Tracking arboviruses, their transmission vectors and potential hosts by nanopore sequencing of mosquitoes

The risk to human health from mosquito-borne viruses such as dengue, chikungunya and yellow fever is increasing due to increased human expansion, deforestation and climate change. To anticipate and predict the spread and transmission of mosquito-borne viruses, a better understanding of the transmission cycle in mosquito populations is needed. We present a pathogen-agnostic combined sequencing protocol for identifying vectors, viral pathogens and their hosts or reservoirs using portable Oxford Nanopore sequencing. Using mosquitoes collected in São Paulo, Brazil, we extracted RNA for virus identification and DNA for blood meal and mosquito identification. Mosquitoes and blood meals were identified by comparing cytochrome c oxidase I (COI) sequences against a curated Barcode of Life Data System (BOLD). Viruses were identified using the SMART-9N protocol, which allows amplified DNA to be prepared with native barcoding for nanopore sequencing. Kraken 2 was employed to detect viral pathogens and Minimap2 and BOLD identified the contents of the blood meal. Due to the high similarity of some species, mosquito identification was conducted using blast after generation of consensus COI sequences using RACON polishing. This protocol can simultaneously uncover viral diversity, mosquito species and mosquito feeding habits. It also has the potential to increase understanding of mosquito genetic diversity and transmission dynamics of zoonotic mosquito-borne viruses.</p

Goodbye Hartmann trial: a prospective, international, multicenter, observational study on the current use of a surgical procedure developed a century ago

Background: Literature suggests colonic resection and primary anastomosis (RPA) instead of Hartmann's procedure (HP) for the treatment of left-sided colonic emergencies. We aim to evaluate the surgical options globally used to treat patients with acute left-sided colonic emergencies and the factors that leading to the choice of treatment, comparing HP and RPA. Methods: This is a prospective, international, multicenter, observational study registered on ClinicalTrials.gov. A total 1215 patients with left-sided colonic emergencies who required surgery were included from 204 centers during the period of March 1, 2020, to May 31, 2020. with a 1-year follow-up. Results: 564 patients (43.1%) were females. The mean age was 65.9 ± 15.6&nbsp;years. HP was performed in 697 (57.3%) patients and RPA in 384 (31.6%) cases. Complicated acute diverticulitis was the most common cause of left-sided colonic emergencies (40.2%), followed by colorectal malignancy (36.6%). Severe complications (Clavien-Dindo ≥ 3b) were higher in the HP group (P &lt; 0.001). 30-day mortality was higher in HP patients (13.7%), especially in case of bowel perforation and diffused peritonitis. 1-year follow-up showed no differences on ostomy reversal rate between HP and RPA. (P = 0.127). A backward likelihood logistic regression model showed that RPA was preferred in younger patients, having low ASA score (≤ 3), in case of large bowel obstruction, absence of colonic ischemia, longer time from admission to surgery, operating early at the day working hours, by a surgeon who performed more than 50 colorectal resections. Conclusions: After 100&nbsp;years since the first Hartmann's procedure, HP remains the most common treatment for left-sided colorectal emergencies. Treatment's choice depends on patient characteristics, the time of surgery and the experience of the surgeon. RPA should be considered as the gold standard for surgery, with HP being an exception

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant

P180 External validation of the Southend GCA Probability Score (GCAPS) as a screening tool for referrals with possible GCA

Abstract Background We run a rheumatologist-led, ultrasound-driven giant cell arteritis (GCA) fast track pathway (FTP). Currently, no specific referral criteria are required. Sensitive referral criteria are now needed to safely reduce referrals, which have risen year-on-year (92 in Year 3, 84% greater than Year 1). Methods The following were collected for all patients referred to our GCA-FTP from 1/4/2018-31/3/2019 (Year 3): Final diagnosis of imaging/biopsy confirmed-GCA, unconfirmed clinical-GCA or not-GCA using the electronic patient record to September 2019; Rheumatologist-determined clinical probability of GCA (low, moderate, high) before imaging/biopsy; Presence of ≥ 3 ACR 1990 GCA Classification Criteria (biopsy excluded, adapted to increase sensitivity, see table); Presence of Southend GCAPS≥10 (Based on our clinical experience, polymyalgic symptoms were also counted if patients had recently taken prednisolone for PMR). Results 88 consecutive patients were analysed (total 92: 2 missing data; 2 passed through twice). 25/88 (27%) were diagnosed with GCA 24 were imaging/biopsy confirmed. The single patient with unconfirmed clinical-GCA had high clinical probability, indeterminate ultrasound and biopsy after &amp;gt;1-week glucocorticoid. GCA patients were mean age 77.3y (range 63-94), 76% female, all White, with mean GCAPS 15.3 (range 10-25). Our adaptations of the ACR criteria increased ACR-criteria sensitivity: 24% GCA patients had new generalised headache and 16% had ESR&amp;lt;50, but CRP&amp;gt;10. 14% referrals were non-White, although GCA is rare in this group. GCAPS was based on a largely White population. If GCAPS did not remove 3 points for alternative diagnoses, then 5 additional non-White patients would have scored ≥10. Conclusion This study externally validates GCAPS≥10 as a screening tool for referrals with possible GCA. It captured all GCA patients and screened out 44% referrals. For this indication, it performed better than a consultant rheumatologist. Despite adaptations to improve sensitivity, ACR criteria missed a quarter of cases. To improve GCAPS specificity when scored by a non-rheumatologist, GCAPS should be adapted to reflect the low likelihood of GCA in non-Whites. We plan to only accept patients with GCAPS≥10, where 3 points are removed for non-Whites if not already removed for alternative diagnoses. We predict referrals will reduce but anticipate referrers will need education to limit over-scoring. Disclosures V. Quick None. M. Hughes None. N. Mothojakan None. D. Fishman None. </jats:sec