Characterization of Norovirus and Other Human Enteric Viruses in Sewage and Stool Samples Through Next-Generation Sequencing

Strubbia, Sofia; Phan, My V. T.; Schaeffer, Julien; Cotten, Matthew; Guyader, Françoise S. Le

doi:10.1007/s12560-019-09402-3

Cited by 40 publications

(30 citation statements)

References 54 publications

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“…From a virological point of view, the analysis of a larger fragment of the RdRp gene in comparison to available studies 12,13,18,19 revealed a high genetic variability of swine NoVs in North East Italy, therefore suggesting that efforts should be made in the generation of longer RdRp swine NoV sequences which are more informative. Clearly, next generation sequencing (NGS) methods, allowing full genome or nearly full genome sequencing, represents the ideal approach, as proven for human NoVs [40][41][42] and animal NoVs 43 . Whether these methods could be applicable for swine NoV, should be tested in future studies.…”

Section: Discussionmentioning

confidence: 99%

Unrevealed genetic diversity of GII Norovirus in the swine population of North East Italy

Cavicchio

Tassoni

Laconi

et al. 2020

Sci Rep

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noroviruses (noVs) are one of the major causative agents of non-bacterial gastroenteritis in humans worldwide. NoVs, belonging to Caliciviridae, are classified into ten genogroups (G) and eight P-groups based on major capsid protein (VP1) and of the RNA-dependent-RNA-polymerase (RdRp), respectively. In swine, the main genogroup and P-group identified are GII and GII.P; which can infect humans too. To date, only one case of GIIP.11 have been identified in swine in Italy while the circulation of other P-types is currently unknown. In the present study, 225 swine faecal samples were collected from 74 swine herds in Veneto region through on-farm monitoring. noV circulation was particularly high in older pigs. The phylogenetic analysis showed the co-circulation of NoVs belonging to two different P-types: GII.P11 and GII.P18, here described for the first time in Italy, presenting an extensive genetic diversity, never described before worldwide. Distinct noV genetic subgroups and unique amino acid mutations were identified for each P-type for the first time. This study demonstrated the co-circulation of diverse swine NoVs subgroups in Italy, raising questions on the origin of such diversity and suggesting that continuous monitoring of swine noVs is needed to track the emergence of potentially zoonotic viruses by recombination events. Food-and water-borne infections, which are mainly manifested with gastroenteritis in humans, represent a significant public health burden. Among food-borne viruses, Noroviruses (NoVs) are a leading pathogen, causing epidemic gastroenteritis cases worldwide 1. Low infectious dose, environmental resistance, strain diversity, and the shedding from asymptomatic persons, render human NoVs highly contagious pathogens. NoVs are transmitted through ingestion of contaminated food or water, either via the faecal-oral route or via airborne particles and contact with contaminated surfaces. NoV belongs to the Caliciviridae family, which includes small non-enveloped viruses of approximately 35 nm in diameter with single stranded positive RNA genome of 7.4-8.3 kb 2. Five genera: Vesivirus, Lagovirus, Sapovirus, Nebovirus and Norovirus as well as unassigned viruses are included in this family 3. Norovirus and Sapovirus genera contain human and animal enteric viruses. The NoV genome possesses 3 Open Reading frames (ORFs) encoding: a polyprotein (ORF1) that by protease processing produces six non-structural proteins, including a RNA-dependent-RNA-polymerase (RdRp), a major capsid protein, VP1 (ORF2), and a minor one, VP2 (ORF3). NoVs are classified into ten genogroups (G) based on the variation of the major capsid protein (VP1), and are further divided into 49 genotypes 3. Due to the recombination events that occur between ORF1 and ORF2, a dual nomenclature based on VP1 and RdRp was recently proposed 3. Based on the RdRp sequence, NoVs are classified into eight P (polymerase)-groups and further divided into 60 P-types. Human NoV infections are caused by GI, GII, and GIV genotypes, with a higher frequency of ...

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Section: Discussionmentioning

confidence: 99%

Unrevealed genetic diversity of GII Norovirus in the swine population of North East Italy

Cavicchio

Tassoni

Laconi

et al. 2020

Sci Rep

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“…In the present study, ultracentrifugation was selected as the concentration methodology since it was previously applied by our team successfully [18,22,24] and its performance showed to be comparable to other methods such as aluminium hydroxide adsorption-precipitation procedure [26]. Currently, RT-qPCR is the golden standard used to study viral loads [26,44,45] from sewage samples but next generation sequencing (NGS) methodologies have emerged strongly in the field in two modalities, sequencing the total virome with or without enrichment [46][47][48] and the NGS sequencing of PCR amplicons [49].…”

Section: Discussionmentioning

confidence: 99%

Epidemiological Surveillance of Norovirus and Rotavirus in Sewage (2016–2017) in Valencia (Spain)

Santiso-Bellón,

Randazzo,

Pérez-Cataluña

et al. 2020

Microorganisms

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The aim of the present study was to perform the molecular epidemiology of rotaviruses and noroviruses detected in sewage samples from a large wastewater facility from the city of Valencia, Spain. A total of 46 sewage samples were collected over a one-year period (September 2016 to September 2017). Norovirus and rotavirus were detected and quantified by RT-qPCR, genotyped by semi-nested RT-PCR and further characterized by sequencing and phylogenetic analyses. Noroviruses and rotaviruses were widely distributed in sewage samples (69.6% for norovirus GI, 76.0% norovirus GII, and 71.7% rotaviruses) and viral loads varied from 4.33 to 5.75 log PCRU/L for norovirus GI, 4.69 to 6.95 log PCRU/L for norovirus GII, and 4.08 to 6.92 log PCRU/L for rotavirus. Overall, 87.5% (28/32) of GI noroviruses could not be genotyped, 6.25% (2/32) of the samples contained GI.2 genotype, and another 6.25% (2/32) were positive for GI.4 genotype. The most common genotype of GII noroviruses was GII.2 (40%, 14/35), followed by GII.6 (8.6%, 3/35) and GII.17 (5.7%, 2/35) while the remaining GII strains could not be typed (45.7%, 16/35). Rotavirus VP4 genotype P[8] was the only one found in 19 out of 33 rotavirus-positive samples (57.7%). G2 was the most prevalent rotavirus VP7 genotype (15.2%, 5/33) followed by G3, G9, and G12, with two positive samples for each genotype (6.1%, 2/33). In one sample both G1 and G2 genotypes were detected simultaneously (3%). The results presented here show that the surveillance of noroviruses and rotaviruses in sewage is useful for the study of their transmission in the population and their molecular epidemiology.

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“…This is even more difficult when studying the viral diversity on a population level, since a large number of clinical and non-clinical samples would need to be sequenced. Various reports have shown that it is possible to detect enteric viruses in wastewater, and also respiratory viruses such as Influenza A, SARS-CoV and SARS-CoV-2 [14][15][16][17][18][19] . This has led to the recognition of the potential of wastewater-based epidemiology as a valuable tool to assess the spread of the disease at a community level.…”

Section: Introductionmentioning

confidence: 99%

Monitoring SARS-CoV-2 circulation and diversity through community wastewater sequencing

Izquierdo-Lara

Elsinga

Heijnen

et al. 2020

Preprint

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The current SARS-CoV-2 pandemic has rapidly become a major global health problem for which public health surveillance is crucial to monitor virus spread. Given the presence of viral RNA in feces in around 40% of infected persons, wastewater-based epidemiology has been proposed as an addition to disease-based surveillance to assess the spread of the virus at the community level. Here we have explored the possibility of using next-generation sequencing (NGS) of sewage samples to evaluate the diversity of SARS-CoV-2 at the community level from routine wastewater testing, and compared these results with the virus diversity in patients from the Netherlands and Belgium. Phylogenetic analysis revealed the presence of viruses belonging to the most prevalent clades (19A, 20A and 20B) in both countries. Clades 19B and 20C were not identified, while they were present in clinical samples during the same period. Low frequency variant (LFV) analysis showed that some known LFVs can be associated with particular clusters within a clade, different to those of their consensus sequences, suggesting the presence of at least 2 clades within a single sewage sample. Additionally, combining genome consensus and LFV analyses we found a total of 57 unique mutations in the SARS-CoV-2 genome which have not been described before. In conclusion, this work illustrates how NGS analysis of wastewater can be used to approximate the diversity of SARS-CoV-2 viruses circulating in a community.

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Characterization of Norovirus and Other Human Enteric Viruses in Sewage and Stool Samples Through Next-Generation Sequencing

Cited by 40 publications

References 54 publications

Unrevealed genetic diversity of GII Norovirus in the swine population of North East Italy

Unrevealed genetic diversity of GII Norovirus in the swine population of North East Italy

Epidemiological Surveillance of Norovirus and Rotavirus in Sewage (2016–2017) in Valencia (Spain)

Monitoring SARS-CoV-2 circulation and diversity through community wastewater sequencing

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