| Literature DB >> 29301542 |
Hui Zhu1, Fang Yuan2, Zhaokang Yuan3, Rong Liu1, Fei Xie1, Ling Huang1, Xiaojun Liu1, Xiaoqing Jiang1, Jian Wang1, Qunying Xu1, Zhiqiang Shen4, Donghan Liu1, Ronghao Zhang1, Yuanan Lu5,6.
Abstract
BACKGROUND: Recreational water contaminated with fecal pollution poses a great public health concern, as fecal waste may cause serious waterborne illnesses. Current recreational water standards using fecal indicator bacteria (FIB) have their limitations for human protection especially in developing countries such as China.Entities:
Keywords: Enteric virus; Poyang Lake; RT-PCR; Water quality indicator
Mesh:
Substances:
Year: 2018 PMID: 29301542 PMCID: PMC5755429 DOI: 10.1186/s12985-017-0916-0
Source DB: PubMed Journal: Virol J ISSN: 1743-422X Impact factor: 4.099
Fig. 1Map showing six sampling sites along Poyang Lake for this study. Water samples were collected monthly from each of these six locations of the lake between October 2016 and January 2017
Sites sampled in the Poyang Lake
| Location | Details | GPS coordinates | |
|---|---|---|---|
| Latitude Longitude | |||
| Qing Shan Zha | In the south branch of Gan River, nearly the city of Nanchang | 28°43′28” | 115°55′47” |
| Guan Niao Tai | Belong to Jiangxi Provincial nature reserve, in the southwestern of Poyang Lake, Nanchang | 28°41′13” | 115°53′56” |
| Tuo Shan | Belong to Jiangxi Provincial nature reserve, in the southwestern of Poyang Lake, Nanchang | 28°56′17” | 116°21′12” |
| Wu Cheng | In the north-central of Poyang Lake, Jiujiang City | 29°26′17” | 116°2′41” |
| Xing Zi | In the north of Jiangxi Province, Jiujiang City | 29°26′17” | 116°2′42” |
| Du Kou | The only junction of Poyang Lake and Yangtze River in Jiujiang City | 29°44′47” | 116°12′56” |
List of PCR primers used in this study with optimal amplification conditions
| Virus | Primer name | Primer Sequence (5′ → 3′) | Length (bp) | Amplification condition | Reference | |||
|---|---|---|---|---|---|---|---|---|
| TA | Mg (mM) | Primer (μM) | BSA | |||||
| NoV GI | QNIF4 | CGCTGGATGCGNTTCCAT | 8 | 58 | 2.0 | 0.4 | Yes | Loisy et al., 2005 |
| NV1LCR | CCTTAGACGCCATCATCATTTAC | |||||||
| NoV GII | COG2F | CARGARBCNATGTTYAGRTGGATGAG | 9 | 58 | 2.0 | 0.8 | Yes | Kageyama et al., 2003 |
| COG2R | TCGACGCCATCTTCATTCACA | |||||||
| EoV | EQ-1 | ACATGGTGTGAAGAGTCTATTGAGCT | 1 | 60 | 1.5 | 0.6 | Yes | Dierssen et al., 2008 |
| EQ-2 | CCAAAGTAGTCGGTTCCGC | |||||||
| AdV | ADV-F | GCCACGGTGGGGTTTCTAAACTT | 1 | 54 | 1.5 | 0.6 | Yes | Gunson et al., 2009 |
| ADV-R | GCCCCAGTGGTCTTACATGCACATC | |||||||
aNoV GI, human norovirus genotype I; NoV GII, human norovirus genotype II; EoV, human enterovirus; AdV, human adenovirus
Fig. 2Agarose gel electrophoresis of RT-PCR and PCR detection of four enteric viruses from six sampling sites of Poyang Lake. The image of enteric virus detection in October (a) and November (b) in 2016. NoV GI, human norovirus genotype I; NoV GII, human norovirus genotype II; EoV, human enterovirus; AdV, human adenovirus. Lanes: 1 = Guan Niao Tai, 2 = Tuo Mountain, 3 = Qing Shan Zha, 4 = Du Kou, 5 = Xing Zi, and 6 = Wu City. Lanes M = 50 bp DNA marker; C+ = positive control; Lane C- = negative control containing no template
Detection of human enteric viruses in water samples of Poyang Lake, Jiangxi, China
| Sampling | NoV GI | NoV GII | EoV | AdV | |
|---|---|---|---|---|---|
| Date | Site* | ||||
| October 10 | 1 | – | – | – | + |
| 2 | – | – | + | + | |
| 3 | + | – | – | + | |
| October 28 | 4 | + | – | + | + |
| 5 | + | – | + | + | |
| 6 | + | – | + | + | |
| November 10 | 1 | + | + | – | – |
| 2 | + | + | + | – | |
| 3 | + | – | + | – | |
| November 28 | 4 | + | – | + |
|
| 5 | – | – | + | + | |
| 6 | – | – | + | + | |
| December 10 | 1 | + | + | – | – |
| 2 | + | + | – | – | |
| 3 | + | – | – | + | |
| December 28 | 4 | – | + | – | + |
| 5 | – | – | – | + | |
| 6 | – | + | + | + | |
| January 10 | 1 | – | – | + | – |
| 2 | – | – | – | – | |
| 3 | – | – | – | – | |
| January 28 | 4 | + | + | + | + |
| 5 | – | + | + | + | |
| 6 | – | + | + | + | |
| Total | 12 | 9 | 14 | 16 | |
* 1 -Qing shan zha; 2 - Guan Niao Tai; 3 - Tuo Shan; 4 -Wu Cheng; 5 - Xing Zi; 6 - Du Kou
Sequence results of amplified PCR fragments
| Site | Blast | Matched DNA | E value | Identity | Sequence |
|---|---|---|---|---|---|
| 3.2 | KC911703.1 | Norovirus Hu/GII/NEC-365/THA/ | 5.00E-10 | 98% | ATAATCATTACCCAAGTTTAAATGAAGAGGAGACGCATCTGGCTCCCAGTTTTGTGAAT |
| 1.2 | EU151450.1 | Swine vesicular disease virus strain SVDV Itl. 1–92 | 5.00E-33 | 96% | CCATGGCTAGGACTGACTACTTTGATACGGCTAATCCTCACTCGCGTGAGCAGATACCCA |
| 1.3; 2.4 | GU236215.1 | Human echovirus 11 isolate 39,351.82 5’ UTR | 6.00E-42 | 100% | AAGGTGAGGACCAGTACTCCTGAATGCGGCTAATCCTAACTGCGGAGCAGATACCCAC |
| 1.1 | KX458103.1 | Norovirus GI.9 strain | 1.00E-09 | 98% | GGGGGTGGCGTCTAAGACATCTCCTACCCGATTATGTAAATGATGATGGCGTCTAAGGA |
| 2.6 | KF303071.1 | Human adenovirus 41 isolate 10–4851 | 2.00E-31 | 98% | TGGGAACCTGCCTTAAGTCGATATCTCGTGGCGCGGGCAAACTGCACCAGGCCCGGA |
| 2.5 | GU236272.1 | Human echovirus 25 isolate 06.048.1621 5’ UTR | 1.00E-40 | 99% | GAGGACGAACACAGACCAACCGCCCACTGGTGTGTGGGTATCTGCTCCGCAGTTAGGAT |
| 2.5; 4.6; 4.5; 4.4 | LT628548.1 | Human adenovirus 41 partial Hexon gene for Hexon gene pseudogene, strain Muonio/11V1867_3/2012/FIN | 5.00E-32 | 97% | TAGGCCTTGGTCTTAATTCGATATCTGGTGGCGCGGGCAAACTGCACCAGGCCCGGACT |
| 3.2; 5.3 | JX412882.1 | Human adenovirus 41 isolate CR6724 hexon gene | 5.00E-37 | 100% | TGCTGGCGAGTCGTATCGGTGGCGCGGGCAAACTGCACCAGGCCCGGACTCAGATA |
| 3.3; 4.4 | AB112114.1 | Human norovirus Saitama gene for RNA dependent RNA polymerase, | 3.00E-15 | 100% | AGGGGCCGTGATTGCGATCTCCTGTCCACAAGCTCAAGTCATGGAACCGCATCCAGCGA |
| 3.3 | JX412882.1 | Human adenovirus 41 isolate CR6724 hexon gene | 5.00E-37 | 100% | TAGACGGCCGAGTCGTATCGGTGGCGCGGGCAAACTGCACCAGGCCCGGACTCAGATA |
| 4.6 | KX907729.1 | Norovirus Hu/USA/2011/GI.P7_GI.7/CS5567 | 5.00E-13 | 98% | GGTAGGCGTCTGATCGCACTCTCCTACCCGATTATGTAAATGATGATGGCGTCTAAGGA |
| 4.5 | AB504701.1 | Norovirus sewage/GI.7/Toyama/SW0703–10/2007/JP genes | 1.00E-15 | 100% | ACGACTGTGATTGCGATCTCCTGTCCACAAGCTCAAGTCATGGAAACGCATCCAGCGA |
| 3.1 | JX439815.1 | Norovirus Hu/GII/Seoul1055/KOR/2010 | 3.00E-12 | 98% | TGGTCCGACTCCGGCGCCGACAATCGGGCGCTCCGCAATCTGGCTCCCAGTTTTGTGA |
| 4.5 | KJ489414.1 | Human coxsackievirus B3 strain 2679 | 1.00E-40 | 96% | GGTCATTCGACGACTGCGCACTGGTGTGTGGGTATCTGCTCCGCAGTTAGGATTAGCCG |
| 5.1; 5.2 | LC147086.1 | Norovirus Hu/GI/Toyama/outbreakApr3741 /2010/JP | 9.00E-10 | 100% | GGCATGCGTCTGACGCATCTCCTACCCGATTATGTAAATGATGATGGCGTCTAAGAGA |
| 5.1 | KC911664.1 | Norovirus Hu/GII/CC-685/THA/2006 RNA polymerase and capsid genes | 2.00E-14 | 98% | TTGCCCCAGACGGGCATCGGTAGGTGGGGCGATCGCATCTGGCTCCCAGTTTTGTGA |
| 6.4 | KX446506.1 | Norovirus GII strain GII/Hu/NL/2010/GII | 1.00E-21 | 97% | CAACGGATCTGAGCCGTGGGAGGGCGATCGCATCTGGCTCCCAGTTTTGTGAATGAAGATGGCGTCGA |
| 6.6; 7.1; 8.6 | JX976770.1 | Human coxsackievirus B3 isolate CVB3SD2012CHN | 1.00E-39 | 99% | ACCTTGCCGTACACAGTACACTGTATGCGGCTAATCCTAACTGCGGAGCAGATACC |
Detection of fecal indicator bacteria for the water samples of Poyang Lake
| Sampling Site* | Aerobic bacterial Count (CFU/ml) | Total Coliform (CFU/100 ml) | Fecal Coliform (CFU/100 ml) | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Oct. | Nov. | Dec. | Jan. | Oct. | Nov. | Dec. | Jan. | Oct.. | Nov. | Dec. | Jan. | |
| 1 | 3.1 × 104 | 1.4 × 104 | 5.0 × 101 | 5.0 × 101 | 0 | 2.2 × 105 | 0 | 0 | 0 | 2.4 × 105 | 0 | 0 |
| 2 | 1.9 × 102 | 1.2 × 102 | 1.0 × 101 | 0.5 × 101 | 0 | 1 × 102 | 0 | 0 | 0 | 1 × 102 | 0 | 0 |
| 3 | 1.0 × 102 | 9.5 × 102 | 2.0 × 101 | 2.0 × 101 | 0.5 × 102 | 0 | 0 | 0 | 0 | 0 | 0.5 × 103 | 0.5 × 101 |
| 4 | 5.1 × 104 | 4.4 × 104 | 3.7 × 104 | 2.5 × 104 | 1 × 102 | 1 × 102 | 0.5 × 102 | 0 | 1 × 102 | 1 × 102 | 0 | 0 |
| 5 | 3.9 × 102 | 3.0 × 102 | 3.5 × 102 | 2.8 × 102 | 0.5 × 102 | 0.5 × 102 | 2.0 × 102 | 0 | 1 × 102 | 1 × 102 | 0.5 × 102 | 0 |
| 6 | 2.2 × 103 | 1.6 × 103 | 3.1 × 103 | 3.9 × 102 | 0 | 0 | 0 | 0 | 0.5 × 102 | 0.5 × 102 | 0 | 0 |
*1 -Qing Shan zha; 2 - Guan Niao Tai; 3 - Tuo Shan; 4 -Wu Cheng; 5 - Xing Zi; 6 - Du Kou
Correlation of enteric viruses between bacteriological index in Poyang Lake (p < 0.05)
| Spearman’s correlation coefficients ( | ||||
|---|---|---|---|---|
| NoV I | NoV II | EoV | AdV | |
| TC | −0.503(0.196) | −0.353(0.260) | 0.359(0.452) | 0.052(0.921) |
| FC | 0.078(0.878) | −0.685(0.016) | −0.462(0.113) | 0.221(0.618) |
|
| −0.334(0.326) | −0.587(0.088) | 0.213(0.727) | −0.213(0.727) |