Analysis of complete capsid sequences of the emerging norovirus GII.17 Kawasaki 308 from 13 countries demonstrated that they originated from a single haplotype since the initial emergence in China in late 2014. Global spread of a sublineage SL2 was identified. A new sublineage SL3 emerged in China in 2016.

Aims:  This study investigated the survival and transport of sewage sludge‐borne pathogenic organisms in soils. Methods and Results:  Undisturbed soil cores were treated with Salmonella enterica ssp. enterica serovar Typhimurium‐lux (STM‐lux) and human adenovirus (HAdV)‐spiked sewage sludge. Following an artificial rainfall event, these pathogens were analysed in the leachate and soil sampled from different depths (0–5 cm, 5–10 cm and 10–20 cm) after 24 h, 1 and 2 months. Significantly more STM‐lux and HAdV leached through the soil cores when sewage sludge was present. Significantly more STM‐lux were found at all soil depths, at all time periods in the sewage sludge treatments, compared to the controls. The rate of decline of STM‐lux in the controls was more rapid than in the sewage sludge treatments. Survival and transport of HAdV were minimal. Conclusions:  The presence of sewage sludge can significantly influence the transport and survival of bacterial pathogens in soils, probably because of the presence of organic matter. Environmental contamination by virus is unlikely because of strong soil adsorption. Significance and Impact of the Study:  This study suggests that groundwater contamination from vertical movement of pathogens is a potential risk and that it highlights the importance of the treatment requirements for biosolids prior to their application to land.

bThe etiology of an outbreak of gastroenteritis in humans cannot always be determined, and ϳ25% of outbreaks remain unsolved in New Zealand. It is hypothesized that novel viruses may account for a proportion of unsolved cases, and new unbiased highthroughput sequencing methods hold promise for their detection. Analysis of the fecal metagenome can reveal the presence of viruses, bacteria, and parasites which may have evaded routine diagnostic testing. Thirty-one fecal samples from 26 gastroenteritis outbreaks of unknown etiology occurring in New Zealand between 2011 and 2012 were selected for de novo metagenomic analysis. A total data set of 193 million sequence reads of 150 bp in length was produced on an Illumina MiSeq. The metagenomic data set was searched for virus and parasite sequences, with no evidence of novel pathogens found. Eight viruses and one parasite were detected, each already known to be associated with gastroenteritis, including adenovirus, rotavirus, sapovirus, and Dientamoeba fragilis. In addition, we also describe the first detection of human parechovirus 3 (HPeV3) in Australasia. Metagenomics may thus provide a useful audit tool when applied retrospectively to determine where routine diagnostic processes may have failed to detect a pathogen. Outbreaks of acute gastroenteritis are associated with significant global morbidity and mortality, particularly in pediatric populations (1). Bacterial pathogens are well-described causes of gastroenteritis, e.g., Escherichia coli O157:H7, Salmonella, Campylobacter, and Shigella (2, 3), but are known to occur less frequently than viral pathogens as the cause of acute gastroenteritis (4). Noroviruses, sapoviruses, group A rotaviruses, enteric adenoviruses, and astroviruses have been recognized as the main etiological agents in viral gastroenteritis, although it has been suggested that a number of other viruses may also be involved (5, 6). Parasites such as Dientamoeba fragilis have also been implicated in gastroenteritis; however, there is still debate surrounding their pathogenicity (2, 7).In New Zealand, no causative agent is identified in approximately 25% of reported gastroenteritis outbreaks at the conclusions of public health investigations (8). A proportion of unsolved cases may be due to the presence of a novel pathogen. Viral pathogens are particularly problematic to discover because well-established methods such as electron microscopy, PCR, or viral culture are not always effective; they may be too specific, lack high-throughput capability, or not be sensitive enough to detect low numbers of organisms within a sample (9). High-throughput sequencing holds promise for resolving the etiology of unsolved gastroenteritis outbreaks, as large volumes of unbiased metagenomic data are produced, allowing for the sequences from all viruses, bacteria, parasites, and fungi present in the sample to be revealed (10). Any knowledge gained from identifying previously unknown pathogens causing outbreaks of gastroenteritis will facilitate public health investigati...

To assist public health responses to COVID-19, wastewater-based epidemiology (WBE) is being utilised internationally to monitor SARS-CoV-2 infections at the community level. However, questions remain regarding the sensitivity of WBE and its use in low prevalence settings. In this study, we estimated the total number of COVID-19 cases required for detection of SARS-CoV-2 RNA in wastewater. To do this, we leveraged a unique situation where, over a 4-month period, all symptomatic and asymptomatic cases, in a population of approximately 120,000, were precisely known and mainly located in a single managed isolation and quarantine facility (MIQF) building. From 9 July to 6 November 2020, 24-hr composite wastewater samples ( n = 113) were collected daily from the sewer outside the MIQF, and from the municipal wastewater treatment plant (WWTP) located 5 km downstream. New daily COVID-19 cases at the MIQF ranged from 0 to 17, and for most of the study period there were no cases outside the MIQF identified. SARS-CoV-2 RNA was detected in 54.0% (61/113) at the WWTP, compared to 95.6% (108/113) at the MIQF. We used logistic regression to estimate the shedding of SARS-CoV-2 RNA into wastewater based on four infectious shedding models. With a total of 5 and 10 COVID-19 infectious cases per 100,000 population (0.005 % and 0.01% prevalence) the predicated probability of SARS-CoV-2 RNA detection at the WWTP was estimated to be 28 and 41%, respectively. When a proportional shedding model was used, this increased to 58% and 87% for 5 and 10 cases, respectively. In other words, when 10 individuals were actively shedding SARS-CoV-2 RNA in a catchment of 100,000 individuals, there was a high likelihood of detecting viral RNA in wastewater. SARS-CoV-2 RNA detections at the WWTP were associated with increasing COVID-19 cases. Our results show that WBE provides a reliable and sensitive platform for detecting infections at the community scale, even when case prevalence is low, and can be of use as an early warning system for community outbreaks.

Noroviruses are the most common cause of acute non-bacterial gastroenteritis outbreaks worldwide, including New Zealand. New Zealand has a population of 4.4 million, which allows for centralized outbreak surveillance and a Norovirus Reference Laboratory, which facilitates efficient diagnosis, surveillance, and tracking of norovirus outbreaks. Norovirus outbreak strains are identified, sequenced, and compared with international reference strains. Between January 2002 and December 2009, 1,206 laboratory-confirmed norovirus outbreaks were recorded. The predominant outbreak settings were healthcare institutions for the elderly and acute care patients. Other outbreak settings included catering establishments, cruise ships, homes, community events, school camps, child-related settings, and consumption of contaminated shellfish. Of the 1,206 outbreaks, 105 (8.7%) were caused by norovirus genogroup I (GI) strains, 1,085 (89.9%) were caused by genogroup II (GII) strains, and both GI and GII strains were detected in 9 (0.8%) outbreaks. The genogroup was not identified in 7 (0.6%) outbreaks. A range of norovirus genotypes, including GI genotypes 1-6, GII genotypes 2-8, and GII.12, were associated with these outbreaks. The predominant genotype was GII.4, which was identified in 825 (68.4%) outbreaks. Norovirus GII.4 variant strains, including 2002 (Farmington Hills), 2004 (Hunter), 2006a (Laurens, Yerseke), 2006b (Minerva), and 2010 (New Orleans) implicated in overseas outbreaks also occurred in New Zealand, providing evidence of global spread.