Improved SARS-CoV-2 sequencing surveillance allows the identification of new variants and signatures in infected patients

Background

Genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the only approach to rapidly monitor and tackle emerging variants of concern (VOC) of the COVID-19 pandemic. Such scrutiny is crucial to limit the spread of VOC that might escape the immune protection conferred by vaccination strategies or previous virus exposure. It is also becoming clear now that efficient genomic surveillance would require monitoring of the host gene expression to identify prognostic biomarkers of treatment efficacy and disease progression. Here we propose an integrative workflow to both generate thousands of SARS-CoV-2 genome sequences per week and analyze host gene expression upon infection.

Methods

In this study we applied an integrated workflow for RNA extracted from nasal swabs to obtain in parallel the full genome of SARS-CoV-2 and transcriptome of host respiratory epithelium. The RNA extracted from each sample was reverse transcribed and the viral genome was specifically enriched through an amplicon-based approach. The very same RNA was then used for patient transcriptome analysis. Samples were collected in the Campania region, Italy, for viral genome sequencing. Patient transcriptome analysis was performed on about 700 samples divided into two cohorts of patients, depending on the viral variant detected (B.1 or delta).

Results

We sequenced over 20,000 viral genomes since the beginning of the pandemic, producing the highest number of sequences in Italy. We thus reconstructed the pandemic dynamics in the regional territory from March 2020 to December 2021. In addition, we have matured and applied novel proof-of-principle approaches to prioritize possible gain-of-function mutations by leveraging patients’ metadata and isolated patient-specific signatures of SARS-CoV-2 infection. This allowed us to (i) identify three new viral variants that specifically originated in the Campania region, (ii) map SARS-CoV-2 intrahost variability during long-term infections and in one case identify an increase in the number of mutations in the viral genome, and (iii) identify host gene expression signatures correlated with viral load in upper respiratory ways.

Conclusion

In conclusion, we have successfully generated an optimized and cost-effective strategy to monitor SARS-CoV-2 genetic variability, without the need of automation. Thus, our approach is suitable for any lab with a benchtop sequencer and a limited budget, allowing an integrated genomic surveillance on premises. Finally, we have also identified a gene expression signature defining SARS-CoV-2 infection in real-world patients’ upper respiratory ways.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13073-022-01098-8.

Ultrasonic Microplotting of Microgel Bioinks

Material scaffolds that mimic the structure, function, and bioactivity of native biological tissues are in constant development. Recently, material scaffolds composed of microgel particles have shown promise for applications ranging from bone regeneration to spheroid cell growth. Previous studies with poly N-isopropylacrylamide microgel scaffolds utilized a layer-by-layer (LBL) technique where individual, uniform microgel layers are built on top of each other resulting in a multilayer scaffold. However, this technique is limited in its applications due to the inability to control microscale deposition or patterning of multiple particle types within a microgel layer. In this study, an ultrasonic microplotting technique is used to address the limitations of LBL fabrication to create patterned microgel films. Printing parameters, such as bioink formulation, surface contact angle, and print head diameter, are optimized to identify the ideal parameters needed to successfully print microgel films. It was found that bioinks composed of 2 mg/mL of microgels and 20% polyethylene glycol by volume (v/v), on bovine serum albumin-coated glass, with a print head diameter of 50 μm resulted in the highest quality prints. Patterned films were created with a maximum resolution of 50 μm with the potential for finer resolutions to be achieved with alternative bioink compositions and printing parameters. Overall, ultrasonic microplotting can be used to create more complex microgel films than is possible with LBL techniques and offers the possibility of greater printing resolution in 3D with further technology development.

Treatment of Acute Liver Failure with Hemodetoxification Techniques

The exact pathogenesis of hepatic coma is unknown and this fact has stimulated research in the field of hemodetoxification treatment. We studied 31 patients (19 M and 12 F) with acute hepatic failure and used different detoxification techniques such as hemodialysis, hemoperfusion, hemofiltration and plasmaferesis. We evaluated blood tests, degree of coma and serum levels of middle-molecular weight substances (by gel-chromatography) for each patient.

Our results show that there was an improvement of consciousness and general clinical state in 40% of patients who underwent HD, in 50% of patients treated with HP, in 37.5% of those treated with PF and 78% of patients treated with HF. Unfortunately, the improvement did not last long.

In conclusion we can say that artificial support improves hepatic coma and state of consciousness. This improvement could be due to the better regeneration possibilities of hepatic cells. For this reason hemodetoxification treatment should be started as soon as possible.

Parenteral iron supplementation for the treatment of iron deficiency anemia in children

Iron-deficiency anemia impairs growth and intellectual development in children, which can be reversed only by early diagnosis and iron supplementation. Oral supplementation can efficiently replace stores, but in many cases parenteral iron is needed. Unfortunately some adverse reactions have limited its use in children. We compared the efficacy and safety of intramuscular and intravenous administration in 33 evaluable children with severe iron deficiency and/or iron-deficiency anemia who failed to respond to oral iron supplementation. Nineteen children received intravenous infusion and 14 intramuscular injections. All children showed recovery from iron-deficiency anemia, with statistically similar improvement in hemoglobin levels. The duration of treatment was longer in those receiving intramuscular injection. Parenteral iron therapy for the treatment of iron-deficiency anemia is a rapid, easy, and definitive solution to a long-troubling situation. We suggest the use of parenteral iron, in particular intravenous iron, in children who do not recover from severe iron-deficiency anemia after oral therapy. We should consider the physical and neuropsychological sequelae of long-lasting iron deficiency in children and the fact that oral supplementation is less likely to replace iron stores.

HCV infection in hemodialyzed patients: incidence and correlation with dialytic age

Hemodialyzed patients mean an high-risk population for hepatitis C infection. Our work was performed to evaluate the incidence of hepatitis C virus (HCV) infection in 51 hemodialyzed patients; the presence of anti-HCV antibodies was studied using the EIA and RIBA test of 1st and 2nd generation. 18 patients (35.29%) showed anti-HCV antibodies with the 1st test; 27 patients (52.94%) showed the presence of anti-HCV antibodies using 2nd generation test. The incidence of test positivity is not related to blood transfusions while it is strictly related with dialytic age. All HCV seropositive patients show antibodies against the c22-3 protein of "virus core". The presence in serum of anti-c22-3 antibodies means that in these patients, there is viral replication.

[Pedodontic patient: child psychology in relation to the dental sphere]

The Authors emphasize how difficult is for the dental surgeon to approach the young patients. The researches carried out on school children (6-11 years old), of different social conditions, emphasis the psychological reality of the visited children and suggest some contrivances for a less traumatic possible meeting with an unknown world, source of anxiety, stress and fear.

Treatment of acute liver failure with hemodetoxification techniques

The exact pathogenesis of hepatic coma is unknown and this fact has stimulated research in the field of hemodetoxification treatment. We studied 31 patients (19 M and 12 F) with acute hepatic failure and used different detoxification techniques such as hemodialysis, hemoperfusion, hemofiltration and plasmaferesis. We evaluated blood tests, degree of coma and serum levels of middle-molecular weight substances (by gel-chromatography) for each patient. Our results show that there was an improvement of consciousness and general clinical state in 40% of patients who underwent HD, in 50% of patients treated with HP, in 37.5% of those treated with PF and 78% of patients treated with HF. Unfortunately, the improvement did not last long. In conclusion we can say that artificial support improves hepatic coma and state of consciousness. This improvement could be due to the better regeneration possibilities of hepatic cells. For this reason hemodetoxification treatment should be started as soon as possible.

Our experience with combined hemodialysis-hemoperfusion treatment in chronic uremia

Hemodialysis can remove only substances that are highly diffusable, non protein bound and with small and middle-molecular weights. The combination of Hemodialysis-Hemoperfusion (HD-HF) takes advantage of both techniques. Uremic patient could reduce the number of weekly dialysis sessions. Fourteen uremic patients were submitted twice a week to a combined HD-HP treatment for 16 months. Polymethacrylate coated charcoal was inserted in the dialysis circuit before the dialyzer. The treatment resulted in improvement of: MNCV (30.5 + -6 to 38.7 + -5.6 m/sec.) subjective symptoms (disappearance of pruritus and insomnia) and hematological status (red blood cells 3.1 x 106 to 4.02 x 106; and hematocrits 28.3 to 36.1). Good control of serum biochemistries. Creatinine and urea clearances of 228 and 236 ml/min respectively. Significant removal of middle-molecules uremic toxins determinated by gel-filtration on Sephadex G15. In conclusion, we state that combined HD-HP improves the detoxication possibilities in chronic uremia.

A method for the identification of in-vivo segmental stiffness properties of the spine

A numerical algorithm is used to estimate in-vivo segmental stiffness properties of individual spine segments based upon existing load-displacement data. A static nonlinear finite element model stimulates a pathological spine and corrective instrumentation system. A systematic procedure for establishing the model's stiffness parameters is described, in the form of a nonlinear constrained optimal design problem. The numerical method is demonstrated using as an example a case of adolescent idiopathic scoliosis requiring corrective surgery.