovirus (AAstV). MAstV and AAstV have been known to infect many mammalian and avian species, respectively. Astroviruses identified thus far have been classified on the basis of their host tropism and viral genomic variation by the International Committee on Taxonomy of Viruses (ICTV). Currently, 19 species within the Mamastrovirus genus (MAstV1-19) and 3 species within Avastrovirus (AAstV1-3) have been officially approved (Fig. 4.3.1). Recently, several novel astroviruses from different animal host species have been discovered, mostly by metagenomic pyrosequencing.

Figure 4.3.1 Phylogenetic relationship among the members in Astroviridae family.
The phylogenetic tree was constructed by neighbor-joining clustering method using MEGA5.2. Scale bar indicates nucleotide substitutions per site and bootstrap values (>80) are indicated at the corresponding nodes. The representative reference strains from each species were obtained from GenBank. MAstV, Mamastrovirus; AAstv, Avastrovirus.

The prototype astrovirus species was originally isolated from humans, called the classic human astrovirus (HAstV) and now belongs to MAstV1 species. The classic human astroviruses are genetically highly diversed and have been classified into eight genotypes (HAstV1-HAstV8). Beside MAstV1, three additional astrovirus species, MAstV6, MAstV8, and MAstV9 have been recently identified in human stool samples. The MAstV6 or MLB1 was detected during an outbreak of diarrhea in Australia (Finkbeiner et al., 2008). MAstV8 is comprised of the human astrovirus strains VA2, VA4, and HMOAstV-A, while MAstV9 includes the VA1, VA3, HMOAstV-B, and HMOAstV-C strains (Finkbeiner et al., 2009a,b; Jiang et al., 2013; Kapoor et al., 2009). Therefore, it is evident that there are at least three clades or genetic clusters of astroviruses cocirculating in humans: MAstV1 (classic human astrovirus: HAstV), MAstV6 (MLB clade), and MAstV8 together with MAstV9 (VA clade). In addition to humans, a wide range of animals has been found to be infected by different astrovirus species, such as cats, pigs, dogs, dolphin, mink, and sheep, infected by MAstV2, 3, 5, 7, 10, and 13, respectively. Moreover, California sea lions have been discovered to be infected by MAstV4 and 11, while several bat species are reported to be positive for MAstV12 and MAstV14–19 (Bosch et al., 2014; De Benedictis et al., 2011). The avian astroviruses are clustered exclusively within the Avastrovirus genus (AAstV); most recently a mammalian-like astrovirus has been reported in birds in 2011 (Pankovics et al., 2015).

3. Detection and diagnosis

By electron microscopy, the astrovirus particle is a small, round virus with a distinctive 5–6 pointed star-like structure (Appleton and Higgins, 1975; Madeley and Cosgrove, 1975). In 1981, the virus was successfully propagated in a primary cell culture, initially using human kidney epithelial cells (HEK) and later a human colon carcinoma (CaCo-2) cell line, which has been found to be more sensitive for the propagation of most human astrovirus strains (Willcocks et al., 1990). In addition, astroviruses could be propagated in several types of adenocarcinoma cell lines (SK-CO-1, T-84, and HT-29) and monkey kidney cell lines (Vero, MA104, and Cos-1) (Brinker et al., 2000). The success of growing human astroviruses in cell cultures was a big step forward in the characterization of these viruses. For the diagnosis of astrovirus infection, several different methods are now available. These include enzyme immunoassay (EIA), an immunochromatography (IC) test, reverse transcription-polymerase chain reaction (RT-PCR), real-time PCR, loop-mediated isothermal amplification, and nucleic acid sequence analysis (Jonassen et al., 1995; Khamrin et al., 2010; Wei et al., 2013). Of all of these methods, RT-PCR and nucleic acid sequence analysis are the most widely used methods for the detection and genotype identification of astroviruses. These techniques have replaced the traditional culture assays and immunological tests and become the gold standard for diagnosis of astrovirus infections in both humans and animal species.

4. Molecular epidemiology

4.1. Human Astroviruses

4.1.1. Classic Human Astroviruses (HAstV)

Since the human astrovirus was discovered, epidemiological studies of classic human astroviruses (HAstVs) have been extensively performed and reported from several countries around the world (Bosch et al., 2014; De Benedictis et al., 2011). The viruses have been identified in sporadic nonbacterial diarrhea cases and have been reported to be associated with a wide range of clinical illnesses including diarrhea, vomiting, fever, abdominal pain, bronchiolitis, and otitis (Mendez and Arias, 2013).

The HAstV positivity rates in acute gastroenteritis patients have been reviewed and summarized in Table 4.3.2. Surveillance of HAstV conducted in several countries worldwide indicate that the prevalence of HAstVs is variable from <1–40% of diarrhea cases. The variations of positivity rates are dependent on geographical area, study periods, age groups, and screening methods. However, in most studies the prevalence rate of HAstVs is approximately 10%. The virus is detected at a lower prevalence in comparison with group A rotavirus (RVA) and norovirus GII (NoV GII) (Chaimongkol et al., 2012; Chhabra et al., 2013). HAstVs predominantly infect young children with the highest rate of infection in children under 2 years of age; mixed infections with RVA are frequently observed (Iturriza Gomara et al., 2008). Although different seasonal peaks have been recorded in HAstV studies, the highest rates of infection have been reported for the cool season in the USA, Netherlands, Spain, China, and Japan (Chan-it et al., 2010; Chhabra et al., 2013; Enserink et al., 2015; Fang et al., 2006; Guix et al., 2002).

Table 4.3.2

Human Astrovirus Positivity Rates in Patients With Acute Gastroenteritis (Reviewed From 60 Studies Worldwide)

Region/Country		Year of sample collection	Detection method	No. of specimens tested	No. astrovirus positive (%)	Age	Coinfecting viruses	Site	References
Asia	Japan	2006–07	RT-PCR	628	15 (2.4%)	≤5 years		O	Dey et al. (2010)
	Japan	2008–09	RT-PCR	662	11 (1.7%)	≤5 years		O	Chan-it et al. (2010)
	Japan	2009–14	RT-PCR	2,908	86 (3%)	≤5 years	NoV	O	Thongprachum et al. (2015)
	Thailand	2000–03, 2005, 2007–08, 2010–11	RT-PCR	1,022	14 (1.4%)	≤5 years	RVA	H	Malasao et al. (2012)
	China	1998–2005	EIA/RT-PCR	1,668	91 (5.5%)	≤5 years		H	Fang et al. (2006)
	China	2005–07	RT-PCR	664	52 (7.8%)	≤13 years		O	Guo et al. (2010)
	China	2007–08	RT-PCR	Children 361 Adult 301	Children 49 (13.6%) Adult 7 (2.3%)	Children ≤3 years Adult ≥50 years		—	Wang et al. (2011)
	China	2008	RT-PCR	279	23 (8.2%)	≤6 years		H	Shan et al. (2009)
	Russia	2009	Real-time PCR	495	7 (1.4%)	≤5 years		H	Chhabra et al. (2014)
	Korea	2002–07	EIA/RT-PCR	106,027	2,057 (1.3%)			—	Jeong et al. (2011)
	Korea	2010–11	RT-PCR	186	3 (1.6%)	≤11 years		H	So et al. (2013)
	Korea	2008–12	RT-PCR	9,597	94 (1%)	≤78 years		O	Ham et al. (2014)
	Taiwan	2009	RT-PCR	989	16 (1.6%)	≤5 years	RVA	H	Tseng et al. (2012)
	Vietnam	2005–06	RT-PCR	502	70 (13.9%)	≤35 years	RVA	B	Nguyen et al. (2008)
	Pakistan	1990–94	RT-PCR	517	58 (11.2%)	≤5 years		H	Phan et al. (2004)
	Pakistan	2009–10	RT-PCR	563	48 (8.5%)	≤31 years		H	Alam et al. (2015)
	India	1999–2004	RT-PCR	857	50 (5.8%)	All ages	RVA	H	Bhattacharya et al. (2006)
	India	2007–09	RT-PCR	2,535	60 (2.4%)	All ages	RVA	H	Pativada et al. (2012)
	Bangladesh	2005–06	RT-PCR	138	13 (9.4%)	≤5 years	NoV, BoV, AdV	H	Mitui et al. (2014)
	Bangladesh	2010–12	RT-PCR	826	26 (3.1%)	≤3 years	RVA, NoV, AdV	H	Afrad et al. (2013)
	Turkey	2004–05	RT-PCR	150	4 (2.7%)	≤5 years	AdV	H	Mitui et al. (2014)
	Saudi Arabia	2002–03	EIA/RT-PCR	1,000	19 (1.9%)	≤6 years		B	Tayeb et al. (2010)
	Qatar	2009	Real-time PCR	288	1 (0.3%)	All ages		—	Al-Thani et al. (2013)
Africa	Egypt	2005–07	EIA	2,112	56 (2.7%)	≤5 years		O	El-Mohammady et al. (2012)
	Egypt	2006–07	EIA/RT-PCR	230	5 (2.2%)	≤18 years	RVA	O	Kamel et al. (2009)
	Egypt	2006–07	RT-PCR	364	23 (6.3%)	≤5 years		—	Ahmed et al. (2011)
	Tunisia	2003–07	EIA/RT-PCR	788	28 (3.6%)	14 days–12 years	RVA	B	Sdiri-Loulizi et al. (2009)
	Nigeria	2002	EIA	134	7 (5.2%)	≤5 years		O	Aminu et al. (2008)
	Nigeria	2007–08	EIA	161	65 (40.4%)	≤5 years		H	Ayolabi et al. (2012)
	Malawi	1997–99	EIA/RT-PCR	In patients 786 Out patients 400	In patients 15 (1.9%) Out patients 9 (2.3%)	≤5 years	RVA	B	Cunliffe et al. (2002)
	Kenya	1999–2005	EIA	476	30 (6.3%)	≤10 years		O	Kiulia et al. (2007)
	Madagascar	2004–05	RT-PCR	237	5 (2.1%)	≤16 years	RVA	—	Papaventsis et al. (2008)
	Ghana	2005–06	RT-PCR	367	12 (3.3%)	≤11 years		O	Silva et al. (2008)
Europe	Italy	1999–2000	EIA/RT-PCR	157	5 (3.2%)	≤2 years		H	De Grazia et al. (2004)
	Italy	2002–05	EIA/RT-PCR	708	28 (4.0%)	≤5 years	RVA	H	De Grazia et al. (2011)
	Italy	2008–09	RT-PCR	1,321	49 (3.7%)	≤5 years		H	De Grazia et al. (2013)
	Spain	1997–2000	Southern Blot Hybridization/RT-PCR	2,341	116 (4.9%)	≤82 years		B	Guix et al. (2002)
	Hungary	2002	RT-PCR	607	10 (1.6%)	49– 60 months		H	Jakab et al. (2004)
	Hungary	2003–05	RT-PCR	449	12 (2.7%)			H	Jakab et al. (2009)
	France	2001–04	EIA/RT-PCR	457	7 (1.5%)	≤15 years		H	Lorrot et al. (2011)
	France	2007	EIA	973	18 (1.8%)	≤6 years		H	Tran et al. (2010)
	UK	2000–03	RT-PCR	685	22 (3.2%)	≤6 years	RVA	B	Iturriza Gomara et al. (2008)
	UK	2006–07	RT-PCR	576	28 (4.9%)	≤16 years	RVA	B	Cunliffe et al. (2010)
	UK	2012–13	RT-PCR	Children 200 Adult 195	Children 35 (17.5%) Adult 1 (0.5%)	Children ≤5 years Adult ≥65 years		H	Borrows and Turner (2014)
	Netherlands	2010–13	Real-time PCR	1802	131 (7.3%)	≤47 years		O	Enserink et al. (2015)
	Bulgaria	2009	RT-PCR	115	7 (6.0%)	40 days– 3 years		H	Mladenova et al. (2015)
North America	USA	2008–09	RT-PCR/Real-time PCR	782	38 (4.9%)	≤5 years	NoV	B	Chhabra et al. (2013)
	Mexico	1988–91	EIA/RT-PCR/Cell culture	365	23 (6.3%)	≤18 months		—	Walter et al. (2001)
	Mexico	1994–95	EIA/IEM/RT-PCR	522	24 (4.6%)	≤5 years		B	Mendez-Toss et al. (2004)
	Guatemala	1987–89	EIA	321	124 (38.6%)	0–3 years		—	Cruz et al. (1992)
South America	Brazil	1994–96, 1998–2003	RT-PCR	1,588	57 (4.1%)	≤5 years		H	Silva et al. (2009)
	Brazil	2000–04	RT-PCR	354	11 (3.1%)	≤3 years	RVA	H	Andreasi et al. (2008)
	Brazil	1994–2008	Real-time PCR	539	19 (6.3%)	≤5 years		O	Ferreira et al. (2012)
	Argentina	1995–98	EIA/RT-PCR	1,070	40 (3.7%)	≤3 years		B	Espul et al. (2004)
	Argentina	1997–98	EIA/RT-PCR	66	5 (7.6%)	≤3 years		O	Bereciartu et al. (2002)
	Argentina	2001–02	EIA	97	12 (12.4%)	≤33 months		O	Giordano et al. (2004)
	Colombia	1997–99	EIA	251	12 (5%)	≤4 years		—	Medina et al. (2000)
	Venezuela	1994–95	RT-PCR	29	3 (10%)	≤4 years		—	Medina et al. (2000)
Australia	Australia	1995	Northern blot hybridization/RT-PCR	378	16 (4.2%)	≤5 years		—	Palombo and Bishop (1996)
	Australia	1995–98	RT-PCR	1,327	40 (3.0%)	≤5 years		—	Mustafa et al. (2000)
	Australia	1997–98	EIA/RT-PCR	414	19 (4.6%)	≤6 years		B	McIver et al. (2000)
	Australia	1995–98	Southern-blot hybridization/RT-PCR	774	33 (4.3%)	3 weeks– 5 years		—	Schnagl et al. (2002)

EIA, Enzyme immunoassay; IEM, immune electron microscopy; RT-PCR, reverse transcription-polymerase chain reaction; RVA, rotavirus of species A; NoV, norovirus; BoV, bocavirus; AdV, adenovirus; H, hospitalized; O, outpatient; B, both hospitalized and outpatient.

Among HAstV circulating in the human population, at least eight genotypes have been described (HAstV1–HAstV8). Based on the genome sequences and phylogenetic analyses, the genotypes of HAstV are tightly correlated with the serotypes (Mendez and Arias, 2013). The HAstV1 has been reported to be the most predominant genotype worldwide in children with diarrhea. However, the detection rate varies by geographical region (Fig. 4.3.2). HAstV1 is a major genotype which represents 30–84% of all HAstV genotypes in each continent. It should be noted that the HAstV1 alone represents over 80% of the strains circulating in Asia, while other genotypes (HAstV2–HAstV8) are found to be uncommon and responsible for only 1–6% of astrovirus infections. Lower detection rates of HAstV1 are observed in North America, South America, and Africa at 30, 43, and 46%, respectively. The HAstV1 together with HAstV2-HAstV4 are found regularly in Europe, North America, and South America, accounting for 89–98% of all astrovirus strains, while HAstV5–HAstV8 are less common and represent only 2–11% of astrovirus infections. In contrast, the distribution of HAstV genotypes in Africa is different from that of other regions since the uncommon genotypes, HAstV8 and HAstV5, are found to be the third and fourth common types after HAstV1 and HAstV3.

Figure 4.3.2 The global distribution of human astrovirus genotypes ascertained by analysis of strains collected between 1998–2014.
Asia: Afrad et al. (2013), Chan-it et al. (2010), Chhabra et al. (2014), Dey et al. (2010), Fang et al. (2006), Guo et al. (2010), Jeong et al. (2011), Malasao et al. (2012), Mitui et al. (2014), Nguyen et al. (2008), Pativada et al. (2012), Phan et al. (2004), Shan et al. (2009), Tayeb et al. (2010), Thongprachum et al. (2015), Tseng et al. (2012), Wang et al. (2011)North America: Chhabra et al. (2013), Mendez-Toss et al. (2004), Walter et al. (2001)South America: Andreasi et al. (2008), Espul et al. (2004), Ferreira et al. (2012), Medina et al. (2000), Silva et al. (2009), Ulloa et al. (2005)Europe: De Grazia et al. (2004), De Grazia et al. (2013), Guix et al. (2002), Jakab et al. (2004, 2009), Mladenova et al. (2015)Africa: Ahmed et al. (2011), Cunliffe et al. (2002), Naficy et al. (2000), Papaventsis et al. (2008), Sdiri-Loulizi et al. (2009), Silva et al. (2008)Australia: McIver et al. (2000), Mustafa et al. (2000), Palombo and Bishop (1996), Schnagl et al. (2002). n, the total number of human astrovirus genotypes reported from each continent.

Within each HAstV genotype, the strains can be further subdivided into lineages or subtypes. Based on the capsid sequences, the new subtype must have a nucleotide sequence divergence of >7% from the existing lineages (Guix et al., 2002). Thus far, HAstV1 has been subdivided into six lineages (1a–1f), HAstV2 into four lineages (2a–2d), HAstV3 into two lineages (3a–3b), and HAstV4 into three lineages (4a–4c) (Martella et al., 2013). In Japan, molecular characterization of HAstV1 lineages from the year 2006–15 demonstrated that during the first half of the surveillance studies from 2006–09 the detection rate of HAstV1d reached a peak of 96% prevalence, while HAstV1a was detected with a low prevalence of 4%. In contrast, from 2010 to 2015 HAstV1a reemerged with the prevalence of up to 98% as a predominant genotype (Chan-it et al., 2010; Dey et al., 2010; Thongprachum et al., 2015). Moreover, a surveillance study in Vietnam carried out in 2005-2006 revealed that HAstV1d was the most predominated astrovirus subtype (Nguyen et al., 2008). In Italy, during the period 2002–05 all HAstV1 were classified as HAstV1d, while during 2008 and 2009 both HAstV1a and HAstV1d subtypes were found to be equally predominant (De Grazia et al., 2013). These data imply that HAstVs cocirculating in children with diarrhea worldwide are genetically highly diverse pathogens.

4.1.2. MLB Astroviruses

The first MLB astrovirus prototype strain was identified in 2008 using the mass genome sequencing approach (Finkbeiner et al., 2008). The virus was detected from archived stool samples collected in 1999 from a 3-year-old boy with acute gastroenteritis in Melbourne, Australia, and later the virus was named as “MLB1.” The complete nucleotide sequence and genetic organization of MLB1 were characterized and demonstrated that MLB1 was considerably distinct from other known classic human astroviruses (HAstV1–HAstV8) and should be classified as a new astrovirus species in the genus Mamastrovirus (Fig. 4.3.1). One year later, the same research group reported the discovery of MLB2 in stool specimens collected from children with diarrhea in the United States and India (Finkbeiner et al., 2009a). In 2013, MLB3 astrovirus strains were identified in five stool specimens which had been collected in India. Within these, four of the MLB3 positive samples were obtained from patients with diarrhea, while 1 positive sample was from an asymptomatic case (Jiang et al., 2013).

The role of astroviruses of the MLB clade as causative agents of gastroenteritis has not been clearly established. Although most of the positive stool samples for this new clade were found in patients with diarrhea, a cohort study with a control population, carried out in Indian children, found no association of MLB1 with diarrhea (Holtz et al., 2011a). In addition, it was reported that MLB1 astrovirus infections were common in an American population since a greater than 60% seropositivity rate was found in children younger than 1-year old and reached 100% by adulthood (Holtz et al., 2014). However, the potential role of a systemic infection being related to febrile illness has been recently described in patient with MLB2 viremia (Holtz et al., 2011b).

After the discovery of the novel MLB astrovirus clade, these viruses have been reported in acute gastroenteritis pediatric patients in the USA, Nigeria, India, Japan, China, Hong Kong, Bhutan, Russia, Italy, Egypt, and Turkey (Bosch et al., 2014). In Japan, during 2013 and 2014, MLB astroviruses were found in 35 out of 330 (10.6%) fecal specimens collected from children with acute diarrhea. Among these, 2 types of MLB were identified (MLB1: n = 32 and MLB2: n = 3). It is interesting to note that the detection rate of MLB astroviruses was higher than that of classic human astroviruses (5.2%); the peak incidence was found in March and April (Khamrin et al., 2016). Since the first MLB astrovirus was identified in 2008, research into MLB astrovirus molecular biology, pathogenicity, and molecular epidemiology remained scarce.

4.1.3. VA Astroviruses

The VA astrovirus prototype strain was initially isolated during a sporadic outbreak of acute diarrhea in a child care center in Virginia, USA, in 2008. Using the pyrosequencing approach, the viral genome was found to be highly divergent from those of all previously known astroviruses, and initially named as “VA1” after the original place of viral discovery (Finkbeiner et al., 2009b). At the same time, another research group also reported the discovery of a novel astrovirus in fecal specimens collected from Nigeria, Pakistan, and Nepal, and the characterization of their genomes revealed that these viruses were phylogentically closely related to mink and ovine astroviruses. Hence, these viruses are provisionally named Human, Mink, and Ovine-like astrovirus (HMOAstV) and subdivided into the three types of HMOAstV-A, HMOAstV-B, and HMOAstV-C (Kapoor et al., 2009). Later, it was found that HMOAstV-C shared a close genetic relationship with VA1 astrovirus. Subsequently, VA2 and VA3 were identified in a cohort study of children with diarrhea in India and the USA (Finkbeiner et al., 2009a). Most recently, VA4 astrovirus strains were identified in two stool specimens collected from children with diarrhea in Nepal (Jiang et al., 2013). Taken together, VA astroviruses are classified into two phylogenetic clusters as VA1 and VA3, together with HMOAstV-B, HMOAstV-C, and are genetically more closely related with Mamastrovirus 9, while VA2, VA4, and HMOAstV-A are grouped together within Manastrovirus 8 (Fig. 4.3.1) (Finkbeiner et al., 2009a; Jiang et al., 2013; Kapoor et al., 2009).

Since the discovery of VA astrovirus was initially published in 2009, the role of VA astrovirus as a cause of gastroenteritis remains unclear (Finkbeiner et al., 2009a; Jiang et al., 2013; Kapoor et al., 2009). Although VA astrovirus infections are thought to be limited to the gastrointestinal tract, some studies have recently described the association of VA1 astrovirus with neurologic disorders in immunocompromised individuals. The VA1 astrovirus has been reported to cause encephalitis in a 15-year-old boy with agammaglobulinemia (Quan et al., 2010). The VA1 astrovirus can escape from the gastrointestinal tract into the circulatory system and is capable of invading the brain, with viral RNA being detected in brain biopsies and cerebrospinal fluid (CSF) (Naccache et al., 2015). In recent epidemiological studies, the virus has been detected at low prevalence rates in sporadic acute gastroenteritis cases in the USA, India, Pakistan, Nepal, Japan, China, and Nigeria (Bosch et al., 2014; Finkbeiner et al., 2009a; Jiang et al., 2013; Kapoor et al., 2009; Khamrin et al., 2016).

4.2. Animal Astroviruses

4.2.1. Ovine Astroviruses (OAstV)

The OAstV was first identified in 1977 in Scotland in lambs suffering from diarrhea shortly after the description of astroviruses in human. The OAstV was identified by electron microscopy (Snodgrass and Gray, 1977) and was purified and characterized structurally in 1981. Subsequently, the nucleotide sequences of the capsid region (ORF2) and the complete genome sequence were determined in the period from 2001 to 2003, and the virus was named OAstV-1 (Y15937) (Jonassen et al., 2003). Recently another OAstV strain was identified in samples taken from healthy domestic sheep in Hungary (Reuter et al., 2012). Sequence and phylogenetic analyses of ORF1b/ORF2/3′UTR of this isolate showed genetic divergence from OAstV-1, and it was therefore named OAstV-2. So far, only two OAstVs have been identified, one from lamb with diarrhea and the other one from a healthy sheep, suggesting that OAstV may not play a crucial causative role of diarrhea in sheep.

4.2.2. Bovine Astroviruses (BoAstV)

The first BoAstV was reported in England in 1978 in samples taken from calves with acute enteritis (Woode and Bridger, 1978). Several years later, another BoAstV, antigenically related to the first BoAstV, was isolated from a calf with diarrhea in Florida, USA. Although, these BoAstVs were isolated from calves with acute diarrhea, they could not induce diarrhea in calves infected experimentally. It was, therefore concluded that BoAstV is not associated with diarrhea in calves under natural conditions. Most recently, three bovine astroviruses associated with neurologic symptoms, so called BoAstV-Neuro S1 (KF233994), were detected in the brain tissue of cattle with histologically confirmed encephalomyelitis and ganglioneuritis, suggesting the virus to be a potential cause of neurologic disease in cattle (Li et al., 2013). Additionally, another bovine neurotropic astrovirus strain (BoAstV-CH13) was identified in cattle with nonsuppurative encephalitis in Switzerland (Bouzalas et al., 2014). Phylogenetically, BoAstV-CH13 was closely related to BoAstV-Neuro S1. These findings support the notion that infection with BoAstV is a common cause of encephalitis in cattle.

4.2.3. Porcine Astroviruses (PoAstV)

The PoAstV was first detected in piglets with diarrhea in association with calicivirus and rotavirus infections (Bridger, 1980). The virus was isolated later in 1990 in an established cell line derived from porcine embryonic kidney tissue. Molecular characterization of the capsid sequence (ORF2 gene) of this isolate was successfully carried out in 2001 and this PoAstV was named as PoAstV-1 (Jonassen et al., 2001). Later, PoAstVs were reported from several countries around the world, suggesting a wide geographical distribution. To date, five different PoAstV types, PoAstV-1–PoAstV-5, have been identified from different countries, including the Czech Republic, Columbia, Canada, the USA, China, and Hungary (De Benedictis et al., 2011). Although PoAstVs were described as a common virus detected in piglets with diarrhea, they were also detected in apparently asymptomatic healthy pigs (Luo et al., 2011). A prevalence of PoAstV infection in pigs of 62% has been reported recently from the United States (Mor et al., 2012). However, examination of the fecal contents of healthy slaughtered finisher pigs revealed a 79% positivity rate for PoAstV (Luo et al., 2011). Taken together, the clinical significance of PoAstV infection in pigs has not been completely elucidated.

4.2.4. Canine Astroviruses (CaAstV)

The CaAstV was first detected by electron microscopy in stool samples of beaglepuppies with gastroenteritis (Williams, 1980). The presumptive identification made by electron microscopy was confirmed by the genetic analysis of viral RNA extracted from clinical specimens. Recently, CaAstV has been propagated in MDCK cell cultures and virus growth induced a clear cytopathic effects (CPE) (Martella et al., 2011a). To date, CaAstVs have been reported from the USA, the UK, Australia, Italy, Germany, France, Brazil, China, Korea, and Japan (De Benedictis et al., 2011; Caddy and Goodfellow, 2015; Takano et al., 2015).

The prevalence of CaAstV infection associated with gastroenteritis in puppies was reported from Italy at 25%, France at 21%, the United Kingdom at 6%, China at 12%, Korea at 2%, and Japan at 10% (De Benedictis et al., 2011; Caddy and Goodfellow, 2015; Takano et al., 2015). It should be noted that the prevalence of CaAstV infection in puppies in Europe is relatively higher than that in Asia. CaAstV was also detected in asymptomatic puppies at an incidence of 9% (Martella et al., 2011a). The information relating to the clinical significance of CaAstV in dogs is limited and requires further investigation.

4.2.5. Feline Astroviruses (FeAstV)

The FeAstV was first detected using electron microscopy in the feces of domestic kittens with diarrhea (Hoshino et al., 1981). Further investigation demonstrated that FeAstV was commonly found in the stools of cats with and without diarrhea (Rice et al., 1993). So far, FeAstV in the feces of domestic cats has been reported from the USA, Australia, Germany, England, New Zealand, and Italy (De Benedictis et al., 2011). The clinical impact of FeAstV infection in cats seems to be low since kittens experimentally infected with FeAstV showed only pyrexia and mild diarrhea (Harbour et al., 1987).

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Tags: Viral Gastroenteritis

Apr 25, 2018 | Posted by admin in MICROBIOLOGY | Comments Off

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Molecular Epidemiology of Astroviruses

Molecular Epidemiology of Astroviruses

Abstract

Keywords

1. Introduction

2. Classification

3. Detection and diagnosis