Journal articles: 'Molecular epidemiology Victoria'

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STOTHARD, J. R., B. L. WEBSTER, T. WEBER, S. NYAKAANA, J. P. WEBSTER, F. KAZIBWE, N. B. KABATEREINE, and D. ROLLINSON. "Molecular epidemiology ofSchistosoma mansoniin Uganda: DNA barcoding reveals substantial genetic diversity within Lake Albert and Lake Victoria populations." Parasitology 136, no. 13 (July 23, 2009): 1813–24. http://dx.doi.org/10.1017/s003118200999031x.

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SUMMARYRepresentative samples of UgandanSchistosoma mansonifrom Lake Albert and Lake Victoria were examined using DNA barcoding, sequence analysis of two partially overlapping regions – ASMIT (396 bp) & MORGAN (617 bp) – of the mitochondrial cytochrome oxidase subunit I (cox1). The Victorian sample exhibited greater nucleotide diversity, 1·4%vs. 1·0%, and a significant population partition appeared as barcodes did not cross-over between lakes. With one exception, Lake Albert populations were more mixed by sampled location, while those from Lake Victoria appeared more secluded. Using statistical parsimony, barcode ASMIT 1 was putatively ancestral to all others and analysis of MORGAN cox1 confirmed population diversity. All samples fell into two of five well-resolved lineages; sub-lineages therein broadly partitioning by lake. It seems that barcode ASMIT 1 (and close variants) was likely widely dispersed throughout the Nilotic environment but later diversifiedin situ, and in parallel, within Lake Albert and Lake Victoria. The genetic uniformity of UgandanS. mansonican no longer be assumed, which might better explain known epidemiological heterogeneities. While it appears plausible that locally evolved heritable traits could spread through most of the Lake Albert populations, it seems unlikely they could quickly homogenise into Lake Victoria or amongst populations therein.

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STANDLEY, C. J., N. B. KABATEREINE, C. N. LANGE, N. J. S. LWAMBO, and J. R. STOTHARD. "Molecular epidemiology and phylogeography of Schistosoma mansoni around Lake Victoria." Parasitology 137, no. 13 (June 21, 2010): 1937–49. http://dx.doi.org/10.1017/s0031182010000788.

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SUMMARYIntestinal schistosomiasis continues to be a major public health problem in sub-Saharan Africa, and is endemic in communities around Lake Victoria. Interest is growing in the molecular evolution and population genetic structure of Schistosoma mansoni and we describe a detailed analysis of the molecular epidemiology and phylogeography of S. mansoni from Lake Victoria. In total, 388 cytochrome oxidase 1 (COI) sequences were obtained from 25 sites along the Ugandan, Tanzanian and Kenyan shorelines of Lake Victoria, and 122 unique barcodes were identified; 9 corresponded to previously discovered barcodes from Lakes Victoria and Albert. A subset of the data, composed of COI sequences from miracidia from 10 individual children, was used for population genetics analyses; these results were corroborated by microsatellite analysis of 4 isolates of lab-passaged adult worms. Overall, 12 barcodes were found to be shared across all 3 countries, whereas the majority occurred singly and were locally restricted. The population genetics analyses were in agreement in revealing high diversity at the level of the human host and negligible population structuring by location. The lack of correlation between genetic distance and geographical distance in these data may be attributed to the confounding influence of high intra-individual diversity as well as human migration between communities.

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McCarty, C. A. "Epidemiology of pterygium in Victoria, Australia." British Journal of Ophthalmology 84, no. 3 (March 1, 2000): 289–92. http://dx.doi.org/10.1136/bjo.84.3.289.

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Globan, M., C. Lavender, D. Leslie, L. Brown, J. Denholm, K. Raios, A. Sievers, H. Kelly, and J. Fyfe. "Molecular epidemiology of tuberculosis in Victoria, Australia, reveals low level of transmission." International Journal of Tuberculosis and Lung Disease 20, no. 5 (May 1, 2016): 652–58. http://dx.doi.org/10.5588/ijtld.15.0437.

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Lemoh, Chris, Claire E. Ryan, Zamberi Sekawi, Anna C. Hearps, Eman Aleksic, Doris Chibo, Jeffrey Grierson, et al. "Acquisition of HIV by African-Born Residents of Victoria, Australia: Insights from Molecular Epidemiology." PLoS ONE 8, no. 12 (December 31, 2013): e84008. http://dx.doi.org/10.1371/journal.pone.0084008.

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Miron, Victor Daniel, Leontina Bănică, Oana Săndulescu, Simona Paraschiv, Marius Surleac, Dragoș Florea, Ovidiu Vlaicu, et al. "Clinical and molecular epidemiology of influenza viruses from Romanian patients hospitalized during the 2019/20 season." PLOS ONE 16, no. 11 (November 12, 2021): e0258798. http://dx.doi.org/10.1371/journal.pone.0258798.

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Two main mechanisms contribute to the continuous evolution of influenza viruses: accumulation of mutations in the hemagglutinin and neuraminidase genes (antigenic drift) and genetic re-assortments (antigenic shift). Epidemiological surveillance is important in identifying new genetic variants of influenza viruses with potentially increased pathogenicity and transmissibility. In order to characterize the 2019/20 influenza epidemic in Romania, 1042 respiratory samples were collected from consecutive patients hospitalized with acute respiratory infections in the National Institute for Infectious Diseases “Prof. Dr. Matei Balș”, Bucharest Romania and tested for influenza A virus, influenza B virus and respiratory syncytial virus (RSV) by real-time PCR. Out of them, 516 cases were positive for influenza, with relatively equal distribution of influenza A and B. Two patients had influenza A and B co-infection and 8 patients had influenza-RSV co-infection. The most severe cases, requiring supplemental oxygen administration or intensive care, and the most deaths were reported in patients aged 65 years and over. Subtyping showed the predominance of A(H3N2) compared to A(H1N1)pdm09 pdm09 (60.4% and 39.6% of all subtyped influenza A isolates, respectively), and the circulation of Victoria B lineage only. Influenza B started to circulate first (week 47/2019), with influenza A appearing slightly later (week 50/2019), followed by continued co-circulation of A and B viruses throughout the season. Sixty-eight samples, selected to cover the entire influenza season and all circulating viral types, were analysed by next generation sequencing (NGS). All A(H1N1)pdm09 sequences identified during this season in Romania were clustered in the 6b1.A clade (sub-clades: 6b1.A.183P -5a and 6b1.A.187A). For most A(H1N1)pdm09 sequences, the dominant epitope was Sb (pepitope = 0.25), reducing the vaccine efficacy by approximately 60%. According to phylogenetic analysis, influenza A(H3N2) strains circulating in this season belonged predominantly to clade 3C.3A, with only few sequences in clade 3C.2A1b. These 3C.2A1b sequences, two of which belonged to vaccinated patients, harbored mutations in antigenic sites leading to potential reduction of vaccine efficacy. Phylogenetic analysis of influenza B, lineage Victoria, sequences showed that the circulating strains belonged to clade V1A3. As compared to the other viral types, fewer mutations were observed in B/Victoria strains, with limited impact on vaccine efficiency based on estimations.

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Chibo, Doris, Christopher J. Birch, Paul A. Rota, and Michael G. Catton. "Molecular characterization of measles viruses isolated in Victoria, Australia, between 1973 and 1998." Journal of General Virology 81, no. 10 (October 1, 2000): 2511–18. http://dx.doi.org/10.1099/0022-1317-81-10-2511.

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Molecular epidemiology studies have made significant contributions to the control of measles virus infection through the identification of source and transmission pathways of the virus. These studies allow observation of changes in measles virus genotypes over time in a particular geographical location, clarification of epidemiological links during measles outbreaks, separation of indigenous strains from newly imported strains and distinction between vaccine- and wild-type virus-associated illness. A total of 35 wild-type measles viruses identified in Victoria, Australia, between 1973 and 1998 were characterized by nucleic acid sequence analysis of the nucleoprotein gene and, in some cases, the haemagglutinin gene. Relatedness between the viruses was studied and genotypes were assigned using a classification scheme recently proposed by the World Health Organization. Five recognized genotypes (C2, D1, D4, D5 and H) and one previously undescribed genotype, which we propose to be D7, were identified. Successive replacement of measles virus genetic lineages occurred in Victoria, with no evidence of temporal overlap, during this 25 year period. This pattern of circulation is likely to represent serial importation of wild-type measles virus strains from overseas foci of measles virus infections.

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Whittington, R. J., A. F. Hope, D. J. Marshall, C. A. Taragel, and I. Marsh. "Molecular Epidemiology of Mycobacterium avium subsp.paratuberculosis: IS900 Restriction Fragment Length Polymorphism and IS1311 Polymorphism Analyses of Isolates from Animals and a Human in Australia." Journal of Clinical Microbiology 38, no. 9 (2000): 3240–48. http://dx.doi.org/10.1128/jcm.38.9.3240-3248.2000.

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The distribution and prevalence of strains of Mycobacterium avium subsp. paratuberculosis were determined among sheep, cattle, and other species with Johne's disease in Australia. A total of 328 isolates were evaluated from numerous farms in New South Wales, Victoria, Tasmania, and South Australia, Australia. Restriction fragment length polymorphism (RFLP) analysis of genomic DNA usingBstEII and an IS900 probe and IS1311 polymorphism analysis using PCR and restriction endonuclease analysis (PCR-REA) was used to classify isolates as cattle (C) or sheep (S) strains. IS1311 PCR-REA provided similar information to IS900 RFLP analysis but was more useful than RFLP analysis where DNA was degraded or scarce. Twelve IS900 RFLP types were found. Johne's disease in sheep was always due to S strains, while cattle were infected only with C strains. RFLP type S1 was the dominant strain in sheep in New South Wales (97% of isolates) and was the only strain found in sheep from Victoria. Seven RFLP types were present in cattle. RFLP types C3 and C1 were most common (collectively, 85% of isolates), but C1 was not found in New South Wales and C3 was present in dairy cattle but not in beef cattle in Victoria. These differences may be explained by restricted livestock trading patterns between different segments of the cattle industry. Up to five RFLP types were present in some geographic regions in Victoria, while up to three RFLP types were found among cattle on some farms. Individual cattle usually were infected with only one RFLP type, but one animal was infected with both C5 and CU4. Two isolates from goats were C type as were three from alpacas, one from a rhinoceros, and two from a human with Crohn's disease. The prevalences of specific RFLP types in Australia differ from those reported in Europe and elsewhere. Given the existence of geographical and farm enterprise differences in IS900 RFLP type, this technique may be applied selectively to trace the spread of Johne's disease, at least in the cattle industries. As these observations reflect past exposure of livestock to M. avium subsp.paratuberculosis, the monitoring of strains present in animals in Australia is continuing.

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Touré, Cheikh Talibouya, Amary Fall, Soa Fy Andriamandimby, Mamadou Malado Jallow, Deborah Goudiaby, Davy Kiori, Sara Sy, et al. "Epidemiology and Molecular Analyses of Influenza B Viruses in Senegal from 2010 to 2019." Viruses 14, no. 5 (May 16, 2022): 1063. http://dx.doi.org/10.3390/v14051063.

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Influenza virus types A and B are responsible for acute viral infections that affect annually 1 billion people, with 290,000 to 650,000 deaths worldwide. In this study, we investigated the circulation of influenza B viruses over a 10-year period (2010–2019). Specimens from patients suspected of influenza infection were collected. Influenza detection was performed following RNA extraction and real-time RT-PCR. Genes coding for hemagglutinin (HA) and neuraminidase (NA) of influenza B viruses were partially sequenced, and phylogenetic analyses were carried out subsequently. During the study period, we received and tested a total of 15,156 specimens. Influenza B virus was detected in 1322 (8.7%) specimens. The mean age of influenza B positive patients was 10.9 years. When compared to reference viruses, HA genes from Senegalese circulating viruses showed deletions in the HA1 region. Phylogenetic analysis highlighted the co-circulation of B/Victoria and B/Yamagata lineage viruses with reassortant viruses. We also noted a clear seasonal pattern of circulation of influenza B viruses in Senegal.

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Bruggink, Leesa D., Jean M. Moselen, and John A. Marshall. "The Comparative Molecular Epidemiology of GII.P7_GII.6 and GII.P7_GII.7 Norovirus Outbreaks in Victoria, Australia, 2012-2014." Intervirology 59, no. 1 (2016): 60–65. http://dx.doi.org/10.1159/000448100.

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Shin, Hyejoo, Bong-Kwang Jung, Seungwan Ryoo, Sooji Hong, Heonwoo Jeong, Hoo-Gn Jeoung, Sunhye Kim, et al. "Molecular Detection of Haplorchis pumilio Eggs in Schoolchildren, Kome Island, Lake Victoria, Tanzania." Emerging Infectious Diseases 28, no. 11 (November 2022): 2298–301. http://dx.doi.org/10.3201/eid2811.220653.

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Seleka, Mpho, Florette K. Treurnicht, Stefano Tempia, Orienka Hellferscee, Senzo Mtshali, Adam L. Cohen, Amelia Buys, et al. "Epidemiology of influenza B/Yamagata and B/Victoria lineages in South Africa, 2005-2014." PLOS ONE 12, no. 5 (May 25, 2017): e0177655. http://dx.doi.org/10.1371/journal.pone.0177655.

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Masse, Shirley, Lisandru Capai, and Alessandra Falchi. "Epidemiology of Respiratory Pathogens among Elderly Nursing Home Residents with Acute Respiratory Infections in Corsica, France, 2013–2017." BioMed Research International 2017 (2017): 1–7. http://dx.doi.org/10.1155/2017/1423718.

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Background. The current study aims to describe the demographical and clinical characteristics of elderly nursing home (NH) residents with acute respiratory infections (ARIs) during four winter seasons (2013/2014–2016/2017), as well as the microbiological etiology of these infections. Methods. Seventeen NHs with at least one ARI resident in Corsica, France, were included. An ARI resident was defined as a resident developing a sudden onset of any constitutional symptoms in addition to any respiratory signs. Nasopharyngeal swabs from ARI residents were screened for the presence of 21 respiratory agents, including seasonal influenza viruses. Results. Of the 107 ARI residents enrolled from NHs, 61 (57%) were positive for at least one of the 21 respiratory pathogens. Forty-one (38.3%) of the 107 ARI residents had influenza: 38 (92%) were positive for influenza A (100% A(H3N2)) and three (8%) for influenza B/Victoria. Axillary fever (≥38°C) was significantly more common among patients infected with influenza A(H3N2). Conclusion. The circulation of seasonal respiratory viruses other than influenza A(H3N2) seems to be sporadic among elderly NH residents. Investigating the circulation of respiratory viruses in nonwinter seasons seems to be important in order to understand better the dynamic of their year-round circulation in NHs.

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Kwong, Jason C., Courtney R. Lane, Finn Romanes, Anders Gonçalves da Silva, Marion Easton, Katie Cronin, Mary Jo Waters, et al. "Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak." PeerJ 6 (January 3, 2018): e4210. http://dx.doi.org/10.7717/peerj.4210.

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BackgroundUntil recently,Klebsiella pneumoniaecarbapenemase (KPC)-producing Enterobacteriaceae were rarely identified in Australia. Following an increase in the number of incident cases across the state of Victoria, we undertook a real-time combined genomic and epidemiological investigation. The scope of this study included identifying risk factors and routes of transmission, and investigating the utility of genomics to enhance traditional field epidemiology for informing management of established widespread outbreaks.MethodsAll KPC-producing Enterobacteriaceae isolates referred to the state reference laboratory from 2012 onwards were included. Whole-genome sequencing was performed in parallel with a detailed descriptive epidemiological investigation of each case, using Illumina sequencing on each isolate. This was complemented with PacBio long-read sequencing on selected isolates to establish high-quality reference sequences and interrogate characteristics of KPC-encoding plasmids.ResultsInitial investigations indicated that the outbreak was widespread, with 86 KPC-producing Enterobacteriaceae isolates (K. pneumoniae92%) identified from 35 different locations across metropolitan and rural Victoria between 2012 and 2015. Initial combined analyses of the epidemiological and genomic data resolved the outbreak into distinct nosocomial transmission networks, and identified healthcare facilities at the epicentre of KPC transmission. New cases were assigned to transmission networks in real-time, allowing focussed infection control efforts. PacBio sequencing confirmed a secondary transmission network arising from inter-species plasmid transmission. Insights from Bayesian transmission inference and analyses of within-host diversity informed the development of state-wide public health and infection control guidelines, including interventions such as an intensive approach to screening contacts following new case detection to minimise unrecognised colonisation.ConclusionA real-time combined epidemiological and genomic investigation proved critical to identifying and defining multiple transmission networks of KPC Enterobacteriaceae, while data from either investigation alone were inconclusive. The investigation was fundamental to informing infection control measures in real-time and the development of state-wide public health guidelines on carbapenemase-producing Enterobacteriaceae surveillance and management.

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Robinson, D. E., J. Lane, R. Craig, A. Judge, J. Bailey, D. Yu, K. Jordan, et al. "FRI0511 THE DESCRIPTIVE EPIDEMIOLOGY AND SECULAR TRENDS OF LOWER BACK PAIN PROCEDURES IN ROUTINE UK NHS CARE FROM 2000 TO 2016." Annals of the Rheumatic Diseases 79, Suppl 1 (June 2020): 854–55. http://dx.doi.org/10.1136/annrheumdis-2020-eular.3230.

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Background:The lifetime prevalence of lower back pain is between 60% and 70%, with surgical treatments spared for those not responding to other options.Objectives:To investigate the age, gender and socio-economic status differences in back pain procedures in the UK between 2000, 2008 and 2016.Methods:Data was obtained from primary care electronic medical records (CPRD GOLD) linked to English hospital admissions data. Lower back procedures in patients aged 35+ were identified using OPCS-4 codes for Decompression (Dc), Fusion (F), Therapeutic injections (TI) and Denervation (Dn). Standardised incidence rates (IR) of each type of lower back procedures were calculated per 10,000 CPRD registered person years for each age group, gender, region and SES strata in 2000, 2008 and 2016. IR were also calculated for combinations of age and gender. Negative binomial regression calculated incidence rate ratios (IRR) and 95% confidence intervals.Results:The IR of lower back procedures was 21.5 [20.7, 22.3] per 10,000 person years in 2000. This doubled by 2008 (45.5 [44.5, 46.5]) and trebled by 2016 (62.5 [60.8, 64.2]). Number of events and incidence rates of each procedure type are shown in table 1 below. The incidence of Dn has increased 6-fold whilst Dc and F have doubled. Female (IR in 2016 of 73.99 [71.43, 76.61] vs 50.08 [47.90, 52.33] in men, IRR 1.50 [1.41, 1.59]) and age are associated with back procedure rates (figure 1). Large socio-economic differences were observed, with higher procedure rates seen in the most deprived areas. These differences did however narrow over time during the study period (figure 2).Table 1.Event numbers and incidence rates of different types of lower back procedure.FusionDecompressionTherapeutic InjectionDenervationEventsIR (95% CI)EventsIR (95% CI)EventsIR (95% CI)EventsIR (95% CI)20001090.86 (0.71, 1.04)4663.69 (3.36, 4.04)203516.11 (15.42, 16.82)910.72 (0.58, 0.88)20083331.77 (1.58, 1.97)11976.35 (6.00, 6.72)628333.35 (32.53, 34.18)5963.16 (2.91, 3.43)20161591.93 (1.65, 2.26)5256.39 (5.85, 6.96)386547.03 (45.56, 48.54)4875.93 (5.41, 6.48)Figure 1.Age and Gender stratified incidence rate ratios of all back procedures in 2000, 2008 and 2016Figure 2.Deprivation status incidence rate ratios by yearConclusion:The incidence of lower back procedures has more than trebled since 2000. Women are more likely to have lower back procedures than men, with patients aged 65-74 the most likely to have a procedure. Procedures in those aged 75+ have become more common over time, potentially increasing the risk of post-operative complications. Socio-economic differences in the incidence of low back procedures are probably related to the known higher prevalence of back pain in deprived areas. Whether the observed narrowing in socio-economic variation over time is explained by a reduced need or by lowered provision needs further research.Disclosure of Interests:Danielle E Robinson: None declared, Jennifer Lane: None declared, Richard Craig: None declared, Andrew Judge: None declared, James Bailey: None declared, Dahai Yu: None declared, Kelvin Jordan: None declared, George Peat: None declared, Ross Wilkie: None declared, Alan Silman: None declared, Victoria Y Strauss: None declared, Daniel Prieto-Alhambra Grant/research support from: Professor Prieto-Alhambra has received research Grants from AMGEN, UCB Biopharma and Les Laboratoires Servier, Consultant of: DPA’s department has received fees for consultancy services from UCB Biopharma, Speakers bureau: DPA’s department has received fees for speaker and advisory board membership services from Amgen

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Panatto, Donatella, Andrea Orsi, Beatrice Marina Pennati, Piero Luigi Lai, Stefano Mosca, Bianca Bruzzone, Patrizia Caligiuri, et al. "No evidence of SARS-CoV-2 in hospitalized patients with severe acute respiratory syndrome in five Italian hospitals from 1st November 2019 to 29th February 2020." PLOS ONE 16, no. 12 (December 7, 2021): e0260947. http://dx.doi.org/10.1371/journal.pone.0260947.

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Background On 9th January 2020, China CDC reported a novel coronavirus (later named SARS-CoV-2) as the causative agent of the coronavirus disease 2019 (COVID-19). Identifying the first appearance of virus is of epidemiological importance to tracking and mapping the spread of SARS-CoV-2 in a country. We therefore conducted a retrospective observational study to detect SARS-CoV-2 in oropharyngeal samples collected from hospitalized patients with a Severe Acute Respiratory Infection (SARI) enrolled in the DRIVE (Development of Robust and Innovative Vaccine Effectiveness) study in five Italian hospitals (CIRI-IT BIVE hospitals network) (1st November 2019 – 29th February 2020). Objectives To acquire new information on the real trend in SARS-CoV-2 infection during pandemic phase I and to determine the possible early appearance of the virus in Italy. Materials and methods Samples were tested for influenza [RT-PCR assay (A/H1N1, A/H3N2, B/Yam, B/Vic)] in accordance with the DRIVE study protocol. Subsequently, swabs underwent molecular testing for SARS-COV-2. [one-step real-time multiplex retro-transcription (RT) PCR]. Results In the 1683 samples collected, no evidence of SARS-CoV-2 was found. Moreover, 28.3% (477/1683) of swabs were positive for influenza viruses, the majority being type A (358 vs 119 type B). A/H3N2 was predominant among influenza A viruses (55%); among influenza B viruses, B/Victoria was prevalent. The highest influenza incidence rate was reported in patients aged 0–17 years (40.3%) followed by those aged 18–64 years (24.4%) and ≥65 years (14.8%). Conclusions In Italy, some studies have shown the early circulation of SARS-CoV-2 in northern regions, those most severely affected during phase I of the pandemic. In central and southern regions, by contrast no early circulation of the virus was registered. These results are in line with ours. These findings highlight the need to continue to carry out retrospective studies, in order to understand the epidemiology of the novel coronavirus, to better identify the clinical characteristics of COVID-19 in comparison with other acute respiratory illnesses (ARI), and to evaluate the real burden of COVID-19 on the healthcare system.

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Isnardi, C. A., R. Quintana, K. Roberts, V. V. Castro Coello, A. A. Reyes, Y. Tissera, M. Cosatti, et al. "POS1208 EPIDEMIOLOGY AND OUTCOMES OF PATIENTS WITH RHEUMATIC DISEASES AND SARS-CoV-2 INFECTION: DATA FROM THE ARGENTINEAN SAR-COVID REGISTRY." Annals of the Rheumatic Diseases 80, Suppl 1 (May 19, 2021): 887.1–887. http://dx.doi.org/10.1136/annrheumdis-2021-eular.2250.

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Background:In the last time, many papers about SARS-CoV-2 have been published in the world. However, data from latinamerican patients is still scarce. In order to assess the impact of SARS-CoV-2 infection in patients with rheumatic diseases in our country and contribute to the global knowledge about the effect of immunosuppressive therapies in this group, the Argentine Society of Rheumatology has developed the National Registry of Patients with Rheumatic Diseases and COVID-19 (SAR-COVID).Objectives:The aim of this study was to evaluate clinical characteristics and outcomes of SARS-CoV-2 infection in patients with rheumatic diseases, treated or not with immunomodulators and/or immunosuppressants.Methods:SAR-COVID is a national, multicenter, prospective and observational registry, in which patients, ≥18 years of age, with a diagnosis of a rheumatic disease who had SARS-CoV-2 infection (PCR or positive serology) are consecutively included between August 13, 2020 and January 17, 2021. Sociodemographic data, comorbidities, underlying rheumatic disease and treatment, clinical characteristics, complications, laboratory and treatment of the SARS-CoV-2 infection were recorded. Hospitalization, mechanical ventilation requirements and death were assessed to evaluate COVID-19 outcome. Statistical analysis: Descriptive analysis. Chi2 or Fischer test and T test or Mann-Whitney U test or ANOVA, as appropriate. Multiple logistic regression.Results:A total of 525 patients were included, 80.4% were female, with a median age of 52 years (IQR 40-62). Comorbidities were reported in half of them (53.3%). The most frequent rheumatological diseases were rheumatoid arthritis (40.4%) and systemic lupus erythematosus (14.9%). At the time of the infection, most of them were in remission or in minimal/low disease activity (68.2%) and 72.9% were receiving immunosuppressive or immunomodulatory treatment.Symptoms were present in 96% of the patients, the most frequent being fever (56.2%), cough (46.7%) and headache (39.2%). During infection, 35.1% received some pharmacological treatment, dexamethasone (20%) the most frequently used. One third (35.1%) of the patients were hospitalized, 11.6% were admitted to the ICU, 10.1% needed mechanical ventilation and 6.9% died due to COVID-19. Complications were reported in 12.4%, being acute respiratory distress syndrome the most prevalent (8.8%).Patients over 65 years of age were more frequently hospitalized, admitted to the ICU, needed mechanical ventilation and died due to COVID-19 (50% vs 31.4%, 22% vs 9%, 16.3% vs 5.2%, 14% vs 5%, respectively; p<0.001 in all cases). Similar results were seen in patients with vasculitis (57.7% vs 33.9%, 46.2 vs 9.8%, 34.6% vs 6 %; 30.8% vs 5.6%, respectively; p< 0.001 in all cases) and those with moderate/high disease activity (55.7% vs 26.5%, 21.3 vs 7.8%, 17.2% vs 4.2 %; 17.2% vs 4.2 %, respectively; p< 0.001 in all cases). Patients with APS were more frequently admitted to the ICU (29.4% vs 11%, p= 0.037). The presence of comorbidities was associated with higher hospitalization (46% vs 22.6%, p<0.001), admission to the ICU (17.2% vs 5.9%, p<0.001) and mechanical ventilation (10.2% vs 4.6%, p= 0.028). Immunosuppressive treatment was not associated with worse outcomes.Conclusion:In this cohort of patients with a wide distribution of rheumatic diseases, we have found clinical characteristics similar to those reported by other international cohorts. Compared with national data, the mortality reported in these patients is higher. However, it should be noted that these are early data collected during isolation and that there may be an underreporting of asymptomatic patients or with mild symptoms who do not attend the rheumatologist.Older patients, those with comorbidities, with vasculitis and with higher disease activity showed poor COVID-19 outcomes.Disclosure of Interests:Carolina Ayelen Isnardi Speakers bureau: Janssen, BMS, Grant/research support from: Unrestricted grants: Pfizer, Abbvie, Elea Phoenix. None of them have access to patient data., Rosana Quintana Grant/research support from: Unrestricted grants: Pfizer, Abbvie, Elea Phoenix. None of them have access to patient data., Karen Roberts Grant/research support from: Unrestricted grants: Pfizer, Abbvie, Elea Phoenix. None of them have access to patient data., Vanessa Viviana Castro Coello Grant/research support from: Unrestricted grants: Pfizer, Abbvie, Elea Phoenix. None of them have access to patient data., Alvaro Andres Reyes Grant/research support from: Unrestricted grants: Pfizer, Abbvie, Elea Phoenix. None of them have access to patient data., Yohana Tissera Grant/research support from: Unrestricted grants: Pfizer, Abbvie, Elea Phoenix. None of them have access to patient data., Micaela Cosatti Grant/research support from: Unrestricted grants: Pfizer, Abbvie, Elea Phoenix. None of them have access to patient data., Romina Rojas Tessel Grant/research support from: Unrestricted grants: Pfizer, Abbvie, Elea Phoenix. None of them have access to patient data., Julia Scafati Grant/research support from: Unrestricted grants: Pfizer, Abbvie, Elea Phoenix. None of them have access to patient data., Tatiana Barbich Grant/research support from: Unrestricted grants: Pfizer, Abbvie, Elea Phoenix. None of them have access to patient data., María Soledad Gálvez Elkin Grant/research support from: Unrestricted grants: Pfizer, Abbvie, Elea Phoenix. None of them have access to patient data., Gustavo Fabian Rodriguez Gil Grant/research support from: Unrestricted grants: Pfizer, Abbvie, Elea Phoenix. None of them have access to patient data., Sebastian Moyano Grant/research support from: Unrestricted grants: Pfizer, Abbvie, Elea Phoenix. None of them have access to patient data., Marina Laura Werner Grant/research support from: Unrestricted grants: Pfizer, Abbvie, Elea Phoenix. None of them have access to patient data., Jonathan Rebak Grant/research support from: Unrestricted grants: Pfizer, Abbvie, Elea Phoenix. None of them have access to patient data., Julieta Morbiducci Grant/research support from: Unrestricted grants: Pfizer, Abbvie, Elea Phoenix. None of them have access to patient data., Victoria Martire Grant/research support from: Unrestricted grants: Pfizer, Abbvie, Elea Phoenix. None of them have access to patient data., María Sol Castaño Grant/research support from: Unrestricted grants: Pfizer, Abbvie, Elea Phoenix. None of them have access to patient data., Carolina Dieguez Grant/research support from: Unrestricted grants: Pfizer, Abbvie, Elea Phoenix. None of them have access to patient data., Gisela Constanza Subils Grant/research support from: Unrestricted grants: Pfizer, Abbvie, Elea Phoenix. None of them have access to patient data., Guillermo Pons-Estel Grant/research support from: Unrestricted grants: Pfizer, Abbvie, Elea Phoenix. None of them have access to patient data.

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Anjum, Hira, Hira Munir, Aftab Ali, Ummara Munir, Tehreem Abaid, and Talha Naeem Cheema. "Patterns of Lip-prints in Undergraduate Medical Students of Bahawalpur." Pakistan Journal of Medical and Health Sciences 16, no. 5 (May 30, 2022): 1582–84. http://dx.doi.org/10.53350/pjmhs221651582.

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Objectives: To determine the frequency of different lip patterns among medical students. Study Design: Cross Sectional Study (Descriptive) Setting and Duration of Study: Department of Forensic Medicine & Toxicology, QAMC/ Bahawal Victoria Hospital, Bahawalpur. From 15th January 2018 to 14 March 2018 Materials and Methods: Total 203 of medical students 18-25 years of age of and both genders was selected. Subjects with any lip deformity or allergic episode with lip stick were excluded. After application of a dark colored, non-glossy, less moist lipstick on lips, lip-prints were obtained on a cellophane tape and then pasted on A4 paper. Results: Out of these 203 subjects, 110 (54.19%) were men and 93 (45.81%) were women with M:F ratio of 1.2:1. In this study, Type I (26.11%) and Type II (20.69%) was the utmost communal lip patterns, trailed by Type-I’ (18.72%), Type III (18.23%), Type IV (10.34%) and Type V (5.91%). Conclusion: This study concluded that cheiloscopy and its pattern recognition in varying circumstances provide valuable information with regards to identification of an individual. Keywords: Cheiloscopy, Identification, Fingerprinting, Geographical Area

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Kamat, Ashish M. "Commentary on “Risks of primary extracolonic cancers following colorectal cancer in lynch syndrome.” Win AK, Lindor NM, Young JP, Macrae FA, Young GP, Williamson E, Parry S, Goldblatt J, Lipton L, Winship I, Leggett B, Tucker KM, Giles GG, Buchanan DD, Clendenning M, Rosty C, Arnold J, Levine AJ, Haile RW, Gallinger S, Le Marchand L, Newcomb PA, Hopper JL, Jenkins MA, Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, Melbourne School of Population Health, The University of Melbourne, Victoria, Australia." Urologic Oncology: Seminars and Original Investigations 31, no. 5 (July 2013): 716. http://dx.doi.org/10.1016/j.urolonc.2013.03.013.

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Yates, M., M. Theobald, and M. Morvell. "The cognitive impairment identifier program: A Victorian hospital alert and education program for cognitive impairment." Alzheimer's & Dementia 5, no. 5 (September 2009): e17-e17. http://dx.doi.org/10.1016/j.jalz.2009.07.036.

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Oliver, Jane, Mathilda Wilmot, Janet Strachan, Siobhan St George, Courtney R. Lane, Susan A. Ballard, Michelle Sait, Katherine Gibney, Benjamin P. Howden, and Deborah A. Williamson. "Recent trends in invasive group A Streptococcus disease in Victoria." Communicable Diseases Intelligence 43 (March 15, 2019). http://dx.doi.org/10.33321/cdi.2019.43.8.

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Background Invasive Group A Streptococcus (iGAS) disease can cause permanent disability and death. The incidence of iGAS has increased in many developed countries since the 1980s. iGAS disease is not nationally notifiable in Australia or at the state level in Victoria. The Victorian Hospital Pathogen Surveillance Scheme (VHPSS) is a voluntary laboratory-based surveillance system established in 1988. We assessed the trends and molecular epidemiology of iGAS disease in Victoria from 2007-2017. Methods A case of iGAS was defined as an individual for whom Group A Streptococcus (GAS) was isolated from a normally sterile body site. Data on all iGAS cases, as reported to the VHPSS, between 1 January 2007 and 31 December 2017 were examined. Results A total of 1,311 iGAS cases had associated isolates, and M Protein Gene (emm) typing was performed for 91.6%. The mean annual incidence was 2.1 (95% CI: 1.8-2.5) per 100,000 population per year, increasing 2.7-fold over the study period. In total, 140 different iGAS emm-types were observed, with the ten most prevalent types comprising 63.1% of the sample. Conclusions Despite limitations in this surveillance data, we observed increasing rates of iGAS disease in Victoria. iGAS incidence exceeded the mean annual incidence for invasive meningococcal disease, calculated using Victorian data from the National Notifiable Diseases Surveillance System (2.1 vs. 0.6 cases per 100,000 population per year, respectively). Mandatory case notification could enhance disease control and prevention. Further, the diversity in emm-types emphasises the importance of effective secondary chemoprophylaxis in prevention, alongside GAS vaccine development.

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Korsun, N. S., S. G. Angelova, I. T. Trifonova, I. L. Georgieva, I. S. Tzotcheva, S. D. Mileva, S. E. Voleva, A. M. Kurchatova, and P. I. Perenovska. "Predominance of influenza B/Yamagata lineage viruses in Bulgaria during the 2017/2018 season." Epidemiology and Infection 147 (2019). http://dx.doi.org/10.1017/s0950268818003588.

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AbstractIn this study, we investigated the antigenic and genetic characteristics of influenza viruses circulating in Bulgaria during the 2017/2018 season. The detection and typing/subtyping of influenza viruses were performed using real-time RT-PCR. Results of antigenic characterisation, phylogenetic and amino acid sequence analyses of representative influenza strains are presented. The season was characterised by the predominance of B/Yamagata viruses, accounting for 77% of detected influenza viruses, followed by A(H1N1)pdm09 (17%), B/Victoria (3.7%) and A(H3N2) (2.4%). The sequenced B/Yamagata, B/Victoria, A(H1N1)pdm09 and A(H3N2) viruses belonged to the genetic groups 3, 1A, 6B.1 and 3C.2a1, respectively. Amino acid analysis of B/Yamagata isolates revealed the presence of three changes in haemagglutinin (HA), eight changes in neuraminidase (NA) and a number of substitutions in internal proteins compared with the B/Phucket/3073/2013 vaccine virus. Despite the amino acid changes, B/Yamagata viruses remained antigenically related to the vaccine strain. B/Victoria isolates fell into a group of viruses with double deletion (Δ162–163) in HA1. Substitutions in HA and NA sequences of B/Victoria, A(H1N1)pdm09 and A(H3N2) viruses were also identified compared with the vaccine strains, including in antigenic sites. The results of this study confirm the genetic variability of circulating influenza viruses and the need for continual antigenic and molecular surveillance.

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Sherry, Norelle L., Courtney R. Lane, Jason C. Kwong, Mark Schultz, Michelle Sait, Kerrie Stevens, Susan Ballard, et al. "Genomics for Molecular Epidemiology and Detecting Transmission of Carbapenemase-Producing Enterobacterales in Victoria, Australia, 2012 to 2016." Journal of Clinical Microbiology 57, no. 9 (July 17, 2019). http://dx.doi.org/10.1128/jcm.00573-19.

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ABSTRACT Carbapenemase-producing Enterobacterales (CPE) are being increasingly reported in Australia, and integrated clinical and genomic surveillance is critical to effectively manage this threat. We sought to systematically characterize CPE in Victoria, Australia, from 2012 to 2016. Suspected CPE were referred to the state public health laboratory in Victoria, Australia, from 2012 to 2016 and examined using phenotypic, multiplex PCR and whole-genome sequencing (WGS) methods and compared with epidemiological metadata. Carbapenemase genes were detected in 361 isolates from 291 patients (30.8% of suspected CPE isolates), mostly from urine (42.1%) or screening samples (34.8%). IMP-4 (28.0% of patients), KPC-2 (25.3%), NDM (24.1%), and OXA carbapenemases (22.0%) were most common. Klebsiella pneumoniae (48.8% of patients) and Escherichia coli (26.1%) were the dominant species. Carbapenemase-inactivation method (CIM) testing reliably detected carbapenemase-positive isolates (100% sensitivity, 96.9% specificity), identifying an additional five CPE among 159 PCR-negative isolates (IMI and SME carbapenemases). When epidemiologic investigations were performed, all pairs of patients designated “highly likely” or “possible” local transmission had ≤23 pairwise single-nucleotide polymorphisms (SNPs) by genomic transmission analysis; conversely, all patient pairs designated “highly unlikely” local transmission had ≥26 pairwise SNPs. Using this proposed threshold, possible local transmission was identified involving a further 16 patients for whom epidemiologic data were unavailable. Systematic application of genomics has uncovered the emergence of polyclonal CPE as a significant threat in Australia, providing important insights to inform local public health guidelines and interventions. Using our workflow, pairwise SNP distances between CPE isolates of ≤23 SNPs suggest local transmission.

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Mao, Haiyan, Yi Sun, Yin Chen, Xiuyu Lou, Zhao Yu, Xinying Wang, Zheyuan Ding, et al. "Co-circulation of influenza A(H1N1), A(H3N2), B(Yamagata) and B(Victoria) during the 2017−2018 influenza season in Zhejiang Province, China." Epidemiology and Infection 148 (2020). http://dx.doi.org/10.1017/s0950268820000412.

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Abstract Influenza is a major human respiratory pathogen. Due to the high levels of influenza-like illness (ILI) in Zhejiang, China, the control and prevention of influenza was challenging during the 2017–2018 season. To identify the clinical spectrum of illness related to influenza and characterise the circulating influenza virus strains during this period, the characteristics of ILI were studied. Viral sequencing and phylogenetic analyses were conducted to investigate the virus types, substitutions at the amino acid level and phylogenetic relationships between sequences. This study has shown that the 2017/18 influenza season was characterised by the co-circulation of influenza A (H1N1) pdm09, A (H3N2) and B viruses (both Yamagata and Victoria lineage). From week 36 of 2017 to week 12 of 2018, ILI cases accounted for 5.58% of the total number of outpatient and emergency patient visits at the surveillance sites. Several amino acid substitutions were detected. Vaccination mismatch may be a potential reason for the high percentage of ILI. Furthermore, it is likely that multiple viral introductions played a role in the endemic co-circulation of influenza in Zhejiang, China. More detailed information regarding the molecular epidemiology of influenza should be included in long-term influenza surveillance.

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Vijaykrishna, Dhanasekaran, Edward C. Holmes, Udayan Joseph, Mathieu Fourment, Yvonne CF Su, Rebecca Halpin, Raphael TC Lee, et al. "The contrasting phylodynamics of human influenza B viruses." eLife 4 (January 16, 2015). http://dx.doi.org/10.7554/elife.05055.

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A complex interplay of viral, host, and ecological factors shapes the spatio-temporal incidence and evolution of human influenza viruses. Although considerable attention has been paid to influenza A viruses, a lack of equivalent data means that an integrated evolutionary and epidemiological framework has until now not been available for influenza B viruses, despite their significant disease burden. Through the analysis of over 900 full genomes from an epidemiological collection of more than 26,000 strains from Australia and New Zealand, we reveal fundamental differences in the phylodynamics of the two co-circulating lineages of influenza B virus (Victoria and Yamagata), showing that their individual dynamics are determined by a complex relationship between virus transmission, age of infection, and receptor binding preference. In sum, this work identifies new factors that are important determinants of influenza B evolution and epidemiology.

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Opere, Wasonga Michael, Maingi John, and Omwoyo Ombori. "Molecular Detection of Human Enteric Adenoviruses in Water Samples Collected from Lake Victoria Waters Along Homa Bay Town, Homa Bay County, Kenya." Food and Environmental Virology, November 3, 2020. http://dx.doi.org/10.1007/s12560-020-09444-y.

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Journal articles on the topic 'Molecular epidemiology Victoria'

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