Structural identifiability of compartmental models for infectious disease transmission is influenced by data type

If model identifiability is not confirmed, inferences from infectious disease transmission models may not be reliable, so they might result in misleading recommendations. Structural identifiability analysis characterises whether it is possible to obtain unique solutions for all unknown model parameters, given the model structure. In this work, we studied the structural identifiability of some typical deterministic compartmental models for infectious disease transmission, focusing on the influence of the data type considered as model output on the identifiability of unknown model parameters, including initial conditions. We defined 26 model versions, each having a unique combination of underlying compartmental structure and data type(s) considered as model output(s). Four compartmental model structures and three common data types in disease surveillance (incidence, prevalence and detected vector counts) were studied. The structural identifiability of some parameters varied depending on the type of model output. In general, models with multiple data types as outputs had more structurally identifiable parameters, than did models with a single data type as output. This study highlights the importance of a careful consideration of data types as an integral part of the inference process with compartmental infectious disease transmission models

Consumers’ preference and associated pathology observed in cattle and goat offals in Kumasi, Ghana

Background: The global population demands high quality meat and the preference for offal continue to be on the increase. This investigation evaluates consumers’ preference and associated pathological conditions observed in cattle and goat offal in Kumasi, Ghana.Materials and Methods: Cross sectional survey and structured questionnaires involving 200 adult respondents were adopted. 105 samples of cattle and goat offal from selected retailers or vendors were also evaluated for associated pathological conditions.Results: From the questionnaire, results showed that on the average, one (1) pound of offal was consumed by a household of seven (7) per meal twice a week. The most preferred offal was the fore-stomach (52.70%) followed by the liver (38.10%). However, 75% and 50% of the liver sampled had one or more lesions in the goat and cattle respectively with presence of abscesses, metazoan parasites and granuloma. Factors like availability, affordability, nutritional value, taste, customs and level of education influenced the consumer’s preference for edible offal.Conclusion: Presence of metazoan parasites, granuloma and microabbscesses further undermine the quality of the offal supply in Ghana and it calls for further investigation into causal agents of these pathological conditions; hence, strict inspection and assessment should be enforced and maintained for continual provision of edible and wholesome offal.Keywords: Offal, Preference, Lesions, Ruminants, Ghan

Catch composition and efficiency of major fishing gears used in stratum II of the Volta lake– implications for managing the fisheries

Catch composition and efficiency of major fishing gears viz; gillnets, basket traps, net traps and ‘atidza’ (brush park), deployed by fishers on the Volta lake at Dzemeni (Stratum II), was assessed over a 16-month period to determine how their deployment can impact on the fish stocks. Fifty thousand seven hundred and ninety four individual specimens were recorded during the study period. This represented 13 taxonomic families, 21 genera and 32 fish species. Only five genera constituted 95 per cent and 84 per cent by number and weight, respectively, of the total catch. Chrysichthys spp. was the most abundant genus (59.1%) followed by the tilapias (15.7%), Hydrocynus spp. (9.7%), Synodontis spp. (8.8%) and Bagrus spp. (2.6%). Catches by ‘atidza’ and basket traps were predominantly Tilapias and Chrysichthys spp., respectively, while that by gillnets and net traps were more heterogeneous. The highest catch of 20 t during the period was made by basket traps, while that from the other gears ranged from 0.33 to 6 t indicating that basket traps were very efficient. Knowledge about the catch composition by the various gears and their efficiency will help to regulate their use when it comes to formulating measures to manage the fisheries of the lake

CONSUMERS PREFERENCE AND ASSOCIATED PATHOLOGY OBSERVED IN CATTLE AND GOAT OFFALS IN KUMASI, GHANA

Background: The global population demands high quality meat and the preference for offal continue to be on the increase. This investigation evaluates consumers’ preference and associated pathological conditions observed in cattle and goat offal in Kumasi, Ghana. Materials and Methods: Cross sectional survey and structured questionnaires involving 200 adult respondents were adopted. 105 samples of cattle and goat offal from selected retailers or vendors were also evaluated for associated pathological conditions. Results: From the questionnaire, results showed that on the average, one (1) pound of offal was consumed by a household of seven (7) per meal twice a week. The most preferred offal was the fore-stomach (52.70%) followed by the liver (38.10%). However, 75% and 50% of the liver sampled had one or more lesions in the goat and cattle respectively with presence of abscesses, metazoan parasites and granuloma. Factors like availability, affordability, nutritional value, taste, customs and level of education influenced the consumer’s preference for edible offal. Conclusion: Presence of metazoan parasites, granuloma and microabbscesses further undermine the quality of the offal supply in Ghana and it calls for further investigation into causal agents of these pathological conditions; hence, strict inspection and assessment should be enforced and maintained for continual provision of edible and wholesome offal

Ten months of temporal variation in the clinical journey of hospitalised patients with COVID-19: an observational cohort

Background: There is potentially considerable variation in the nature and duration of the care provided to hospitalised patients during an infectious disease epidemic or pandemic. Improvements in care and clinician confidence may shorten the time spent as an inpatient, or the need for admission to an intensive care unit (ICU) or high density unit (HDU). On the other hand, limited resources at times of high demand may lead to rationing. Nevertheless, these variables may be used as static proxies for disease severity, as outcome measures for trials, and to inform planning and logistics. Methods: We investigate these time trends in an extremely large international cohort of 142,540 patients hospitalised with COVID-19. Investigated are: time from symptom onset to hospital admission, probability of ICU/HDU admission, time from hospital admission to ICU/HDU admission, hospital case fatality ratio (hCFR) and total length of hospital stay. Results: Time from onset to admission showed a rapid decline during the first months of the pandemic followed by peaks during August/September and December 2020. ICU/HDU admission was more frequent from June to August. The hCFR was lowest from June to August. Raw numbers for overall hospital stay showed little variation, but there is clear decline in time to discharge for ICU/HDU survivors. Conclusions: Our results establish that variables of these kinds have limitations when used as outcome measures in a rapidly-evolving situation. Funding: This work was supported by the UK Foreign, Commonwealth and Development Office and Wellcome [215091/Z/18/Z] and the Bill and Melinda Gates Foundation [OPP1209135]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Autosomal dominant optic atrophy and cataract “plus” phenotype including axonal neuropathy

Objective To characterize the phenotype in individuals with OPA3-related autosomal dominant optic atrophy and cataract (ADOAC) and peripheral neuropathy (PN). Methods Two probands with multiple affected relatives and one sporadic case were referred for evaluation of a PN. Their phenotype was determined by clinical ± neurophysiological assessment. Neuropathologic examination of sural nerve and skeletal muscle, and ultrastructural analysis of mitochondria in fibroblasts were performed in one case. Exome sequencing was performed in the probands. Results The main clinical features in one family (n = 7 affected individuals) and one sporadic case were early-onset cataracts (n = 7), symptoms of gastrointestinal dysmotility (n = 8), and possible/confirmed PN (n = 7). Impaired vision was an early-onset feature in another family (n = 4 affected individuals), in which 3 members had symptoms of gastrointestinal dysmotility and 2 developed PN and cataracts. The less common features among all individuals included symptoms/signs of autonomic dysfunction (n = 3), hearing loss (n = 3), and recurrent pancreatitis (n = 1). In 5 individuals, the neuropathy was axonal and clinically asymptomatic (n = 1), sensory-predominant (n = 2), or motor and sensory (n = 2). In one patient, nerve biopsy revealed a loss of large and small myelinated fibers. In fibroblasts, mitochondria were frequently enlarged with slightly fragmented cristae. The exome sequencing identified OPA3 variants in all probands: a novel variant (c.23T>C) and the known mutation (c.313C>G) in OPA3. Conclusions A syndromic form of ADOAC (ADOAC+), in which axonal neuropathy may be a major feature, is described. OPA3 mutations should be included in the differential diagnosis of complex inherited PN, even in the absence of clinically apparent optic atrophy

StopCOVID cohort : An observational study of 3,480 patients admitted to the Sechenov University hospital network in Moscow city for suspected COVID-19 infection

© 2020 Oxford University Press. This is a pre-copyedited, author-produced PDF of an article accepted for publication in Clinical Infectious Diseases following peer review. The version of record is available online at: https://doi.org/10.1093/cid/ciaa1535.BACKGROUND: The epidemiology, clinical course, and outcomes of COVID-19 patients in the Russian population are unknown. Information on the differences between laboratory-confirmed and clinically-diagnosed COVID-19 in real-life settings is lacking. METHODS: We extracted data from the medical records of adult patients who were consecutively admitted for suspected COVID-19 infection in Moscow, between April 8 and May 28, 2020. RESULTS: Of the 4261 patients hospitalised for suspected COVID-19, outcomes were available for 3480 patients (median age 56 years (interquartile range 45-66). The commonest comorbidities were hypertension, obesity, chronic cardiac disease and diabetes. Half of the patients (n=1728) had a positive RT-PCR while 1748 were negative on RT-PCR but had clinical symptoms and characteristic CT signs suggestive of COVID-19 infection.No significant differences in frequency of symptoms, laboratory test results and risk factors for in-hospital mortality were found between those exclusively clinically diagnosed or with positive SARS-CoV-2 RT-PCR.In a multivariable logistic regression model the following were associated with in-hospital mortality; older age (per 1 year increase) odds ratio [OR] 1.05 (95% confidence interval (CI) 1.03 - 1.06); male sex (OR 1.71, 1.24 - 2.37); chronic kidney disease (OR 2.99, 1.89 - 4.64); diabetes (OR 2.1, 1.46 - 2.99); chronic cardiac disease (OR 1.78, 1.24 - 2.57) and dementia (OR 2.73, 1.34 - 5.47). CONCLUSIONS: Age, male sex, and chronic comorbidities were risk factors for in-hospital mortality. The combination of clinical features were sufficient to diagnoseCOVID-19 infection indicating that laboratory testing is not critical in real-life clinical practice.Peer reviewe

The Micronemal Plasmodium Proteins P36 and P52 Act in Concert to Establish the Replication-Permissive Compartment Within Infected Hepatocytes

Within the liver, Plasmodium sporozoites traverse cells searching for a “suitable” hepatocyte, invading these cells through a process that results in the formation of a parasitophorous vacuole (PV), within which the parasite undergoes intracellular replication as a liver stage. It was previously established that two members of the Plasmodium s48/45 protein family, P36 and P52, are essential for productive invasion of host hepatocytes by sporozoites as their simultaneous deletion results in growth-arrested parasites that lack a PV. Recent studies point toward a pathway of entry possibly involving the interaction of P36 with hepatocyte receptors EphA2, CD81, and SR-B1. However, the relationship between P36 and P52 during sporozoite invasion remains unknown. Here we show that parasites with a single P52 or P36 gene deletion each lack a PV after hepatocyte invasion, thereby pheno-copying the lack of a PV observed for the P52/P36 dual gene deletion parasite line. This indicates that both proteins are equally important in the establishment of a PV and act in the same pathway. We created a Plasmodium yoelii P36mCherry tagged parasite line that allowed us to visualize the subcellular localization of P36 and found that it partially co-localizes with P52 in the sporozoite secretory microneme organelles. Furthermore, through co-immunoprecipitation studies in vivo, we determined that P36 and P52 form a protein complex in sporozoites, indicating a concerted function for both proteins within the PV formation pathway. However, upon sporozoite stimulation, only P36 was released as a secreted protein while P52 was not. Our results support a model in which the putatively glycosylphosphatidylinositol (GPI)-anchored P52 may serve as a scaffold to facilitate the interaction of secreted P36 with the host cell during sporozoite invasion of hepatocytes

Determinants of brain swelling in pediatric and adult cerebral malaria.

Cerebral malaria (CM) affects children and adults, but brain swelling is more severe in children. To investigate features associated with brain swelling in malaria, we performed blood profiling and brain MRI in a cohort of pediatric and adult patients with CM in Rourkela, India, and compared them with an African pediatric CM cohort in Malawi. We determined that higher plasma Plasmodium falciparum histidine rich protein 2 (PfHRP2) levels and elevated var transcripts that encode for binding to endothelial protein C receptor (EPCR) were linked to CM at both sites. Machine learning models trained on the African pediatric cohort could classify brain swelling in Indian children CM cases but had weaker performance for adult classification, due to overall lower parasite var transcript levels in this age group and more severe thrombocytopenia in Rourkela adults. Subgrouping of patients with CM revealed higher parasite biomass linked to severe thrombocytopenia and higher Group A-EPCR var transcripts in mild thrombocytopenia. Overall, these findings provide evidence that higher parasite biomass and a subset of Group A-EPCR binding variants are common features in children and adult CM cases, despite age differences in brain swelling