Gemykibivirus detection in acute encephalitis patients from Nepal.

Acute encephalitis syndrome (AES) causes significant morbidity and mortality worldwide. In Nepal, Japanese encephalitis virus (JEV) accounts for ~5-20% of AES cases, but ~75% of AES cases are of unknown etiology. We identified a gemykibivirus in CSF collected in 2020 from an 8-year-old male patient with AES using metagenomic next-generation sequencing. Gemykibiviruses are single stranded, circular DNA viruses in the family Genomoviridae. The complete genome of 2,211 nucleotides was sequenced, which shared 98.69% nucleotide identity to its closest relative, Human associated gemykibivirus 2 isolate SAfia-449D. Two real-time PCR assays were designed, and screening of 337 cerebrospinal fluid (CSF) and 164 serum samples from AES patients in Nepal collected in 2020 and 2022 yielded 11 CSF and 1 serum sample that were positive in both PCR assays. Complete genomes of seven of the positives were sequenced. These results identify a potential candidate etiologic agent of encephalitis in Nepal. IMPORTANCE: Viral encephalitis is a devastating disease, but unfortunately, worldwide, the causative virus in many cases is unknown. Therefore, it is important to identify viruses that could be responsible for cases of human encephalitis. Here, using metagenomic sequencing of CSF, we identified a gemykibivirus in a male child from Nepal with acute encephalitis syndrome (AES). We subsequently detected gemykibivirus DNA in CSF or serum of 12 more encephalitis patients by real-time PCR. The virus genomes we identified are highly similar to gemykibiviruses previously detected in CSF of three encephalitis patients from Sri Lanka. These results raise the possibility that gemykibivirus could be an underrecognized human pathogen.

Gemykibivirus detection in acute encephalitis patients from Nepal.

Acute Encephalitis Syndrome (AES) causes significant morbidity and mortality worldwide. In Nepal, Japanese encephalitis virus (JEV) accounts for ~ 5-20% of AES cases, but ~75% of AES cases are of unknown etiology. We identified a gemykibivirus in CSF collected in 2020 from a male child with AES using metagenomic next-generation sequencing. Gemykibiviruses are single stranded, circular DNA viruses in the family Genomoviridae. The complete genome of 2211 nucleotides was sequenced which shared 98.69% nucleotide identity to its closest relative, Human associated gemykibivirus 2 isolate SAfia-449D. Two real-time PCR assays were designed, and screening of 337 CSF and 164 serum samples from AES patients in Nepal collected in 2020 and 2022 yielded 11 CSF and 1 serum sample that were positive in both PCR assays. Complete genomes of 7 of the positives were sequenced. These results identify a candidate etiologic agent of encephalitis in Nepal.

Isolation of a rhesus calicivirus that can replicate in human cells.

Recoviruses (rhesus enteric caliciviruses) are members of the Caliciviridae family. They are a valuable model for studying human caliciviruses such as noroviruses. It has been suggested that some recoviruses may infect humans, which necessitates detailed studies on the cell type tropism of recoviruses. For the recoviruses that have been cultured to date, successful growth has only been reported in monkey kidney cell lines, precluding their use to study virus interactions with human cells. We isolated and characterized a new recovirus, Recovirus Mo/TG30/2012, from monkey stool which grew efficiently in the monkey kidney cell line LLC-MK2. Notably, the virus can infect and replicate in several human cell lines derived from different organs. The ability to infect a human cell culture system with a recovirus expands our understanding of the potential for spillover to humans as well as increases the value of recoviruses as a model of human caliciviruses.

Role of the nifB1 and nifB2 Promoters in Cell-Type-Specific Expression of Two Mo Nitrogenases in the Cyanobacterium Anabaena variabilis ATCC 29413.

Anabaena variabilis ATCC 29413 has one Mo nitrogenase that is made under oxic growth conditions in specialized cells called heterocysts and a second Mo nitrogenase that is made only under anoxic conditions in vegetative cells. The two large nif gene clusters responsible for these two nitrogenases are under the control of the promoter of the first gene in the operon, nifB1 or nifB2 Despite differences in the expression patterns of nifB1 and nifB2, related to oxygen and cell type, the regions upstream of their transcription start sites (tss) show striking homology, including three highly conserved sequences (CS). CS1, CS2, and the region just upstream from the tss were required for optimal expression from the nifB1 promoter, but CS3 and the 5' untranslated region (UTR) were not. Hybrid fusions of the nifB1 and nifB2 upstream regions revealed that the region including CS1, CS2, and CS3 of nifB2 could substitute for the similar region of nifB1; however, the converse was not true. Expression from the nifB2 promoter region required the CS1, CS2, and CS3 regions of nifB2 and also required the nifB2 5' UTR. A hybrid promoter that was mostly nifB2 but that had the region from about position -40 to the tss of nifB1 was expressed in heterocysts and in anoxic vegetative cells. Thus, addition of the nifB1 promoter region (from about position -40 to the tss of nifB1) in the nifB hybrid promoter supported expression in heterocysts but did not prevent the mostly nifB2 promoter from also functioning in anoxic vegetative cells. IMPORTANCE: In the filamentous cyanobacterium Anabaena variabilis, two Mo nitrogenase gene clusters, nif1 and nif2, function under different environmental conditions in different cell types. Little is known about the regulation of transcription from the promoter upstream of the first gene of the cluster, which drives transcription of each of these two large operons. The similarity in the sequences upstream of the primary promoters for the two nif gene clusters belies the differences in their expression patterns. Analysis of these nif promoters in strains with mutations in the conserved sequences and in strains with hybrid promoters, comprising parts from nif1 and nif2, provides strong evidence that each promoter has key elements required for cell-type-specific expression of the nif1 and nif2 gene clusters.

Guidelines to identify abnormalities after childhood urinary tract infections: a prospective audit.

OBJECTIVE: To compare the childhood urinary tract infection (UTI) guidelines from the Royal College of Physicians (RCP) in 1991 and from National Institute of Health and Care Excellence (NICE) (CG54) in 2007 by measuring their efficiency at detecting urinary tract abnormalities. DESIGN: Children with UTIs within the Newcastle Primary Care Trust (population 70,800 children) were referred and imaged according to the RCP guidelines during 2008, and these were compared to the activity that would have been undertaken if we had implemented the CG54 guidelines, including following them through 2011 to identify those with recurrent UTIs. MAIN OUTCOME MEASURES: The numbers of children imaged, the imaging burden and efficiency, and urinary tract abnormalities detected by each guideline. RESULTS: Fewer children would have been imaged by CG54 than RCP (150 vs 427), but its sensitivity was lower, at 44% for detecting scarring, 10% for identifying vesicoureteric reflux and 40% for other abnormalities. Overall, it would have only detected one-quarter of the abnormal cases (8 vs 32) and would have missed five of nine children with scarring, including three with multiple lesions and one with renal impairment. Imposing an age restriction of <8 years to the RCP guidelines would reduce its screening rate by 20% and still detect 90% of the abnormalities. INTERPRETATION: The CG54 guidelines do not alter the imaging efficiency compared to the RCP guidelines, but they are considerably less sensitive.

Does prompt treatment of urinary tract infection in preschool children prevent renal scarring: mixed retrospective and prospective audits.

OBJECTIVE: To test whether active management of urinary tract infections (UTI) in young children by general practitioners can reduce kidney scarring rates. DESIGN: A comparison of two audits in Newcastle, of children aged <8 years, presenting with UTIs ; a retrospective audit of conventional management during 1992-1995 (1990s) versus a prospective audit of direct access management during 2004-2011 (2000s). MAIN OUTCOME MEASURES: Kidney scarring rates, and their relationship with time-to-treat. RESULTS: Children with a first UTI in the 2000s compared to those in the 1990s, were referred younger, were half as likely to have a renal scar (girls OR 0.47, 95% CI 0.29 to 0.76; boys 0.35, 0.16 to 0.81), and were about 12 times more likely to have vesicoureteric reflux without scarring (girls 11.9, 4.3 to 33.5; boys 14.4, 4.3 to 47.6). In the 2000s, general practitioners treated about half the children at first consultation. Children who were treated within 3 days of their symptoms starting were one-third as likely to scar as those whose symptoms lasted longer (0.33, 0.12 to 0.72). INTERPRETATION: Most kidney defects seen in children after UTIs, are acquired scars, and in Newcastle, active management in primary care has halved this rate.

Complexity of the decision-making process of ambulance staff for assessment and referral of older people who have fallen: a qualitative study.

BACKGROUND: Older people who fall commonly present to the emergency ambulance service, and approximately 40% are not conveyed to the emergency department (ED), despite an historic lack of formal training for such decisions. This study aimed to understand the decision-making processes of emergency ambulance staff with older people who have fallen. METHODS: During 2005 ambulance staff in London tested a clinical assessment tool for use with the older person who had fallen. Documented use of the tool was low. Following the trial, 12 staff participated in semistructured interviews. Interviews were recorded and transcribed. Thematic analysis was carried out. RESULTS: The interviews revealed a similar assessment and decision-making process among participants: Prearrival: forming an early opinion from information from the emergency call. Initial contact: assessing the need for any immediate action and establishing a rapport. Continuing assessment: gathering and assimilating medical and social information. Making a conveyance decision: negotiation, referral and professional defence, using professional experience and instinct. CONCLUSIONS: An assessment process was described that highlights the complexity of making decisions about whether or not to convey older people who fall and present to the emergency ambulance service, and a predominance of informal decision-making processes. The need for support for ambulance staff in this area was highlighted, generating a significant challenge to those with education roles in the ambulance service. Further research is needed to look at how new care pathways, which offer an alternative to the ED may influence decision making around non-conveyance.