Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria

Effective infectious disease surveillance in high-risk regions is critical for clinical care and pandemic preemption; however, few clinical diagnostics are available for the wide range of potential human pathogens. Here, we conduct unbiased metagenomic sequencing of 593 samples from febrile Nigerian patients collected in three settings: i) population-level surveillance of individuals presenting with symptoms consistent with Lassa Fever (LF); ii) real-time investigations of outbreaks with suspected infectious etiologies; and iii) undiagnosed clinically challenging cases. We identify 13 distinct viruses, including the second and third documented cases of human blood-associated dicistrovirus, and a highly divergent, unclassified dicistrovirus that we name human blood-associated dicistrovirus 2. We show that pegivirus C is a common co-infection in individuals with LF and is associated with lower Lassa viral loads and favorable outcomes. We help uncover the causes of three outbreaks as yellow fever virus, monkeypox virus, and a noninfectious cause, the latter ultimately determined to be pesticide poisoning. We demonstrate that a local, Nigerian-driven metagenomics response to complex public health scenarios generates accurate, real-time differential diagnoses, yielding insights that inform policy.

Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: a guide and case study in setting up an emergency-use, laboratory-developed molecular microbiological assay

Developing and deploying new diagnostic tests are difficult, but the need to do so in response to a rapidly emerging pandemic such as COVID-19 is crucially important. During a pandemic, laboratories play a key role in helping healthcare providers and public health authorities detect active infection, a task most commonly achieved using nucleic acid-based assays. While the landscape of diagnostics is rapidly evolving, PCR remains the gold-standard of nucleic acid-based diagnostic assays, in part due to its reliability, flexibility and wide deployment. To address a critical local shortage of testing capacity persisting during the COVID-19 outbreak, our hospital set up a molecular-based laboratory developed test (LDT) to accurately and safely diagnose SARS-CoV-2. We describe here the process of developing an emergency-use LDT, in the hope that our experience will be useful to other laboratories in future outbreaks and will help to lower barriers to establishing fast and accurate diagnostic testing in crisis conditions.

Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: A guide and case study in setting up an emergency-use, laboratory-developed molecular assay

Developing and deploying new diagnostic tests is difficult, but the need to do so in response to a rapidly emerging pandemic such as COVID-19 is crucially important for an effective response. In the early stages of a pandemic, laboratories play a key role in helping health care providers and public health authorities detect active infection, a task most commonly achieved using nucleic acid-based assays. While the landscape of diagnostics is rapidly evolving, polymerase chain reaction (PCR) remains the gold-standard of nucleic acid-based diagnostic assays, in part due to its reliability, flexibility, and wide deployment. To address a critical local shortage of testing capacity persisting during the COVID-19 outbreak, our hospital set up a molecular based laboratory developed test (LDT) to accurately and safely diagnose SARS-CoV-2. We describe here the process of developing an emergency-use LDT, in the hope that our experience will be useful to other laboratories in future outbreaks and will help to lower barriers to fast and accurate diagnostic testing in crisis conditions.

Lassa Virus Genetics

In a pattern repeated across a range of ecological niches, arenaviruses have evolved a compact four-gene genome to orchestrate a complex life cycle in a narrow range of susceptible hosts. A number of mammalian arenaviruses cross-infect humans, often causing a life-threatening viral hemorrhagic fever. Among this group of geographically bound zoonoses, Lassa virus has evolved a unique niche that leads to significant and sustained human morbidity and mortality. As a biosafety level 4 pathogen, direct study of the pathogenesis of Lassa virus is limited by the sparse availability, high operating costs, and technical restrictions of the high-level biocontainment laboratories required for safe experimentation. In this chapter, we introduce the relationship between genome structure and the life cycle of Lassa virus and outline reverse genetic approaches used to probe and describe functional elements of the Lassa virus genome. We then review the tools used to obtain viral genomic sequences used for phylogeny and molecular diagnostics, before shifting to a population perspective to assess the contributions of phylogenetic analysis in understanding the evolution and ecology of Lassa virus in West Africa. We finally consider the future outlook and clinical applications for genetic study of Lassa virus.

Real-time Metagenomic Analysis of Undiagnosed Fever Cases Unveils a Yellow Fever Outbreak in Edo State, Nigeria

Fifty patients with unexplained fever and poor outcomes presented at Irrua Specialist Teaching Hospital (ISTH) in Edo State, Nigeria, an area endemic for Lassa fever, between September 2018 - January 2019. After ruling out Lassa fever, plasma samples from these epidemiologically-linked cases were sent to the African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria, where we carried out metagenomic sequencing which implicated yellow fever virus (YFV) as the etiology of this outbreak. Twenty-nine of the 50 samples were confirmed positive for YFV by reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR), 14 of which resulted in genome assembly. Maximum likelihood phylogenetic analysis revealed that these YFV sequences formed a tightly clustered clade more closely related to sequences from Senegal than sequences from earlier Nigerian isolates, suggesting that the YFV clade responsible for this outbreak in Edo State does not descend directly from the Nigerian YFV outbreaks of the last century, but instead reflects a broader diversity and dynamics of YFV in West Africa. Here we demonstrate the power of metagenomic sequencing for identifying ongoing outbreaks and their etiologies and informing real-time public health responses, resulting in accurate and prompt disease management and control.

An evaluation of the influence of teeth and the labial soft tissues on the perceived aesthetics of a smile

Objective The aim of this study was to investigate how the lips and teeth may affect the perceived aesthetics of a given smile. Lips and teeth were collectively assessed in different fields of view to see how they may contribute to smile aesthetics. The perception of 'beauty' was assessed to determine whether differences existed between; dentists, non-dentists, males and females.Methods Five subjects were photographed to produce the following views: 1) retracted anterior teeth; 2) lips at rest; 3) zoomed smile; and 4) smile showing the lower face. Images were compiled in a survey questionnaire and shown to respondents who ranked the subjects in order of aesthetic appeal. Kendall's coefficient of concordance (W) and median rank scores were used to determine the statistical significance.Results All groups demonstrated statistically significant agreement in the perception of beauty. Both the teeth and lips seemed to contribute similarly to the attractiveness of a smile. Dentists seemed to be more influenced by teeth in a zoomed smile view, however, this was negated when viewing a broader field of view. All other groups showed no difference in perception of aesthetics with changing field of view.Conclusion Both lips and teeth seem to contribute to the aesthetic appeal of a smile. Dentists may have a tendency to place a disproportionate weight to teeth when assessing a smile close up.

Simulation study of Hemodynamic in Bifurcations for Cerebral Arteriovenous Malformation using Electrical Analogy

BACKGROUND AND OBJECTIVE

Cerebral Arteriovenous Malformation (CAVM) hemodynamic is disease condition, results changes in the flow and pressure level in cerebral blood vessels. Measuring flow and pressure without catheter intervention along the vessel is big challenge due to vessel bifurcations/complex bifurcations in Arteriovenous Malformation patients. The vessel geometry in CAVM patients are complex, composed of varying diameters, lengths, and bifurcations of various angles. The variations in the vessel diameter and bifurcation angle complicate the measurement and analysis of blood flow features invasively or non-invasively.

METHODS

In this paper, we proposed a lumped model for the bifurcation for symmetrical and asymmetrical networks in CAVM patients. The models are created using MATLAB Simulation software for various bifurcation angles. Each bifurcation angle created using electrical network- RLC. The segmentation and pre-processing of bifurcation vessels are implemented using adaptive segmentation. The proposed network address clinicians problem by measuring hemodynamic non-invasively. The method is applicable for any types of bifurcation networks with different bifurcation angles in CAVM patients.

RESULTS

In this work, we constructed a mathematical model, measured hemodynamic for 23 patients (actual and simulated cases) with 60 vessel bifurcation angles variations. The results indicate that comparisons evidenced highly significant correlations between values computed by the lumped model and simulated mechanical model for both networks with p < 0.0001. A P value of less than 0.05 considered statistically significant.

CONCLUSION

In this paper, we have modelled different bifurcation types and automatically display pressure and flow non-invasively at different node and at different angles of bifurcation in the complex vessel with help of bifurcation parameters, using lumped parameter model. We have simulated for different bifurcation angles and diameters of vessel for various imaging modality and model extend for different organs. This will help clinicians to measure haemodynamic parameters noninvasively at various bifurcations, where even catheter cannot be reached.

Current concepts on the management of tooth wear: part 2. Active restorative care 1: the management of localised tooth wear

This second of the four part series of articles on the current concepts of tooth wear management will focus on the provision of active restorative care, where the implementation of a preventative, passive approach may prove insufficient to meet the patient's expectations, or indeed prove to be sufficiently adequate to address the extent of the underlying pathology to the desired level of clinical satisfaction. The active restorative management of cases presenting with localised tooth wear (of either the anterior, posterior, maxillary or mandibular variety) will be considered in depth in this paper, including a description of the commonly applied techniques and treatment strategies, where possible illustrated by case examples.

Active spatial perception in the vibrissa scanning sensorimotor system

Haptic perception is an active process that provides an awareness of objects that are encountered as an organism scans its environment. In contrast to the sensation of touch produced by contact with an object, the perception of object location arises from the interpretation of tactile signals in the context of the changing configuration of the body. A discrete sensory representation and a low number of degrees of freedom in the motor plant make the ethologically prominent rat vibrissa system an ideal model for the study of the neuronal computations that underlie this perception. We found that rats with only a single vibrissa can combine touch and movement to distinguish the location of objects that vary in angle along the sweep of vibrissa motion. The patterns of this motion and of the corresponding behavioral responses show that rats can scan potential locations and decide which location contains a stimulus within 150 ms. This interval is consistent with just one to two whisk cycles and provides constraints on the underlying perceptual computation. Our data argue against strategies that do not require the integration of sensory and motor modalities. The ability to judge angular position with a single vibrissa thus connects previously described, motion-sensitive neurophysiological signals to perception in the behaving animal.

Rats explore the world with their whiskers (vibrissae). Although the sensations of touch that an animal experiences while exploring an object either in front of its head or to its side can be similar, the two sensations tell the animal different things about its nearby environment. The translation from passive touch to knowledge of an object's location requires that the nervous system keep track of the location of the animal's body as it moves. We studied this process by restricting a rat's whisking information to that provided by a single actively moving vibrissa. We found that even with such limited information, rats can search for, locate, and differentiate objects near their heads with astonishing speed. Their behavior during this search reflects the computations performed by their nervous systems to locate objects based on touch, and this behavior demonstrates that rats keeps track of their vibrissa motion with a resolution of less than 0.1 s. Understanding how these computations are performed will bring us closer to understanding how the brain integrates the sense of touch with its sense of self.

Rats can localize objects with their specialized vibrissa system by the integration of feed-forward sensory events and motor feedback. This discovery provides a behavioral model for understanding how sensorimotor loops derive the perception of space from the sensation of touch.

Frisking the whiskers: patterned sensory input in the rat vibrissa system

How are two prominent environmental features, surface texture and object location, transduced and encoded as rats whisk? Recent papers show that textures may excite intrinsic mechanical vibrations of the vibrissae. Although these vibrations are too rapid to be directly followed by cortical neurons, there is evidence that their speed is encoded by contact-dependent sensory signals. In addition to contact, sensory signals exist that report the angular position of the vibrissae. The combination of contact and reference signals may be used to decode spatial variations in the environment, particularly the location of objects in head-centered coordinates.

Reversing cerebellar long-term depression

The discovery of a postsynaptically expressed form of cerebellar parallel fiber-Purkinje cell long-term potentiation (LTP) raises the question whether this is the long-sought resetting mechanism for long-term depression (LTD). Extracellular monitoring of PC spikes enables stable prolonged recordings of parallel fiber-Purkinje cell synaptic efficacy. LTD, saturated by repeated induction protocols, can be reversed by a single round of postsynaptic LTP or nitric oxide (NO), enabling LTD to be reinduced. Conversely, after postsynaptic LTP has been saturated, one round of LTD permits fresh postsynaptic LTP. By contrast, after saturation of LTD, induction of presynaptic LTP or application of forskolin leaves LTD still saturated. Likewise, presynaptic LTP cannot be reversed by LTD. Therefore postsynaptic LTP mediated by NO without postsynaptic Ca2+ elevation, unlike presynaptic LTP mediated by cAMP, is a true counterbalance to LTD mediated by coincidence of NO plus postsynaptic Ca2+

Nasal hyposensitization and hay fever

A clinical trial of pre-seasonal hyposensitization with intra-nasal grass pollen extract was carried out in forty-two patients. Results were assessed subjectively, by clinical examination during the pollen season, and by measurements of nasal air flow. Useful relief of symptoms was considered to have occurred in fifteen out of twenty-one patients who had pre-seasonal treatment with pollen extract and in five out of twenty-one patients who had similar treatment with carbol saline as a placebo. Of twelve patients who were symptom free in the pollen season ten had nasal hyposensitization. It is concluded that this simple and safe method of treatment gives results comparable with those of pre-seasonal injections.