| Literature DB >> 33755873 |
Ke Song1, Xiaojuan Lin2, Yao Liu2, Feng Ji2, Li Zhang2, Peng Chen3, Chenxu Zhao4, Yanyan Song5, Zexin Tao6, Aiqiang Xu2,4.
Abstract
Human sapovirus (SaV) is an important causative agent of nonbacterial gastroenteritis in humans. However, little is known about its circulation in China. To study the prevalence and diversity of human SaV genotypes circulating in eastern China, a 3-year environmental surveillance combined with next generation sequencing (NGS) technology was conducted. A total of 36 raw sewage samples were collected from January 2017 to December 2019 in Jinan and processed. Thirty-five (97.22%) samples were positive for human SaV genome in quantitative RT-PCR assay; 33 (91.67%) samples were positive in nested RT-PCR assay on partial capsid VP1 sequence and all amplicons were further analyzed separately by NGS. Among those, ten genotypes belonging to the genogroups of GI, GII, GIV, and GV were identified by NGS, including 4 major genotypes (GI.2, GI.1, GV.1 and GI.3) and 6 uncommon genotypes (GII.5, GII.1, GII.NA1, GII.3, GI.6 and GIV.1). A temporal switch of predominant genotype was observed from GI.2 to GI.1 around June 2019. Local and foreign sequences clustered together in some branches according to phylogenetic analysis, indicating frequent transmission of various lineages in different regions of the world. Environmental surveillance provides a comprehensive picture of human SaV in China. NGS-based environmental surveillance improves our knowledge on human SaV circulating in communities greatly and should be encouraged as a sensitive surveillance tool.Entities:
Keywords: Environmental surveillance; Human sapovirus; Next generation sequencing; Phylogenetics
Year: 2021 PMID: 33755873 PMCID: PMC7985922 DOI: 10.1007/s12560-021-09469-x
Source DB: PubMed Journal: Food Environ Virol ISSN: 1867-0334 Impact factor: 2.778
Fig. 1Sapovirus concentration (copies per liter) in sewage monthly from January 2017 to December 2019, by month (a) and by season (b). The sample collected in February 2019 was negative in SaV qRT-PCR assay, and is not included in b
Fig. 2Sapovirus genotype distribution in sewage samples from NGS in three years (a). Monthly distribution of major genotypes (>1% of monthly identified sequences) in raw sewage in Jinan, China from 2017 to 2019 (b)
The number of sapovirus reads detected in raw sewage, by month and by genotype
| Genotype | 2017 | 2018 | 2019 | Viral detection frequency (%) | ||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Jan | Feb | Mar | Apr | May | Jun | Jul | Aug | Sept | Oct | Nov | Dec | Jan | Feb | Mar | Apr | May | Jun | Jul | Aug | Oct | Nov | Dec | Jan | Mar | Apr | May | Jun | Jul | Aug | Oct | Nov | Dec | ||
| GI.1 | 2.9E+06 | 1.9E+06 | 9.7E+06 | 1.3E+06 | 4.4E+05 | 1.2E+06 | 4.7E+06 | 3.7E+06 | 6.7E+05 | 8.6E+04 | 2.7E+06 | 3.9E+06 | 6.0E+05 | 4.1E+06 | 4.9E+06 | 7.2E+06 | 5.1E+06 | 8.4E+06 | 9.2E+06 | 1.2E+07 | 20/33 (60.61) | |||||||||||||
| GI.2 | 3.2E+06 | 8.1E+06 | 9.1E+06 | 2.6E+04 | 8.3E+06 | 8.5E+06 | 7.9E+06 | 9.2E+06 | 8.5E+06 | 1.7E+06 | 7.8E+06 | 3.8E+06 | 5.8E+06 | 1.0E+07 | 6.3E+06 | 7.7E+06 | 7.9E+06 | 9.7E+06 | 9.5E+06 | 9.0E+06 | 8.8E+06 | 7.1E+06 | 4.2E+03 | 1.2E+07 | 1.1E+07 | 7.9E+06 | 4.4E+06 | 6.3E+05 | 6.6E+04 | 1.6E+06 | 30/33 (90.91) | |||
| GI.3 | 3.2E+06 | 1.9E+04 | 7.3E+01 | 7.1E+01 | 9.7E+02 | 1.9E+05 | 1.1E+05 | 8.2E+01 | 9.3E+01 | 6.9E+05 | 4.8E+02 | 3.4E+04 | 12/33 (36.36) | |||||||||||||||||||||
| GI.6 | 3.9E+03 | 1/33 (3.03) | ||||||||||||||||||||||||||||||||
| GII.1 | 1.7E+02 | 6.2E+01 | 1.5E+02 | 7.9E+01 | 9.6E+01 | 8.6E+01 | 1.8E+04 | 1.1E+03 | 8/33 (24.24) | |||||||||||||||||||||||||
| GII.3 | 8.7E+01 | 1.2E+02 | 8.8E+01 | 3.4E+03 | 7.2E+01 | 8.8E+01 | 9.5E+01 | 6.7E+01 | 2.2E+02 | 1.1E+02 | 10/33 (30.30) | |||||||||||||||||||||||
| GII.5 | 4.6E+04 | 1.2E+03 | 5.8E+03 | 1.4E+04 | 2.4E+03 | 8.0E+01 | 9.3E+01 | 8.7E+02 | 4.6E+02 | 1.1E+03 | 10/33 (30.30) | |||||||||||||||||||||||
| GII.NA1 | 7.4E+01 | 3.8E+03 | 3.1E+02 | 9.0E+01 | 4/33 (12.12) | |||||||||||||||||||||||||||||
| GIV.1 | 1.6E+02 | 1/33 (3.03) | ||||||||||||||||||||||||||||||||
| GV.1 | 6.7E+05 | 2.4E+04 | 5.1E+05 | 3.5E+05 | 2.8E+06 | 4.9E+05 | 1.2E+07 | 1.6E+05 | 8.1E+01 | 7.6E+01 | 1.5E+04 | 11/33 (33.33) | ||||||||||||||||||||||
Fig. 3The Simpson’s diversity index and the number of genotypes monthly in three years
Fig. 4Phylogenetic tree of sapovirus strains based on partial VP1 nucleotide sequences (nt position 5179–5571 corresponding to strain Hu/SaV/Manchester/1993/UK with accession number X86560). The tree was generated using the Neighbor-Joining method with Kimura 2-parameter model and gamma-distributed rates in MegaX, with representative strains derived from sewage in Jinan, China, and reference strains from GenBank. The time of sequences detected in present study is characterized as different shapes: (filled square) for 2017; (filled circle) for 2018; and (filled triangle) for 2019. The origin of sequences in the tree was presented in other shapes: (filled star) from human stool; (open star) from sewage; and (filled inverted triangle) from shellfishes