Coronavirus in water environments: Occurrence, persistence and concentration methods – A scoping review

Authors

Giuseppina La Rosa, Lucia Bonadonna, Luca Lucentini, Sebastien Kenmoe, Elisabetta Suffredini

Coronaviruses (CoV) are a large family of viruses causing a spectrum of disease ranging from the common cold to more severe diseases as Middle East Respiratory Syndrome (MERS-CoV) and Severe Acute Respiratory Syndrome (SARS-CoV). The recent outbreak of coronavirus disease 2019 (COVID-19) has become a public health emergency worldwide. SARS-CoV-2, the virus responsible for COVID-19, is spread by human-to-human transmission via droplets or direct contact. However, since SARS-CoV-2 (as well as other coronaviruses) has been found in the fecal samples and anal swabs of some patients, the possibility of fecal-oral (including waterborne) transmission need to be investigated and clarified.

This scoping review was conducted to summarize research data on CoV in water environments. A literature survey was conducted using the electronic databases PubMed, EMBASE, and Web Science Core Collection. This comprehensive research yielded more than 3000 records, but only 12 met the criteria and were included and discussed in this review.

In detail, the review captured relevant studies investigating three main areas: 1) CoV persistence/survival in waters; 2) CoV occurrence in water environments; 3) methods for recovery of CoV from waters.

The data available suggest that: i) CoV seems to have a low stability in the environment and is very sensitive to oxidants, like chlorine; ii) CoV appears to be inactivated significantly faster in water than non-enveloped human enteric viruses with known waterborne transmission; iii) temperature is an important factor influencing viral survival (the titer of infectious virus declines more rapidly at 23°C–25 °C than at 4 °C); iv) there is no current evidence that human coronaviruses are present in surface or ground waters or are transmitted through contaminated drinking-water; v) further research is needed to adapt to enveloped viruses the methods commonly used for sampling and concentration of enteric, non enveloped viruses from water environments.

The evidence-based knowledge reported in this paper is useful to support risk analysis processes within the drinking and wastewater chain (i.e., water and sanitation safety planning) to protect human health from exposure to coronavirus through water.

Metagenomic Analysis of the Diversity of DNA Viruses in the Surface and Deep Sea of the South China Sea

Authors

Yantao Liang, Long Wang, Zengmeng Wang, Jiulong Zhao, Qingwei Yang, Min Wang, Kaiguang Yang, Lihua Zhang, Nianzhi Jiao, and Yongyu Zhang

A metagenomic analysis of the viral community from five surface and five deep sea water (>2000 m below the surface, mbs) samples collected from the central basin of the South China Sea and adjacent Northwest Pacific Ocean during July–August 2017 was conducted herein. We builded up a South China Sea DNA virome (SCSV) dataset of 29,967 viral Operational Taxonomic Units (vOTUs), which is comparable to the viral populations from the original Tara Ocean and Malaspina expeditions. The most abundant and widespread viral populations were from the uncultivated viruses annotated from the viral metagenomics. Only 74 and 37 vOTUs have similarity with the reported genomes from the cultivated viruses and the single-virus genomics, respectively. The community structures of deep sea viromes in the SCSV were generally different from the surface viromes. The carbon flux and nutrients (PO₄ and NOx) were related to the surface and deep sea viromes in the SCSV, respectively. In the SCSV, the annotated vOTUs could be affiliated to the cultivated viruses mainly including Pelagibacter (SAR11) phage HTVC010P, Prochlorococcus phages (P-GSP1, P-SSM4, and P-TIM68), Cyanophages (MED4-184 and MED4-117) and Mycobacterium phages (Sparky and Squirty). It indicated that phage infection to the SAR11 cluster may occur ubiquitously and has significant impacts on bathypelagic SAR11 communities in the deep sea. Meanwhile, as Prochlorococcus is prominently distributed in the euphotic ocean, the existence of their potential phages in the deep sea suggested the sedimentation mechanism might contribute to the formation of the deep sea viromes. Intriguingly, the presence of Mycobacterium phages only in the deep sea viromes, suggests inhabitance of endemic viral populations in the deep sea viromes in the SCSV. This study provided an insight of the viral community in the South China Sea and for the first time uncovered the deep sea viral diversity in the central basin of the South China Sea.

Distribution patterns of bacterial communities and their potential link to variable viral lysis in temperate freshwater reservoirs

Authors

Angia Sriram Pradeep Ram, Jitendra Keshri, Telesphore Sime-Ngando

Man-made reservoirs which receive substantial inputs of terrestrial organic matter are characterized by physiologically diverse and distinct bacterial communities. Here we examined bacterial community structure using Illumina MiSeq sequencing of 16S rRNA genes and evaluated the potential role of viruses in influencing them in two productive freshwater reservoirs namely, Villerest and Grangent (Central France). Two dimensional non-metric multidimensional scaling analyses indicated that bacterial communities in both reservoirs were structurally different in time and space, with Villerest harboring more diverse communities than Grangent reservoir. The bacterial communities in both reservoirs were dominated by hgcI clade (Actinobacteria) and Limnohabitans (Betaproteobacteria) which are known to have adaptive life strategies towards top-down mechanisms and resource utilization. In Villerest, thermal stratification of water column which resulted in temporary anoxia especially during summer promoted the occurrence of anoxygenic phototrophic and methanotrophic bacteria. Overall, low bacterial richness which was linked to viral lytic infection possibly suggests that a relatively small number of highly active bacterial populations sustained high bacterial activity and viral abundances. Weighted UniFrac analysis indicated that a minimum threshold viral infection and virus-to-bacteria ratio (serve as a proxy) of 10% and 10, respectively, is required to exert its impact on phylogenetic structure of bacterial community. Therefore depending on the levels of viral infection we suggest that viruses at times can prevail over other trophic or top-down factors in shaping and structuring bacterial communities in such man-made artificial freshwater systems.

Cyanophage Propagation in the Freshwater Cyanobacterium Phormidium Is Constrained by Phosphorus Limitation and Enhanced by Elevated pCO2

Authors

Kai Cheng, Thijs Frenken, Corina P. D. Brussaard and Dedmer B. Van de Waal

Intensification of human activities has led to changes in the availabilities of CO₂ and nutrients in freshwater ecosystems, which may greatly alter the physiological status of phytoplankton. Viruses require hosts for their reproduction and shifts in phytoplankton host physiology through global environmental change may thus affect viral infections as well. Various studies have investigated the impacts of single environmental factors on phytoplankton virus propagation, yet little is known about the impacts of multiple factors, particularly in freshwater systems. We therefore tested the combined effects of phosphorus limitation and elevated pCO₂ on the propagation of a cyanophage infecting a freshwater cyanobacterium. To this end, we cultured Phormidium in P-limited chemostats under ambient (400 μatm) and elevated (800 μatm) pCO₂ at growth rates of 0.6, 0.3, and 0.05 d^-1. Host C:P ratios generally increased with strengthened P-limitation and with elevated pCO₂. Upon host steady state conditions, virus growth characteristics were obtained in separate infection assays where hosts were infected by the double-stranded DNA cyanophage PP. Severe P-limitation (host growth 0.05 d^-1) led to a 85% decrease in cyanophage production rate and a 73% decrease in burst size compared to the 0.6 d^-1 grown P-limited cultures. Elevated pCO₂ induced a 96% increase in cyanophage production rate and a 57% increase in burst size, as well as an 85% shorter latent period as compared to ambient pCO₂ at the different host growth rates. In addition, elevated pCO₂ caused a decrease in the plaquing efficiency and an increase in the abortion percentage for the 0.05 d^-1 P-limited treatment, while the plaquing efficiency increased for the 0.6 d^-1 P-limited cultures. Together, our results demonstrate interactive effects of elevated pCO₂ and P-limitation on cyanophage propagation, and show that viral propagation is generally constrained by P-limitation but enhanced with elevated pCO₂. Our findings indicate that global change will likely have a severe impact on virus growth characteristics and thereby on the control of cyanobacterial hosts in freshwater ecosystems.

Precipitation of calcium carbonate mineral induced by viral lysis of cyanobacteria: evidence from laboratory experiments

Authors

Hengchao Xu, Xiaotong Peng, Shijie Bai, Kaiwen Ta, Shouye Yang, Shuangquan Liu, Ho Bin Jang, and Zixiao Guo

Viruses have been acknowledged as being important components of the marine system for the past 2 decades, but their role in the functioning of the geochemical cycle has not been thoroughly elucidated to date. Virus-induced rupturing of cyanobacteria is theoretically capable of releasing intracellular bicarbonate and inducing the homogeneous nucleation of calcium carbonate; however, experiment-based support for virus-induced calcification is lacking. In this laboratory study, both water carbonate chemistry and precipitates were monitored during the viral infection and lysis of host cells. Our results show that viral lysis of cyanobacteria can influence the carbonate equilibrium system remarkably and promotes the formation and precipitation of carbonate minerals. Amorphous calcium carbonate (ACC) and aragonite were evident in the lysate, compared with the Mg(OH)₂ (brucite in this paper) precipitate in noninfected cultures, implying that a different precipitation process had occurred. Based on the carbonate chemistry change and microstructure of the precipitation, we propose that viral lysis of cyanobacteria can construct a calcification environment where carbonate is the dominant inorganic carbon species. Numerous virus particles available in lysate may coprecipitate with the calcium carbonate. The experimental results presented in this study demonstrate both the pathway and the outcome with respect to how viruses influence the mineralization of carbonate minerals. It is suggested that viral calcification offers new perspectives on mechanisms of CaCO₃ biomineralization and may play a crucial role within the Earth system.

New insight into the RNA aquatic virosphere via viromics

Author

Alexander Culley

RNA viruses that infect microbes are now recognized as an active, persistent and important component of the aquatic microbial community. While some information about the diversity and dynamics of the RNA virioplankton has been derived from culture-based and single gene approaches, research based on viromic and metatransciptomic methods has generated unprecedented insight into this relatively understudied class of microbes. Here, the relevant literature is summarized and discussed, including viromic studies of extracellular aquatic RNA viral assemblages, and transcriptomic studies of active and associated RNA viruses from aquatic environments followed by commentary on the present challenges and future directions of this field of research.

Host Traits Drive Viral Life Histories across Phytoplankton Viruses

Authors

Kyle F. Edwards and Grieg F. Steward

Viruses are integral to ecological and evolutionary processes, but we have a poor understanding of what drives variation in key traits across diverse viruses. For lytic viruses, burst size, latent period, and genome size are primary characteristics controlling host-virus dynamics. Here we synthesize data on these traits for 75 strains of phytoplankton viruses, which play an important role in global biogeochemistry. We find that primary traits of the host (genome size, growth rate) explain 40%–50% of variation in burst size and latent period. Specifically, burst size and latent period both exhibit saturating relationships versus the host∶virus genome size ratio, with both traits increasing at low genome size ratios while showing no relationship at high size ratios. In addition, latent period declines as host growth rate increases. We analyze a model of latent period evolution to explore mechanisms that could cause these patterns. The model predicts that burst size may often be set by the host genomic resources available for viral construction, while latent period evolves to permit this maximal burst size, modulated by host metabolic rate. These results suggest that general mechanisms may underlie the evolution of diverse viruses. Future extensions of this work could help explain viral regulation of host populations, viral influence on community structure and diversity, and viral roles in biogeochemical cycles.

Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations

Authors

Jessica Chopyk, Sarah Allard, Daniel J. Nasko, Anthony Bui, Emmanuel F. Mongodin and Amy R. Sapkota

Agricultural ponds have a great potential as a means of capture and storage of water for irrigation. However, pond topography (small size, shallow depth) leaves them susceptible to environmental, agricultural, and anthropogenic exposures that may influence microbial dynamics. Therefore, the aim of this project was to characterize the bacterial and viral communities of pond water in the Mid-Atlantic United States with a focus on the late season (October–December), where decreasing temperature and nutrient levels can affect the composition of microbial communities. Ten liters of freshwater from an agricultural pond were sampled monthly, and filtered sequentially through 1 and 0.2 μm filter membranes. Total DNA was then extracted from each filter, and the bacterial communities were characterized using 16S rRNA gene sequencing. The remaining filtrate was chemically concentrated for viruses, DNA-extracted, and shotgun sequenced. Bacterial community profiling showed significant fluctuations over the sampling period, corresponding to changes in the condition of the pond freshwater (e.g., pH, nutrient load). In addition, there were significant differences in the alpha-diversity and core bacterial operational taxonomic units (OTUs) between water fractions filtered through different pore sizes. The viral fraction was dominated by tailed bacteriophage of the order Caudovirales, largely those of the Siphoviridaefamily. Moreover, while present, genes involved in virulence/antimicrobial resistance were not enriched within the viral fraction during the study period. Instead, the viral functional profile was dominated by phage associated proteins, as well as those related to nucleotide production. Overall, these data suggest that agricultural pond water harbors a diverse core of bacterial and bacteriophage species whose abundance and composition are influenced by environmental variables characteristic of pond topology and the late season.

Geospatial distribution of viromes in tropical freshwater ecosystems

Authors

Xiaoqiong Gu, Qi Xiang Martin Tay, Shu Harn Te, Nazanin Saeidi, Shin Giek Goh, Ariel Kushmaro, Janelle R. Thompson, Karina Yew-Hoong Gin

This study seeks to understand the general distribution of virome abundance and diversity in tropical freshwater ecosystems in Singapore and the geospatial distribution of the virome under different landuse patterns. Correlations between diversity, environmental parameters and land use patterns were analyzed and significant correlations were highlighted. Overall, the majority (65.5%) of the annotated virome belonged to bacteriophages. The percentage of Caudovirales was higher in reservoirs whereas the percentages of Dicistroviridae, Microviridae and Circoviridae were higher in tributaries. Reservoirs showed a higher Shannon-index virome diversity compared to upstream tributaries. Land use (urbanized, agriculture and parkland areas) influenced the characteristics of the virome distribution pattern. Dicistroviridae and Microviridae were enriched in urbanized tributaries while Mimiviridae, Phycodnaviridae, Siphoviridae and Podoviridae were enriched in parkland reservoirs. Several sequences closely related to the emerging zoonotic virus, cyclovirus, and the human-related virus (human picobirnavirus), were also detected. In addition, the relative abundance of PMMoV (pepper mild mottle virus) sequences was significantly correlated with RT-qPCR measurements (0.588 < r < 0.879, p < 0.05). This study shows that spatial factors (e.g., reservoirs/tributaries, land use) are the main drivers of the viral community structure in tropical freshwater ecosystems.

Spatiotemporal dynamics of river viruses, bacteria and microeukaryotes

Authors

Thea Van Rossum, Miguel I Uyaguari-Diaz, Marli Vlok, Michael A Peabody, Alvin Tian, Kirby I Cronin, Micheal Chan, Matthew A Croxen, William WL Hsiao, Judith Isaac-Renton, Patrick KC Tang, Natalie A Prystajecky, Curtis A Suttle, Fiona SL Brinkman

Freshwater is an essential resource of increasing value, as clean water sources diminish. Microorganisms in rivers, a major source of renewable freshwater, are significant due to their role in drinking water safety, signalling environmental contamination, and driving global nutrient cycles. However, a foundational understanding of microbial communities in rivers is lacking, especially temporally and for viruses. No studies to date have examined the composition of the free-floating river virome over time, and explanations of the underlying causes of spatial and temporal changes in riverine microbial composition, especially for viruses, remain unexplored. Here, we report relationships among riverine microbial communities and their environment across time, space, and superkingdoms (viruses, bacteria, and microeukaryotes), using metagenomics and marker-based microbiome analysis methods. We found that many superkingdom pairs were synchronous and had consistent shifts with sudden environmental change. However, synchrony strength, and relationships with environmental conditions, varied across space and superkingdoms. Variable relationships were observed with seasonal indicators and chemical conditions previously found to be predictive of bacterial community composition, emphasizing the complexity of riverine ecosystems and raising questions around the generalisability of single-site and bacteria-only studies. In this first study of riverine viromes over time, DNA viral communities were stably distinct between sites, suggesting the similarity in riverine bacteria across significant geographic distances does not extend to viruses, and synchrony was surprisingly observed between DNA and RNA viromes. This work provides foundational data for riverine microbial dynamics in the context of environmental and chemical conditions and illustrates how a bacteria-only or single-site approach would lead to an incorrect description of microbial dynamics. We show how more holistic microbial community analysis, including viruses, is necessary to gain a more accurate and deeper understanding of microbial community dynamics.