Molecular detection and characterization of human enteroviruses in Korean surface water

Direct typing of human enteroviruses from wastewater samples

A RT-PCR approach for the direct detection and typing of human enteroviruses in the environment is described in this study. A semi-nested RT-PCR using COnsensus-DEgenerated Hybrid Oligonucleotide Primers (CODEHOP) designed from the VP2 genome region has been developed for the direct typing of enteroviruses in clinical samples (Ibrahim et al., 2013). This CODEHOP/VP2 PCR strategy as well as the CODEHOP/VP1 technique described by Nix et al. (2006), were tested for the detection and typing of enteroviruses in wastewater samples. Virus particles were first extracted and concentrated from wastewater samples by using respectively beef extract and polyethylene glycol 6000, and the presence of enteroviruses was screened by a RT-PCR method using primers from the 5'-end non-coding region (5'NCR). Fifty-two of 172 samples (30.2%) were revealed positive by the 5'NCR method. From these 52 samples, only 19 samples (36.5%) were found positive by at least one of the two CODEHOP techniques, with the following distribution: VP1(+)/VP2(+)=4 (7.7%), VP1(-)/VP2(+)=13 (25%) and VP1(+)/VP2(-)=2 (3.8%). These results illustrate that the direct typing of enteroviruses in environmental samples is insensitive, possibly due to the presence of large amounts of amplification inhibitors; however, the VP2 method was found able to allow the direct detection and typing of c. one-third of the positive environmental samples.

Evolutionary pattern of 5'-UTR of enteroviruses and primer update for the detection of enteroviral RNA in environmental samples

OBJECTIVE

To study the recombination events among enterovirus strains and the development of specific primers for the detection of enteroviruses in environmental samples.

METHODS

Nucleotide sequence analysis of enteroviruses deposited in the international database GenBank (www.ncbi.nlm.nih.gov/Genbank) was conducted to develop specific primers for the detection of these viruses. The specificity and sensitivity of the method were tested using coxackievirus B3 strain Nancy, environmental isolate of human hepatitis A virus and human rotavirus strain WA. Seventy sewage samples were analyzed.

RESULTS

Enterovirus genome was detected in all positive samples. The genome of enterovirus was not detected in negative samples. The level of detection of these viruses was 10(2) TCID(50)/mL.

CONCLUSIONS

The development of new primers is an important issue for the detection of enteroviruses in the environment and the assessment of risk factors to human health.

Detection and molecular characterization of human noroviruses in Korean groundwater between 2008 and 2010

RT-PCR, nucleotide sequencing, and phylogenetic analysis were performed for genotyping and molecular characterization of noroviruses isolated from Korean groundwater. Among 160 samples collected from 80 sites between 2008 and 2010, 14 samples (8.7 %) from 12 sites were positive for noroviruses (NoVs). The percentages of NoV-positive samples in 2008, 2009, and 2010 were 22.2, 3.2, and 0 %, respectively, representing a yearly decrease. GII-positive samples (n = 9, 5.6 %) outnumbered GI-positive samples (n = 5, 3.1 %). The genotypes of the GI NoVs were GI.2, GI.5, and GI.6, and the genotypes of the GII NoVs were all GII.4. One sample, HM623465, was very similar to CUK-3 and CBNU2 and two GII.4 sequences isolated from the stool of Korean gastroenteritis patients. A BLASTN search revealed several nucleotide sequences highly similar to those of NoVs isolated in this study. The original isolation sources for these similar NoVs were mostly stool (n = 731, 80.0 %) and groundwater (n = 135, 14.8 %), and all the countries from which they were isolated were almost in Asia (96.0 %); specifically, China (n = 192, 21.0 %), Japan (n = 383, 41.9 %), Korea (n = 296, 32.4 %), and other Asian countries (n = 6, 0.7 %). These results suggest that Korean groundwater might be contaminated with NoVs from the stool of infected patients and that these NoVs in turn cause new cases of gastroenteritis through a typical fecal-oral route with region-specific circulation. Therefore, it is important to properly treat sewage, which may include waterborne viruses and manage point sources in groundwater for national health and sanitation. In addition, continuous molecular surveillance remains important for understanding circulating NoVs.

Complete genomic sequence analysis of norovirus isolated from South Korea

The complete nucleotide and deduced amino acid sequences of the RNA genome of a recently isolated norovirus (NoV) from Korea, designated Hu/GII-4/CBNU2/2007/KR (CBNU2), were determined and characterized by phylogenetic comparison with several genetically diverse NoV sequences. The RNA genome of CBNU2 is 7,560 nucleotides in length, excluding the 3' poly (A) tract. It includes three open reading frames (ORFs): ORF1, which encodes the nonstructural polyprotein (5-5,104); ORF2, which encodes VP1 (5,085-6,707); and ORF3, which encodes VP2 (6,707-7,513). ORF2-based phylogenetic analysis revealed that CBNU2 belonged to the GII.4 genotype, the most prevalent genotype, and formed a cluster with NoVs isolated from Asian regions, between 2006 and 2008. Comparative analysis with the consensus sequence of 207 completely sequenced NoV genomes showed 47 mismatched nucleotides: 26 in ORF1, 14 in ORF2, and 7 in ORF3, resulting in 8 amino acid changes: 3 in ORF1, 2 in ORF2, and 3 in ORF3. Phylogenetic analysis with full genome ORF1, ORF2, and ORF3 nucleotide sequences obtained from CBNU2 and each of the other representative NoV genomes suggested that CBNU2 had not undergone recombination with any of the other NoVs. A SimPlot analysis further supported this finding.