Introduction

Viral gastroenteritis is one of the most common diseases in humans. The major etiologic agents of viral diarrhea include rotaviruses (RVs), astroviruses (AstVs), adenoviruses (AdVs), noroviruses (NoVs), and sapoviruses (SaVs) [11]. Fecal-oral transmission is the primary route of transmission for these viruses. Food contamination, water contamination, and direct person-to-person contact have all been implicated in gastroenteritis outbreaks [27]. NoVs and SaVs are recognized as major causes of both sporadic and epidemic gastroenteritis [14]. In particular, NoVs are the most common cause of acute viral gastroenteritis in humans worldwide [23]. Acute NoV-associated gastroenteritis is characterized by the sudden onset of watery diarrhea and/or vomiting. Additional symptoms include nausea, malaise, fever, anorexia, headache, and myalgia.

NoVs and SaVs are members of the family Caliciviridae and are non-enveloped viruses whose genome contains a positive-sense single-stranded RNA [36]. NoVs have a single positive-strand RNA genome of approximately 7.4–7.7 kb, enclosed in a non-enveloped protein coat that contains distinct cup-shaped depressions. The human NoVs include more than 40 different viral strains that are divided into five genogroups (GI to GV) based on the VP1 capsid sequence [34]. The GI and GII genogroups account for the majority of human NoV cases and are further subdivided into 9 and 19 genotypes, respectively, of which GII.4 is responsible for >85 % of outbreaks [28]. SaV is a pathogen that causes acute gastroenteritis and is divided into five genogroups (GI to GV). Of these genogroups, members of GI, GII, GIV, and GV are capable of infecting humans. The SaV genome is a single-strand 7.5-kb RNA molecule with positive polarity. Based on the nucleotide sequence of the capsid gene, we categorized human SaVs into 16 genotypes (GI.1–7, GII.1–7, GIV, and GV). Real-time polymerase chain reaction (PCR) and reverse-transcription polymerase chain reaction (RT-PCR) have been employed to detect these viral pathogens in clinical specimens. However, little comprehensive epidemiological data have been reported concerning acute gastroenteritis and HuCV infections.

Shenzhen, a city located on the southern coast of China, is involved in extensive trading with other regions in Southeast Asia and has a relatively high incidence of HuCV infection. In this study, stool samples were tested for the presence of AdV, RV, NoV, and AstV, and then grouped according to month collected, age, and gender. Subsequently, all specimens were genotyped by RT-PCR and nucleotide sequencing. Phylogenetic analysis of genotype sequences was performed for HuCVs, which include NoV and SaV.

Materials and methods

Stool specimens

Stool specimens were collected from 983 patients (573 male and 410 female) with acute gastroenteritis from January 2011 to December 2011. For this study, diarrhea was defined as less than or at least three bouts of unformed (loose and watery) stool a day. Acute gastroenteritis was defined as the occurrence of diarrhea and other symptoms such as nausea, vomiting, fever, and abdominal cramps. The patients used in this study ranged from neonates to 60-year-old patients. The specimens were collected at clinics during the symptomatic period, transferred to the Shenzhen People’s Hospital, and stored at −80 °C until use.

The study was approved by the ethics committee of the Shenzhen Center for Disease Control and Prevention, and it was conducted in compliance with the principles of the Declaration of Helsinki. Written informed consent was obtained from the parents or legal guardians of all subjects.

RNA extraction and real-time PCR

Nucleic acids were extracted from 140 μl of a 10 % (w/v) stool suspension using a QIAamp Viral RNA Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol. In order to confirm the diagnosis of acute gastroenteritis and identify potential causes, we screened for pathogens of viral gastroenteritis. Quantitative and genogroup-specific TaqMan-based real-time PCR was performed for NoV, group A RoV, AdV, and AstV [35]. NoV was screened using primers for GIIF/GIIR targeting the viral ORF1-ORF2 [1]. The group A RoV primers, namely, VP3-Fbeg/VP3-R1, targeted the gene encoding non-structural protein 3 (NSP3), and the probe incorporated a FAM reporter and a BHQ1 quencher [31]. To detect AdV and AstV, we used previously described primers [22, 42]. For each reaction, the final volume was 25 μl, and it contained 5 μl RNA and 20 μl RT-PCR master mix, which was aliquoted into a 96-well reaction plate. Quantitative RT-PCR was performed using an Applied Biosystems 7500 Real-Time PCR System (Applied Biosystems, Foster City, CA). Amplification conditions were set according to the manufacturer’s instructions: reverse transcription at 50 °C for 20 min, initial denaturation at 95 °C for 5 min, followed by 40 cycles of amplification with denaturation at 95 °C for 15 s and annealing and extension at 60 °C for 1 min. Samples were scored as positive if cycle threshold (Ct) values were less than 40.

RT-PCR and phylogenetic analysis of NoV and SaV

RT-PCR was performed to target and amplify NoV G1, NoV GII, and SaV. The GI-SKF/GI-SKR and GoG2F/ G2-SKR primer sets were employed to detect NoV G1 and NoV GII [25], and the SLV5317/SLV5749 primers were used to detect SaV [17]. The final volume for each reaction was 25 μl, and it consisted of 2.5 μl of cDNA, 2.5 μl of 10× ExTaq DNA polymerase buffer, 2.0 μl of 2.5 mM dNTPs, 1.6 μl of each primer, 0.125 μl of ExTaq DNA polymerase (5 U/ml), and 16.275 μl of distilled water. The PCR cycling conditions were as follows: 50 °C for 30 min, 95 °C for 3 min, 40 cycles of 95 °C for 10 s, 55 °C for 30 s, and 72 °C for 30 s, and a final 7-min elongation at 72 °C. The temperature was held at 4 °C until use. The expected product sizes were 330 bp for NoV G1, 387 bp for NoV GII, and 434 bp for SaV. All PCR products were purified using a QIAquick Gel Extraction Kit (QIAGEN), and the purified DNA was sequenced using a Big Dye Terminator Cycle Sequencing Kit (Applied Biosystems) and an ABI 3100 Automated Sequencer (PE Biosystems). The sequences obtained were compared to the NoV and SaV reference strains deposited in GenBank using BLAST searches (http://www.ncbi.gov/BLAST/). Phylogenetic analysis was performed using the Kimura two-parameter model for nucleotide substitution and the neighbor-joining method to reconstruct the phylogenetic tree using MEGA 5.0. Statistical significance for the constructed phylogenies was estimated by bootstrap analysis, with 1,000 pseudoreplicated datasets.

Nucleotide sequence accession numbers

The partial nucleotide sequences of the capsid gene were deposited in GenBank under accession numbers KC820420–KC820487 for the NoV strains and KC820488–KC820502 for the SaV strains.

Results

Pathogen detection in patients with acute gastroenteritis

Our data revealed that, of the 983 stool samples collected from patients with gastrointestinal symptoms, 402 (40.9 %) contained at least one of the pathogens. NoV was the most common and was detected in 210 (21.4 %) samples, followed by group A RoV in 173 (17.6 %), AstV in 10 (1.0 %), AdV in 15 (1.5 %), and SaV in 15 (1.5 %). Mixed infections involving two viruses were found in 21 of the 402 (5.2 %) positive samples, and the combinations were as follows: RoV + NoV in 16 cases, NoV + AstV in two cases, NoV + AdV in one case, RoV + AdV in one case, and RoV + AstV in one case. The monthly distribution for the positive samples indicated a peak infection period from July to October (Fig. 1).

Fig. 1
figure 1

Monthly distribution of viral gastroenteritis in Shenzhen City, China, 2011. The bar represents the number of detected cases, and lines represent the positive rate of RV and NoV infection. Co-infections are shown as NoV–RV, NoV–AstV, NoV–AdV, RV–AdV, and RV–AstV

Full size image

The distribution of viral etiologic agents according to age is shown in Fig. 2. Of the total number of strains, 33.8 % (332 of 983) were obtained from adults aged 21 years and older, while 60.1 % (591 of 983) were obtained from children 5 years of age and younger. From the 5 year old and younger group, 45.5 % of the positive isolates were obtained from infants less than 1 year old. In all positive samples, NoV was the most prevalent viral agent of acute gastroenteritis (52.2 %) and was followed by RV (43.0 %). In infants aged 1 year or younger, the occurrence of NoV, RV, AdV, and AstV was 47.4 % (82 of 173), 41.0 % (86 of 210), 53.3 % (8 of 15), and 40.0 % (4 of 10), respectively. Mixed infections occurred in 5.4 % of isolates, with the majority of these (76.2 %; 16 of 21 isolates) being found in 0- to 5-year-old subjects. The most common viral co-infections were RV + NoV (76.2 %; 16 of 21 isolates).

Fig. 2
figure 2

Distribution of viral agents of gastroenteritis by age in Shenzhen, China, 2011. Co-infections are shown as NoV–RV, NoV–AstV, NoV–AdV, RV–AdV, and RV–AstV. The number of positive samples = RV + NoV + AdV + AstV − “co-infection”

Full size image

Distribution of NoV genotypes

Genome sequences of 983 fecal specimens were amplified by RT-PCR, and 68 NoV strains (5 G1 and 63 GII) were successfully sequenced. Based on the capsid sequence, five strains from the G1 group were further genotyped as two G1.1, one G1.3, one G1.4, and one G1.8. Sixty-three GII strains were clustered into five genotypes, including 41 (65.1 %) G II.4 (36 GII.4 2006b and five GII.4 New Orleans), 18 (28.6 %) GII.3, 2 (3.2 %) GII.2, 1 (1.6 %) GII.6, and one (1.6 %) GII.13.

Phylogenetic analysis of these NoV strains (Fig. 3) revealed that 36 GII.4 2006b strains detected in Shenzhen, China, during 2011 were closely related to the strains detected in Japan (AB291542) that spread in a health care setting during 2006 [18]. Another five GII.4 strains were closely related to the GII.4 New Orleans strain, which was first detected during October 2009 in the United States (GU445325) [39]. NoV GII.3 was identified as the second most common genotype and is closely related to the (HM635113) strain isolated from Seoul, Korea, during 2010. In addition, the NoV GII.2 strains (SHZH11–039 and SHZH11–135) were related to the NoV strains isolated from the United States (AY134748), while NoV GII.13 (SHZH11-391) strains were related to strains isolated from Vietnam (JF262607), and GII.6 (SHZH11–067) strains were closely related to the GII.6 strain detected in Tokyo, Japan, during 2000 (AB039778).

Fig. 3
figure 3

Phylogenetic analysis of partial nucleotide capsid sequence of NoVs detected in acute gastroenteritis in Shenzhen in 2011. The tree was constructed by the neighbor-joining method using the MEGA 5 software package, and the numbers on each branch indicate the bootstrap values. The strains detected in this study are marked by ∆ and are in bold. The scale represents the nucleotide substitutions per site

Full size image

SaV genotype distribution

Of the 983 fecal specimens screened for SaV, 15 (1.5 %) were successfully sequenced. Based on partial sequencing analysis of the of partial capsid gene, 12 SaV isolates belonged to the SaV G1.2 genogroup, and one belonged to the NoV GII.4 2006b genogroup. The remaining three SaV strains belonged to the SaV GII genogroup.

Phylogenetic analysis of the SaV strains (Fig. 4) revealed that the SaV G1.2 strains detected in our study were related to the strain found in Houston during 1997 (U95644) and a strain isolated from a gastroenteritis outbreak in the United Kingdom during 2006. The SaV GII (SHZH11–024, SHZH11–397, SHZH11–116) formed a cluster as a sublineage of SAV GII that is separate from the Hu/C12/00/JP/AY603425, Hu/Mc10/00/TH/AY237420, and Hu/Cruise ship/00//AY289804 cluster [10].

Fig. 4
figure 4

Phylogenetic trees constructed from partial nucleotide sequences of the capsid genes of SaVs. The isolate numbers of the samples tested are marked by ∆ and are in bold. The calibration scale indicates the percent divergence among nucleotide sequences. The reference sequences were obtained from GenBank

Full size image

Discussion

This one-year surveillance study of outpatients with gastroenteritis, based on real-time PCR detection, successfully identified viral pathogens in 39.7 % of specimens. Over the past decade, NoV has been well documented as a major etiological agent that causes sporadic diarrhea in infants and young children [2, 4, 11, 23]. In this study, NoV exhibited a relatively high detection rate and was found in 21.4 % of all samples tested. This is a much higher incidence when compared to data obtained from studies conducted in Vietnam and India [6, 29]. However, this rate is lower than that observed in a recent study from Brazil and Thailand [12, 38, 41], where RV was identified in 173 (17.6 %) of 983 patients. This rate is also lower than previously reported in community-based studies of developed countries in which RV was detected in 19–28 % of gastroenteritis patients [19, 21]. The monthly distribution of the positive samples in this study revealed that NoV could be detected throughout the year. Higher activity of NoV was observed between July (late summer) and August (early autumn). However, peak RV infection was observed during the winter months (Fig. 1), with the highest activity of RV infection spanning from autumn to spring and peaking during winter. Viruses infect individuals of all ages, with children below the age of 3 years exhibiting the highest incidence of infection. Notably, this finding was consistent with recent reports from the United States, India, and Taiwan [3, 15, 26].

The phylogenetic trees generated from partial and complete capsid genome sequences revealed that most NoV strains in Shenzhen belonged to the GII genogroup. The NoV genotypes identified in this study are diverse, and GII.4 was the predominant NoV strain, followed by the GII.3 strain. This result is consistent with studies from other regions of China and various countries [5, 8, 40]. Since NoV was first isolated in the mid-1990s, novel GII.4 genotype variants have been detected in multiple populations [2, 33]. The last pandemic GII.4 variant, GII.4 2006b or GII.4 Minerva, was identified in late 2005/early 2006 and has since been identified as the predominant strain involved in outbreaks across the United States [7, 9, 43]. Recently, novel NoV GII.4 variants have been discovered, namely, the GII.4 New Orleans, which first emerged in October 2009 in the United States [39]. Subsequently, NoV GII.4 variant strains have also been report in Vietnam, Taiwan, and Singapore [16, 24, 37]. Notably, in this study, 30 NoV samples were also positive for the GII.4 New Orleans strain from patients in Ho Chi Minh City. It has been suggested that most GII.4 variants originated in the northern hemisphere and migrated to southern countries. In this study, the NV GII.4 subtype comprised GII.4 2006b and GII.4 New Orleans strains. In addition, this is the first time the GII.4 New Orleans strain has been detected in China at such a high rate. This indicates that future studies are required to identify whether the prevalence of this new GII.4 variant will continue to increase. Furthermore, several genotypes of the NoV genogroup are rarely detected, namely, G1.1 and G1.8.

Few studies have used molecular methods to identify SaV infection and compare its prevalence with that of NoV, as performed here. In this study, 15 (1.5 %) SaV were detected by RT-PCR, which is consistent with previous reports [20, 38]. Interestingly, the SaV genogroup I strains are more common than those of genogroup II. This finding differs from reports from the United Kingdom and Japan [13, 17]. Additionally, most SaV strains belong to G1.2 (80 %), and many studies suggest that the GI.1 cluster is the most frequently detected cluster [30, 32]. The difference in the pathogen detection rate may also be partly explained by the differences in the target country, age group, and criteria of severity.

In conclusion, this study characterized viral gastroenteritis and HuCVs in samples collected from hospitalized patients with acute gastroenteritis. Phylogenetic analysis was employed to classify SaV and NoV strains that co-circulated in the studied populations during a defined surveillance period. Systematic surveillance for gastroenteritis pathogens is important to preserve public health. In addition, continuous surveillance for viruses, including NoV and SaV, utilizing novel methodologies is required to elucidate genetic diversity of the viruses within the population, to identify novel viral strains, and to treat gastroenteritis.