Host obesity impacts genetic variation in influenza A viral populations.

Obesity is well established as a risk factor for many noncommunicable diseases; however, its consequences for infectious disease are poorly understood. Here, we investigated the impact of host obesity on influenza A virus (IAV) genetic variation using a diet-induced obesity ferret model and the A/Hong Kong/1073/1999 (H9N2) strain. Using a co-caging study design, we investigated the maintenance, generation, and transmission of intrahost IAV genetic variation by sequencing viral genomic RNA obtained from nasal wash samples over multiple days of infection. We found evidence for an enhanced role of positive selection acting on de novo mutations in obese hosts that led to nonsynonymous changes that rose to high frequency. In addition, we identified numerous cases of mutations throughout the genome that were specific to obese hosts and that were preserved during transmission between hosts. Despite detection of obese-specific variants, the overall viral genetic diversity did not differ significantly between obese and lean hosts. This is likely due to the high supply rate of de novo variation and common evolutionary adaptations to the ferret host regardless of obesity status, which we show are mediated by variation in the hemagglutinin and polymerase genes (PB2 and PB1). We also identified defective viral genomes (DVGs) that were found uniquely in either obese or lean hosts, but the overall DVG diversity and dynamics did not differ between the two groups. Our study suggests that obesity may result in a unique selective environment impacting intrahost IAV evolution, highlighting the need for additional genetic and functional studies to confirm these effects.IMPORTANCEObesity is a chronic health condition characterized by excess adiposity leading to a systemic increase in inflammation and dysregulation of metabolic hormones and immune cell populations. Influenza A virus (IAV) is a highly infectious pathogen responsible for seasonal and pandemic influenza. Host risk factors, including compromised immunity and pre-existing health conditions, can contribute to increased infection susceptibility and disease severity. During viral replication in a host, the negative-sense single-stranded RNA genome of IAV accumulates genetic diversity that may have important consequences for viral evolution and transmission. Our study provides the first insight into the consequences of host obesity on viral genetic diversity and adaptation, suggesting that host factors associated with obesity alter the selective environment experienced by a viral population, thereby impacting the spectrum of genetic variation.

Genetic complementation fosters evolvability in complex fitness landscapes.

The ability of natural selection to optimize traits depends on the topology of the genotype-fitness map (fitness landscape). Epistatic interactions produce rugged fitness landscapes, where adaptation is constrained by the presence of low-fitness intermediates. Here, we used simulations to explore how evolvability in rugged fitness landscapes is influenced by genetic complementation, a process whereby different sequence variants mutually compensate for their deleterious mutations. We designed our model inspired by viral populations, in which genetic variants are known to interact frequently through coinfection. Our simulations indicate that genetic complementation enables a more efficient exploration of rugged fitness landscapes. Although this benefit may be undermined by genetic parasites, its overall effect on evolvability remains positive in populations that exhibit strong relatedness between interacting sequences. Similar processes could operate in contexts other than viral coinfection, such as in the evolution of ploidy.

Limbal advancement technique in managing acute or impending peripheral corneal perforations.

Purpose: To describe the outcomes of a novel technique for the repair of peripheral corneal perforations using autologous limbal tissue. Methods: Two patients with peripheral corneal perforations with contraindications to other corneal procedures underwent limbal advancements. This technique involves creating a pedicle of the limbus, sclera and conjunctiva to cover the perforation. Results: The tissue had optimal integration in both patients; no aqueous leaks or flat anterior chambers were noted. None of the patients had recurrence of perforation or ocular discomfort. Conclusion: In conclusion, this technique is a cost-effective and straightforward alternative for the repair of impending acute peripheral perforations.

Cooperative Virus-Virus Interactions: An Evolutionary Perspective.

Despite extensive evidence of virus-virus interactions, not much is known about their biological significance. Importantly, virus-virus interactions could have evolved as a form of cooperation or simply be a by-product of other processes. Here, we review and discuss different types of virus-virus interactions from the point of view of social evolution, which provides a well-established framework for interpreting the fitness costs and benefits of such traits. We also classify interactions according to their mechanisms of action and speculate on their evolutionary implications. As in any other biological system, the evolutionary stability of viral cooperation critically requires cheaters to be excluded from cooperative interactions. We discuss how cheater viruses exploit cooperative traits and how viral populations are able to counteract this maladaptive process.

The role of spatial structure in the evolution of viral innate immunity evasion: A diffusion-reaction cellular automaton model.

Most viruses have evolved strategies for preventing interferon (IFN) secretion and evading innate immunity. Recent work has shown that viral shutdown of IFN secretion can be viewed as a social trait, since the ability of a given virus to evade IFN-mediated immunity depends on the phenotype of neighbor viruses. Following this idea, we investigate the role of spatial structure in the evolution of innate immunity evasion. For this, we model IFN signaling and viral spread using a spatially explicit approximation that combines a diffusion-reaction model and cellular automaton. Our results indicate that the benefits of preventing IFN secretion for a virus are strongly determined by spatial structure through paracrine IFN signaling. Therefore, innate immunity evasion can evolve as a cooperative or even altruistic trait based on indirect fitness effects that IFN shutdown exerts on other members of the viral population. We identify key factors determining whether evasion from IFN-mediated immunity should evolve, such as population bottlenecks occurring during viral transmission, the relative speed of cellular infection and IFN secretion, and the diffusion properties of the medium.

The effect of genetic complementation on the fitness and diversity of viruses spreading as collective infectious units.

Viruses can spread collectively using different types of structures such as extracellular vesicles, virion aggregates, polyploid capsids, occlusion bodies, and even cells that accumulate virions at their surface, such as bacteria and dendritic cells. Despite the mounting evidence for collective spread, its implications for viral fitness and diversity remain poorly understood. It has been postulated that, by increasing the cellular multiplicity of infection, collective spread could enable mutually beneficial interactions among different viral genetic variants. One such interaction is genetic complementation, whereby deleterious mutations carried by different genomes are compensated. Here, we used simulations to evaluate whether complementation is likely to increase the fitness of viruses spreading collectively. We show that complementation among co-spreading viruses initially buffers the deleterious effects of mutations, but has no positive effect on mean population fitness over the long term, and even promotes error catastrophe at high mutation rates. Additionally, we found that collective spread increases the risk of invasion by social cheaters such as defective interfering particles. We also show that mutation accumulation depends on the type of collective infectious units considered. Co-spreading viral genomes produced in the same cell (e.g. extracellular vesicles, polyploid capsids, occlusion bodies) should exhibit higher genetic relatedness than groups formed extracellularly by viruses released from different cells (aggregates, binding to bacterial or dendritic cell surfaces), and we found that increased relatedness limits the adverse effects of complementation as well cheater invasion risk. Finally, we found that the costs of complementation can be offset by recombination. Based on our results, we suggest that alternative factors promoting collective spread should be considered.

Social evolution of innate immunity evasion in a virus.

Antiviral immunity has been studied extensively from the perspective of virus-cell interactions, yet the role of virus-virus interactions remains poorly addressed. Here, we demonstrate that viral escape from interferon (IFN)-based innate immunity is a social process in which IFN-stimulating viruses determine the fitness of neighbouring viruses. We propose a general and simple social evolution framework to analyse how natural selection acts on IFN shutdown and validate it in cell cultures and mice infected with vesicular stomatitis virus. Furthermore, we find that IFN shutdown is costly because it reduces short-term viral progeny production, thus fulfilling the definition of an altruistic trait. Hence, in well-mixed populations, the IFN-blocking wild-type virus is susceptible to invasion by IFN-stimulating variants and spatial structure consequently determines whether IFN shutdown can evolve. Our findings reveal that fundamental social evolution rules govern viral innate immunity evasion and virulence and suggest possible antiviral interventions.

Beneficial coinfection can promote within-host viral diversity.

In many viral infections, a large number of different genetic variants can coexist within a host, leading to more virulent infections that are better able to evolve antiviral resistance and adapt to new hosts. But how is this diversity maintained? Why do faster-growing variants not outcompete slower-growing variants, and erode this diversity? One hypothesis is if there are mutually beneficial interactions between variants, with host cells infected by multiple different viral genomes producing more, or more effective, virions. We modelled this hypothesis with both mathematical models and simulations, and found that moderate levels of beneficial coinfection can maintain high levels of coexistence, even when coinfection is relatively rare, and when there are significant fitness differences between competing variants. Rare variants are more likely to be coinfecting with a different variant, and hence beneficial coinfection increases the relative fitness of rare variants through negative frequency dependence, and maintains diversity. We further find that coexisting variants sometimes reach unequal frequencies, depending on the extent to which different variants benefit from coinfection, and the ratio of variants which leads to the most productive infected cells. These factors could help drive the evolution of defective interfering particles, and help to explain why the different segments of multipartite viruses persist at different equilibrium frequencies.

Detection of human-derived fecal contamination in Puerto Rico using carbamazepine, HF183 Bacteroides, and fecal indicator bacteria.

The level of fecal pollution in 17 sites in Puerto Rico was determined by Escherichia coli (E.coli) enumeration using an enzyme substrate medium and Quanti-Tray®/2000. Human fecal pollution was identified using an enzyme-linked immunosorbent assay for the detection of carbamazepine (CBZ) and quantitative polymerase chain reaction (qPCR) detection of the human Bacteroides marker, HF183. Carbamazepine was detected in 16 out of 17 sites, including Condado Lagoon, a popular recreational area. Elevated E.coli levels (>410 CFU 100 mL(-1)) were detected in 13 sites. Average CBZ concentrations ranged from 0.005 µg L(-1) to 0.482 µg L(-1) and 7 sites were positive for HF183. Higher CBZ concentrations were associated with the detection of HF183 (Mann-Whitney test; U=42.0; df=7; 1-tailed P value=0.013). This was the second study to determine surface water concentrations of CBZ in the Caribbean and the first in Puerto Rico.

Detection of Helicobacter pylori in the coastal waters of Georgia, Puerto Rico and Trinidad.

Fecal pollution in the coastal marine environments was assessed at eleven sampling locations along the Georgia coast and Trinidad, and nine sites from Puerto-Rico. Membrane filtration (EPA method 1604 and method 1600) was utilized for Escherichia coli and enterococci enumeration at each location. Quantitative polymerase chain reaction (qPCR) amplification of the 16S ribosomal RNA gene was used to determine the presence of the Helicobacter pylori in marine samples. There was no significant correlation between the levels of E. coli, enterococci and H. pylori in these water samples. H. pylori was detected at four of the 31 locations sampled; Oak Grove Island and Village Creek Landing in Georgia, Maracas river in Trinidad, and Ceiba Creek in Puerto Rico. The study confirms the potential public health risk to humans due to the widespread distribution of H. pylori in subtropical and tropical costal marine waters.

Detection of verotoxin producing Escherichia coli in marine environments of the Caribbean.

The goal of this study was to determine the potential for Enterohemorrhagic Escherichia coli O157:H7 (EHEC) contamination in tropical marine waters. Samples were collected from urban, suburban, and rural sites around the islands of Puerto Rico and The Republic of Trinidad and Tobago. Quantification of E. coli and EHEC was evaluated using MI plates and qPCR. EHEC was detected in six sites in Puerto Rico: West of La Parguera Town, Boquilla, Oro Creek, Fishers Association, Joyuda Lagoon, and Boqueron Wetland Creek and in two rural sites in Trinidad: Balandra Bay and Quinam Bay. Plate count enumeration of E. coli was not a reliable indicator for the presence of EHEC. The sites where EHEC was detected on both islands are used for recreational bathing, water sports and recreational/commercial fisheries and therefore pose a public potential health risk.

Molecular detection of atrazine catabolism gene atzA in coastal waters of Georgia, Puerto Rico and Trinidad.

In this study, quantitative polymerase chain reaction targeting the atrazine catabolism gene, atzA, was used to detect the presence of atrazine degrading bacteria as an indicator of atrazine contamination in 11 sites in Georgia, nine coastal sites in Puerto Rico and 11 coastal sites in Trinidad. The atzA gene was detected in five stations in Georgia (Oak Grove Island entrance, Blythe Island Recreation Park, Jekyll Island., Village Creek Landing and Dunbar Creek Sea Island Rd Bridge). In Puerto Rico gene was detected in five sites (Boquilla, Oro Creek, Fishers Association, Ceiba Creek and Sabalos Creek) while seven sites in Trinidad (Carli Bay, Las Cuevas Bay, Quinam Bay, Salybia River, Salybia Bay, Maracas River and Maracas Bay) showed the presence of atzA.

Coastal bacterioplankton community diversity along a latitudinal gradient in Latin America by means of V6 tag pyrosequencing.

The bacterioplankton diversity of coastal waters along a latitudinal gradient between Puerto Rico and Argentina was analyzed using a total of 134,197 high-quality sequences from the V6 hypervariable region of the small-subunit ribosomal RNA gene (16S rRNA) (mean length of 60 nt). Most of the OTUs were identified into Proteobacteria, Bacteriodetes, Cyanobacteria, and Actinobacteria, corresponding to approx. 80% of the total number of sequences. The number of OTUs corresponding to species varied between 937 and 1946 in the seven locations. Proteobacteria appeared at high frequency in the seven locations. An enrichment of Cyanobacteria was observed in Puerto Rico, whereas an enrichment of Bacteroidetes was detected in the Argentinian shelf and Uruguayan coastal lagoons. The highest number of sequences of Actinobacteria and Acidobacteria were obtained in the Amazon estuary mouth. The rarefaction curves and Good coverage estimator for species diversity suggested a significant coverage, with values ranging between 92 and 97% for Good coverage. Conserved taxa corresponded to aprox. 52% of all sequences. This study suggests that human-contaminated environments may influence bacterioplankton diversity.

Comparison of four polymerase chain reaction methods for the rapid detection of human fecal pollution in marine and inland waters.

We compared the effectiveness of three PCR protocols for the detection of Bifidobacterium adolescentis and one PCR protocol for detecting Bacteroidales as indicators of human fecal pollution in environmental samples. Quantitative PCR indicated that a higher concentration of B. adolescentis DNA was recovered from sewage samples on the 0.2 mum filters compared to the 0.45 mum filters, and there was no evidence of qPCR inhibitors in the DNA extracts. With the Matsuki method (1999), B. adolescentis was detected only in undiluted sewage samples. The King method (2007) performed well and detected B. adolescentis in all of the sewage dilutions (from undiluted to 10(-4)). In contrast, the Bonjoch approach (2004) was effective at detecting B. adolescentis at lower dilutions (10(-3)) of sewage samples and it gave false positive results with some (3/8) pig fecal samples. Human-specific Bacteroidales (HuBacs) were detected in the lower diluents of sewage samples but was positive in pig (6/8) and cattle fecal samples. PCR detection of B. adolescentis in marine samples from Puerto Rico and freshwater samples from Georgia indicated that the PCR method of King et al. (2007) and the modified Layton method for HuBac were in agreement in detecting human fecal pollution in most sites.

Assessment of non-point sources of fecal pollution in coastal waters of Puerto Rico and Trinidad.

Traditional and molecular methods (PCR) were used to detect, quantify and identify the source of fecal pollution in coastal sites of Puerto Rico and Trinidad. Enterococci and Escherichia coli standard plate counts were used as a general indicator of fecal contamination while the PCR detection of Bifidobacteria adolescentis and human or bovine specific Bacteroidales were used to examine potential sources. Seven of 14 sites in Trinidad including Maracas Bay which is a major public beach contained significant fecal contamination based on enterococci numbers counts exceeding established thresholds for areas of direct contact. Forty six percent of the 27 stations in Puerto Rico were over the established thresholds for enterococci and 49% according to E. coli counts. About 31% of the stations examined in Puerto Rico had evidence of human derived fecal contamination. Human fecal pollution was detected in only one station from Trinidad. Bovine derived contamination was detected only once.

Contamination of Caribbean coastal waters by the antifouling herbicide Irgarol 1051.

Irgarol 1051 is a s-triazine herbicide used in popular slime-resistant antifouling paints. It has been shown to be acutely toxic to corals, mangroves and sea grasses, inhibiting photosynthesis at low concentrations (>50 ng l(-1)). We present the first data describing the occurrence of Irgarol 1051 in coastal waters of the Northeastern Caribbean (Puerto Rico (PR) and the US Virgin Islands (USVI)). Low level contamination of coastal waters by Irgarol 1051 is reported, the herbicide being present in 85% of the 31 sites sampled. It was not detected in water from two oceanic reference sites. In general, Irgarol 1051was present at concentrations below 100 ng l(-1), although far higher concentrations were reported at three locations within Benner Bay, USVI (223-1,300 ng l(-1)). The known toxicity of Irgarol 1051 to corals and sea grasses and our findings of significant contamination of the Northeastern Caribbean marine environment by this herbicide underscore the importance of understanding, more fully, local and regional exposure of reef and sea grass habitats to Irgarol 1051 and, where necessary, implementing actions to ensure adequate protection of these important ecosystems.

Chlorophyll a and turbidity patterns over coral reefs systems of La Parguera Natural Reserve, Puerto Rico

Abstract:Studies of temporal and spatial changes in phytoplankton biomass and turbidity provide essential information on coral reef ecosystem function and health.Fluctuation of phytoplankton biomass responds to several factors including nutrient inputs,both anthropogenic and natural,while turbidity is mostly affected by sediment resuspension or transport from terrestrial systems.These parameters can be used as sentinels of significant environmental factors "modifying "coral reef systems.A chlorophyll a concentration (Chl a )and turbidity (Turb)in situ logger was installed at 10 stations from June 4 to July 7,2003 in La Parguera Natural Reserve (Southwestern Puerto Rico)to assess short-term temporal and geographic variation in patterns of phytoplankton biomass and turbidity at pre-selected sites as part of an interdisciplinary long-term study.Average station Chl a variation was 0.17-1.12 µg l-1 and 0.2-23.4 NTU for Turb.Results indicate that the western near-coastal stations had higher levels of Turb and Chl a .The easternmost mid shelf station,Romero reef,was similar to coastal stations probably due to nutrient and suspended sediment inputs from a source external to our study area to the east,Guánica Bay.Comparisons between different sampling days indicate significant differences between days for most stations suggesting that one-time discrete sampling may not be representative of average water column conditions and illustrate the dynamic nature of coral reef systems.Further work is warranted to assess seasonal changes that integrate short-term (daily)variability in both Turb and Chl a.