RT-PCR For Influenza Research Articles

Cross-Species Surveillance of Respiratory Viruses in Domestic and Wild Mammals of an Urban Atlantic Forest from Brazil.

Our aim was to investigate respiratory viruses circulating in animals from the urban Atlantic Forest, which is located in the most densely populated area near Rio de Janeiro in Brazil. This study focused on the detection of Influenza A viruses and diverse coronaviruses, including SARS-CoV-2, in domestic and wild animals, including bats, nonhuman primates, rodents, and marsupials. From August 2020 to September 2022, biological samples were collected from a total of 72 pets, 66 primates, 20 rodents, 36 marsupials, and 390 bats. Samples were tested using RT-PCR for Influenza A and coronaviruses, and positive samples were sequenced. When blood samples were available, they were tested for SARS-CoV-2 antibodies. All terrestrial animals were negative for evidence of infection with SARS-CoV-2 and Influenza A viruses. However, samples from 17 phyllostomid bats, including Great fruit-eating bat (Artibeus lituratus), Silky short-tailed bat (Carollia brevicauda), Seba's short-tailed bat (Carollia perspicillata), Common big-eared bat (Micronycteris microtis), Greater spear-nosed bat (Phyllostomus hastatus), White-lined broad-nosed bat (Platyrrhinus lineatus), Little yellow-shouldered bat (Sturnira lilium), Greater round-eared bat (Tonatia bidens), and Common vampire bat (Desmodus rotundus), were positive for bat coronaviruses classified as Alphacoronavirus. Our study adds new information on the occurrence of coronaviruses in bats and contributes to a long-term program of Influenza surveillance. Developing active surveillance for viruses in wildlife species, as implemented in this study, is crucial for understanding zoonotic risks and preventing future global pandemics.

Effectiveness of 2023 southern hemisphere influenza vaccines against severe influenza-associated illness: pooled estimates from eight countries using the test-negative design.

Annual estimates of seasonal influenza vaccine effectiveness can guide global risk communication and vaccination strategies to mitigate influenza-associated illness. We aimed to evaluate vaccine effectiveness in countries using the 2023 southern hemisphere influenza vaccine formulation. We evaluated end-of-season influenza vaccine effectiveness across eight countries (Argentina, Australia, Brazil, Chile, New Zealand, Paraguay, Thailand, and Uruguay) that used the 2023 southern hemisphere vaccine formulation, with use of a test-negative design. All patients who attended participating hospitals with severe acute respiratory illness were tested by RT-PCR for influenza. We calculated country-specific, network-specific, and pooled vaccine effectiveness against hospitalisation. For countries with sufficient data, we also calculated vaccine effectiveness against intensive care unit (ICU) admission by comparing the odds of vaccination among test-positive cases to that among test-negative controls. We evaluated vaccine effectiveness for groups prioritised for vaccination (young children aged 1-4 years, people aged 5-64 years with underlying health conditions, and older adults aged ≥65 years). From March 5 to Nov 27, 2023, 31 368 individuals were admitted to hospital with severe acute respiratory infection in the eight included countries. Of these, 12 609 individuals admitted to hospital (6452 [51·2%] female and 6157 [48·8%] male) who met inclusion criteria and had complete data were included in the analysis, including 4388 test-positive cases and 8221 test-negative controls. Pooled vaccine effectiveness against hospitalisation with any influenza virus was 51·9% (95% CI 37·2-66·7), with substantial heterogeneity across countries (I2 74%). Vaccine effectiveness against ICU admission from any influenza virus was 67·7% (44·5-81·2) in Chile and 69·7% (45·3-83·3) in Australia. Vaccine effectiveness estimates against hospitalisation were highest for young children (70·9% [47·5-94·4]) and lowest for older adults (47·7% [24·9-70·5]). Across eight countries, 2023 southern hemisphere vaccines were effective in reducing hospitalisations from influenza illness. Use of common protocols can facilitate data pooling to provide a comprehensive evaluation of vaccine effectiveness across settings. US Centers for Disease Control and Prevention cooperative agreements to the Pan American Health Organization and the Thailand Ministry of Public Health; the Australian Government Department of Health and Aged Care; and the New Zealand Ministry of Health.

P-2328. Influenza and RSV Surveillance in the US Veterans Health Administration (VHA): 2023-2024 Season

Abstract Background Influenza and Respiratory Syncytial Virus (RSV) cause seasonal epidemics with substantial morbidity and mortality. Veterans Health Administration’s (VHA) large elderly population is at higher risk for complications, including hospitalization and death. Herein we summarize VHA’s annual surveillance data for influenza and RSV activity and vaccinations. Methods Influenza-like-illness (ILI) as well as influenza and RSV-coded outpatient visits and hospitalizations, laboratory testing, and antivirals were obtained from VHA data sources (10/1/2023-4/13/2024) and compared to prior years and CDC data. VHA and community vaccinations were captured starting August 1st each year, with rates calculated based on VHA users in each fiscal year. Influenza RT-PCR positive respiratory samples underwent whole genome sequencing (WGS) to analyze clade and antiviral resistance. Results Influenza vaccinations (including high dose) were increased compared to 2022-2023 (Table). Weekly ILI ranged from 0.6%-1.6% in primary/urgent care settings. Activity was highest for 2023 Week 52, matching national influenza trends and increased compared to last season (Fig.1). There were 28,853 influenza positives among 438,110 tests performed (6.6%). Median length of stay was 3 days in 4,059 hospitalizations. Among 139 deaths, 129 (92.8%) had Influenza A and 10 (7.2%) Influenza B (Table, Fig.2). 310 samples (in 5 states) were sequenced with no drug resistance mutations identified (237 A/H1; 30 A/H3; 43 B/Victoria), representing 4 subclades, which aligned with CDC reporting (Fig.3). Over 270,000 Veterans received an RSV vaccine in 2023-2024 (over 177,000 administered by VHA). RSV visits, hospitalizations and positive tests were increased compared to 2022-2023. Conclusion For 2023-2024, influenza vaccinations (including high dose) increased compared to prior years, and newly licensed RSV vaccines were available in VHA. Influenza and RSV activity was increased compared to the prior season. VHA influenza activity and WGS analysis tracks closely with national CDC reporting. Given risks associated with influenza and RSV in the elderly population, VHA will continue efforts to improve vaccination rates. Disclosures All Authors: No reported disclosures

P-1316. Influenza Antiviral Prescribing Practices for Outpatients with an Acute Respiratory Illness and at Increased Risk for Influenza-Associated Complications pre- and post-COVID-19 pandemic — United States, 2016–2022

Abstract Background Early antiviral treatment (< 2 days after illness onset) can reduce the risk of influenza-associated complications and is recommended for outpatients at increased risk. However, in previous influenza seasons, antivirals have been underprescribed. We describe influenza antiviral prescribing practices for outpatients from 2016-2022. Methods We analyzed influenza antiviral prescription data from 5 US Influenza Vaccine Effectiveness Network sites pre-pandemic, 2016-2017 through 2019-2020, and post-pandemic, 2021–2022 (2020-2021 season not included due to low influenza circulation). Patients enrolled were aged ≥6 months presenting with an acute respiratory illness with a new or worsening cough ≤7 days duration. All had respiratory specimens collected for influenza RT-PCR testing. Patients at increased risk for severe outcome included those aged < 2 years, ≥ 65 years, and those with at least one underlying medical condition. Electronic medical records were examined to determine whether antivirals were prescribed within 7 days after enrollment. Results Among 21,483 patients at increased risk enrolled in the US Flu VE Network between 2016-2017 and 2021-2022, 8% (1,852) were prescribed antivirals within 7 days. In pre-pandemic seasons, the average proportion of those prescribed antivirals was 9.5% overall and lowest during the 2019-2020 season (6%); post-pandemic, this proportion decreased to 1%. Among confirmed influenza cases, 40% (874/2210) of those at increased risk who presented for care < 2 days after illness onset were prescribed antivirals across all 5 seasons. Similarly, during the pre-pandemic seasons the average proportion of patients prescribed antivirals was 40% with the lowest percentage observed during the 2019-2020 season (26%). This proportion continued to trend downward post-pandemic (21%). Conclusion Over the last several seasons, influenza antiviral medications have been infrequently prescribed, including among those at increased risk for severe illness who present early in their illness. Efforts to increase appropriate antiviral prescribing may reduce influenza-associated complications among outpatients presenting early for care. Disclosures All Authors: No reported disclosures

Influenza A in children complicated by encephalitis - case study

Influenza is a seasonal disease that can cause annual outbreaks, especially during the cold periods of the year, in temperate areas. Symptomatology mainly involves the upper and lower respiratory tract, but varies greatly depending on the age and medical history of each person. In this paper we present a clinical case of influenza type A complicated with encephalitis in a female child aged 5 years and 6 months with a personal pathological history of neurological damage (Guillain-Barre syndrome). The diagnosis of influenza was established on the basis of symptoms (productive cough, rhinorrhea, marked physical asthenia, high fever) and confirmed by laboratory tests (rapid influenza antigen test and influenza RT PCR from nasopharyngeal secretions - positive). Neurological involvement was clinically supported by the occurrence of bradykinesia, bradypsy, broad-based gait, confirmed by neurological examination. The diagnosis of encephalitis was completed by analysis of cerebrospinal fluid (CSF) obtained by lumbar puncture in which influenza virus type A was identified and by electroencephalogram (EEG) showing altered tracing. Under antiviral (Oseltamivir), pathogenic (corticosteroid therapy), brain depleting (mannitol solution), non-specific human and symptomatic immunoglobulins treatments, the evolution was slowly favorable with remission of symptoms. The case presented argues that although influenza in immunocompetent children is generally a self-limiting and uncomplicated condition, it can evolve severely with the development of complications and after-effects and sometimes increased mortality especially in immunocompromised hosts.

898. Influenza Surveillance in the US Veterans Health Administration (VHA): 2022-2023 Season

Abstract Background Influenza causes seasonal epidemics with substantial morbidity and mortality. Veterans Health Administration’s (VHA) large elderly population is at higher risk for influenza complications, including hospitalization, and death. Herein we summarize VHA’s national annual surveillance data for influenza activity and vaccinations. Methods Influenza-like-illness (ILI) as well as influenza-coded outpatient visits and hospitalizations, laboratory testing, and antivirals were obtained from VHA data sources (10/2/2022-4/22/23) and compared to prior years and CDC data. Vaccinations were captured starting 8/1/2022, with rates calculated based on VHA users in each fiscal year. Influenza RT-PCR positive respiratory samples underwent whole genome sequencing (WGS) to analyze clade and antiviral resistance. Results Surveillance metrics are presented (Table). Vaccinations were decreased compared to 2021-22, but the used of adjuvanted vaccine was increased. Weekly ILI ranged from 0.4%-1.4% in primary/urgent care settings. Activity was highest for 2022 Week 48, matching national influenza trends (Fig.1). Testing found 23,297 influenza positives of 457,020 tests performed (5.1%). Median length of stay (3 days) for hospitalized patients and deaths (127, 3%) were stable. Among 115 deaths where influenza type was available, 110 had Influenza A and 5 Influenza B. Following two low activity seasons, total influenza positives, outpatient visits, and hospitalizations during 2022-23 tracked closer to seasons prior to the COVID-19 pandemic (Table, Fig.2). 411 samples (in 16 states) were sequenced (410 Flu A: 136 H1, 274 H3; 1 B/Victoria), representing 12 subclades, which aligned with CDC reporting. No drug resistance mutations were found (Fig.3). Conclusion For 2022-23, influenza vaccinations in VHA dropped but percent vaccinated was stable. For the first time, over half of VHA-administered vaccines were adjuvanted formulation. The influenza season was notable for an earlier than usual peak (late Nov/early Dec), with overall increased activity compared to the prior two seasons. Testing for influenza during 2022-23 season was decreased but remained higher than pre-COVID-19 pandemic testing levels. VHA influenza activity and WGS analysis tracks closely with national CDC reporting. Disclosures All Authors: No reported disclosures

A SARS-CoV-2 and influenza rapid antigen test-based hospital isolation policy awaiting RT-PCR, a prospective observational study

This study aimed to evaluate the clinical performance of a combined SARS-CoV-2/influenza rapid antigen test (SIRAT) and to evaluate a SIRAT-based hospital isolation policy awaiting RT-PCR results for patients presenting at the emergency department (ED). We performed a prospective observational study including all adult patients presenting with influenza-like symptoms at the ED of two hospitals from 31 October 2022 to 31 March 2023. A SIRAT and SARS-CoV-2 and influenza RT-PCR were performed on upper respiratory samples. SIRAT results were compared with RT-PCR. Droplet and contact isolation measures (DCIM) were imposed based on SIRAT results awaiting RT-PCR. We monitored symptomatic nosocomial SARS-CoV-2 and influenza infections potentially caused by delayed isolation of patients with false negative SIRAT and the hours of unnecessary DCIM saved. We included 1740 patients of whom 1296 were hospitalized. SARS-CoV-2 and influenza A/B prevalence were 12.7% (221/1740) and 9.9% (171/1740). Sensitivity and specificity of the SIRAT were 67.7% (95% CI 61.1-73.9%) (149/220) and 99.4% (95% CI 99.0-99.8%) (1510/1518) for SARS-CoV-2 and 52.7% (95% CI 44.9-60.4%) (89/169) and 99.1% (95% CI 98.5-99.5%) (1530/1544) for influenza A/B. We found a 0% nosocomial transmission risk for SARS-CoV-2 (95% CI 0-8.8%) and influenza (95% CI 0-10%). In all, 8712hours in total or a median up to 6hours 59minutes (IQR (interquartile range) 11h03) per patient of unnecessary DCIM were saved. A SIRAT-guided hospital isolation policy awaiting RT-PCR results for patients who present at the ED can save unnecessary isolation hours without having to lead to significant symptomatic nosocomial transmission of SARS-CoV-2 or influenza viruses.

Preschool-located influenza vaccination and influenza-like illness surveillance: an Italian pilot experience

BackgroundWe describe the first school-located influenza vaccination campaign with quadrivalent live-attenuated influenza vaccine (LAIV) among pre-school children in Italy, coupled with an innovative school-centred influenza-like illnesses (ILIs) surveillance using a self-sampling non-invasive saliva collection method.MethodsThe pilot study was proposed during the 2021/2022 influenza season to fifteen pre-schools in the Milan municipality. LAIV was offered directly in school to all healthy children without contraindications. ILI differential diagnosis was conducted by real-time RT-PCR for influenza A/B and SARS-CoV-2.ResultsFive pre-schools were involved in the pilot project and overall, 135 families (31.2%) participated in the study, adhering to both surveillance and vaccination; 59% of families had an immigrant background. No pupil experienced adverse reactions after vaccination. Nineteen saliva samples were collected from sixteen children (11.8%). Six samples (31.6%) tested positive for SARS-CoV-2; none was positive for influenza A/B.ConclusionsThe participation in the immunisation campaign was good, considering possible absences due to COVID-19 pandemic, and the intranasal administration was well tolerated and helped to overcome parental hesitancy. Saliva sampling represented a useful tool to reduce children’s stress and increase parents’ compliance. The high participation of families with an immigrant background suggests that school-based interventions can represent an effective strategy to overcome socioeconomic and cultural barriers.

Rapid Multiplex RT-PCR for Influenza A and B by Genesoc®, a Microfluidic PCR System

Rapid antigen tests are widely used to diagnose influenza. However, despite their simplicity and short turnover time, the sensitivity of these tests is relatively low, and molecular tests with greater sensitivity are being sought. In this study, we developed and clinically evaluated a protocol for the rapid multiplex testing of influenza A and B, using a rapid real-time PCR system, GeneSoC®, that is based on microfluidic thermal cycling technology. The specificity of the developed assay was validated using cultured viral strains of influenza A/B, human metapneumovirus, and respiratory syncytial virus. Analytical sensitivity was evaluated using serially diluted RNA synthesized via in vitro transcription and nasopharyngeal swab samples collected from consecutive patients seeking medical attention for a combination of upper respiratory and general symptoms. Cross-validation of GeneSoC® based on comparisons with conventional real-time RT-PCR and rapid antigen tests was performed by parallel testing of influenza-positive clinical specimens. The GeneSoC® assay detected the target sequences of influenza A and B at minimum concentrations of 38 and 65 copies/µL in reaction, respectively. For the analysis of clinical specimens, the positive, negative, and overall agreement between GeneSoC® RT-PCR and a conventional real-time RT-PCR was in all cases 100%, whereas for the comparison between GeneSoC® RT-PCR and the rapid antigen test, the agreements for positive, negative, and overall findings were 100%, 90.9%, and 95.7%, respectively. The mean time for completing GeneSoC® RT-PCR was 16 min 29 s (95% confidence interval, 16 min 18 s to 16 min 39 s). The microfluidic real-time PCR system, GeneSoC®, has an analytical performance comparable to that of conventional real-time RT-PCR with rapid turnover time, and represents a promising alternative to rapid antigen tests for diagnosing influenza A and B.

Developing and validating clinical features-based machine learning algorithms to predict influenza infection in influenza-like illness patients

Seasonal influenza poses a significant risk, and patients can benefit from early diagnosis and treatment. However, underdiagnosis and undertreatment remain widespread. We developed and compared clinical feature-based machine learning (ML) algorithms that can accurately predict influenza infection in emergency departments (EDs) among patients with influenza-like illness (ILI). We conducted a prospective cohort study in five EDs in the US and Taiwan from 2015 to 2020. Adult patients visiting the EDs with symptoms of ILI were recruited and tested by real-time RT-PCR for influenza. We evaluated seven ML algorithms and compared their results with previously developed clinical prediction models. Out of the 2189 enrolled patients, 1104 tested positive for influenza. The eXtreme Gradient Boosting achieved superior performance with an area under the receiver operating characteristic curve of 0.82 (95% confidence interval [CI]=0.79-0.85), with a sensitivity of 0.92 (95% CI=0.88-0.95), specificity of 0.89 (95% CI=0.86-0.92), and accuracy of 0.72 (95% CI=0.69-0.76) in the testing set over cut-offs of 0.4, 0.6 and 0.5, respectively. These results were superior to those of previously proposed clinical prediction models. The model interpretation revealed that body temperature, cough, rhinorrhea, and exposure history were positively associated with and the days of illness and influenza vaccine were negatively associated with influenza infection. We also found the week of the influenza season, pulse rate, and oxygen saturation to be associated with influenza infection. The clinical feature-based ML model outperformed conventional models for predicting influenza infection.

Genetic Evolution of Avian Influenza A (H9N2) Viruses Isolated from Domestic Poultry in Uganda Reveals Evidence of Mammalian Host Adaptation, Increased Virulence and Reduced Sensitivity to Baloxavir.

A (H9N2) avian influenza A viruses were first detected in Uganda in 2017 and have since established themselves in live bird markets. The aim of this study was to establish the subsequent genetic evolution of H9N2 viruses in Uganda. Cloacal samples collected from live bird market stalls in Kampala from 2017 to 2019 were screened by RT-PCR for influenza A virus and H9N2 viruses were isolated in embryonated eggs. One hundred and fifty H9N2 isolates were subjected to whole genome sequencing on the Illumina MiSeq platform. The sequence data analysis and comparison with contemporary isolates revealed that the virus was first introduced into Uganda in 2014 from ancestors in the Middle East. There has since been an increase in nucleotide substitutions and reassortments among the viruses within and between live bird markets, leading to variations in phylogeny of the different segments, although overall diversity remained low. The isolates had several mutations such as HA-Q226L and NS-I106M that enable mammalian host adaptation, NP-M105V, PB1-D3V, and M1-T215A known for increased virulence/pathogenicity and replication, and PA-E199D, NS-P42S, and M2-S31N that promote drug resistance. The PA-E199D substitution in particular confers resistance to the endonuclease inhibitor Baloxavir acid, which is one of the new anti-influenza drugs. Higher EC50 was observed in isolates with a double F105L+E199D substitution that may suggest a possible synergistic effect. These H9N2 viruses have established an endemic situation in live bird markets in Uganda because of poor biosecurity practices and therefore pose a zoonotic threat. Regular surveillance is necessary to further generate the needed evidence for effective control strategies and to minimize the threats.

Incidence and neutralizing antibody seroprevalence of influenza B virus in Egypt: Results of a community-based cohort study.

Since 2000, two lineages of influenza B viruses, Victoria and Yamagata, have been circulating at similar frequencies worldwide. Little is known about the circulation of those viruses in Egypt. This study aims to describe the epidemiology of influenza B virus infections in Egypt, 2017–2019. This was performed through a household prospective cohort study on influenza infections among 2400 individuals from five villages. When a study participant had influenza like symptoms, a nasal swab and an oropharyngeal swab were obtained and tested by RT-PCR for influenza B infections. A serum sample was obtained from all participants annually to detect neutralizing antibodies using microneutralization assay. 9.1% of subjects were positive for influenza B viruses during season 2017–2018 mostly among preschoolers and 7.6% were positive during the season 2018–2019 with higher risk in females, potentially due to mothers being infected after contact with their children. The overall seroprevalence among the participants was 53.2% and 52.2% against the Victoria and Yamagata lineages respectively, the majority of seropositive participants were students. Multivariate analysis showed that age and having chronic diseases were the strongest predictors of infection. Our results show that both influenza B lineages circulated between 2017 and 2020 in Egypt almost in equal proportion. Encouraging the uptake of seasonal influenza vaccines is recommended.

Assessment of seasonal influenza vaccine effectiveness in patients from a central Italy reference hospital: pitfalls and intricacies from a pilot case-control study

Objectives: Influenza vaccination protects high-risk populations from severe outcomes. We assessed the feasibility of testing influenza vaccine effectiveness against hospitalization with laboratory-confirmed influenza.
 Methods: All hospitalized patients with influenza-like illness within 14 days, were swabbed. Cases were positive at RT-PCR for influenza A/B.
 Results: AtRome “GemelliHospital” (Season 2011-2012) 104 patients were contacted and 62 recruited. Considering total sample and target group (n= 47, 76%), only 29% and 38% had been vaccinated. Eighteen patients were laboratory-confirmed for influenza.
 Conclusions: RecruitedILI patients and prevalence of vaccinated subjects were less than expected. Larger numbers are warranted to study vaccine effectiveness against severe influenza outcomes.

Cause-specific student absenteeism monitoring in K-12 schools for detection of increased influenza activity in the surrounding community-Dane County, Wisconsin, 2014-2020.

Schools are primary venues of influenza amplification with secondary spread to communities. We assessed K-12 student absenteeism monitoring as a means for early detection of influenza activity in the community. Between September 2014 and March 2020, we conducted a prospective observational study of all-cause (a-TOT), illness-associated (a-I), and influenza-like illness-associated (a-ILI) absenteeism within the Oregon School District (OSD), Dane County, Wisconsin. Absenteeism was reported through the electronic student information system. Students were visited at home where pharyngeal specimens were collected for influenza RT-PCR testing. Surveillance of medically-attended laboratory-confirmed influenza (MAI) occurred in five primary care clinics in and adjoining the OSD. Poisson general additive log linear regression models of daily counts of absenteeism and MAI were compared using correlation analysis. Influenza was detected in 723 of 2,378 visited students, and in 1,327 of 4,903 MAI patients. Over six influenza seasons, a-ILI was significantly correlated with MAI in the community (r = 0.57; 95% CI: 0.53-0.63) with a one-day lead time and a-I was significantly correlated with MAI in the community (r = 0.49; 0.44-0.54) with a 10-day lead time, while a-TOT performed poorly (r = 0.27; 0.21-0.33), following MAI by six days. Surveillance using cause-specific absenteeism was feasible and performed well over a study period marked by diverse presentations of seasonal influenza. Monitoring a-I and a-ILI can provide early warning of seasonal influenza in time for community mitigation efforts.

Clinical and pathologic evaluation of chorioretinal lesions in wild owl species.

Investigate histopathology and spectral-domain optical coherence tomography (OCT) imaging of wild owls with chorioretinitis and identify any potential correlation with an infectious etiology. Ophthalmic examination and retinal OCT imaging were performed on fifteen great horned (Strix varia) and barred (Bubo virginianus) owls (30 eyes) with chorioretinitis and five owls with normal eyes (10 eyes). Testing to investigate the presence of potential infectious diseases included a complete blood count, biochemistry, protein electrophoresis, West Nile virus (WNV) plaque reduction neutralization test, Toxoplasma gondii modified direct agglutination test, WNV RT-PCR, and Avian Influenza RT-PCR. A necropsy was performed on all owls, including ocular histopathology. Fundus lesions included retinal detachment (7/15 owls), depigmented lesions (12/15), pigment clumping (8/15), and retinal tear (4/15). All birds were negative for WNV and Avian Influenza on RT-PCR. Of the owls with chorioretinitis, 3/15 were seropositive for WNV and 7/15 for T.gondii. Optical coherence tomography of 25/30 affected eyes revealed outer retinal lesions (19/25 eyes), retinal detachment (16/25), and retinal tears (3/25). Histopathological examination revealed outer nuclear layer atrophy (19/30 eyes), retinal detachment (18/30), retinal tears (7/30), suprachoroidal hemorrhage (12/30), scleral rupture (3/30), and ossicle fracture (3/30). Although 20% of birds were seropositive for WNV and 46.6% for T.gondii, histopathologic findings supported that the posterior segment lesions in the study group were likely due to blunt ocular trauma rather than an infectious etiology. The results of OCT imaging and histopathology documented retinal changes most consistent with blunt ocular trauma.

Is it possible to hospitalize patients in multiple-bed room without increasing the risk of hospital-acquired influenza? Description of a pragmatic preventive strategy in a French university hospital

Large inrush of patients through Emergency Department during influenza season can be dramatic. The purpose of this study was to evaluate the impact of an emergency preventive strategy, namely admission of patients with influenza in multiple-bed room with patients free from influenza, on the occurrence of hospital-acquired influenza (HAI). When a patient with an influenza RT-PCR diagnosis was hospitalized in a multiple-bed room, the emergency preventive strategy was applied: selection of non-immunocompromised neighbor, implementation of physical barriers (rigid screen pulled between beds, surgical mask for healthcare workers and visitors), preemptive Oseltamivir therapy for the neighbor. From 29/11/2017 to 10/05/2018 a total of 464 hospitalized influenza patients were included; 318 were placed in multiple-bed room and 141 in single room. Emergency preventive strategy was correctly applied for 75.1% of patients in multiple-bed room. A total of 8 exposed neighbors matched HAI definition despite strategy. 7 were already exposed to the case before the set-up of the strategy. Only one case of documented transmission of influenza occurred after application of an incorrect emergency preventive strategy: preventive posology of Oseltamivir was not correct. These preliminary results suggest that the occurrence of HAI in multiple-bed rooms can be limited by the implementation of maximum precautions and urge us to promote further evaluation of the strategy. A detection bias should be considered without a systematic neighbors monitoring.

Investigating the sequence variation in the influenza A matrix genes during the 2017-2018 and 2018-2019 seasons in samples from a local population in London

Recent publications have highlighted the emergence of mutations in the M1 gene of both influenza A H1N1pdm09 and H3N2 subtypes affecting the performance of commercial RT-PCR assays. Respiratory samples from the 2018/2019 season positive by our in-house RT-PCR for influenza A were analysed for the prevalence and impact of any M1 gene mutations. Sequence information was used to re-design primers for our routine assay and their performance assessed. Forty-five samples, consisting of 11 H1N1pdm09 and 34 H3N2 subtypes, together with the NIBSC H1N1 control were sequenced. All samples displayed the core mutations for H1N1 M1(C154T; G174A and G238A) and for H3N2 M1(C153T; C163T and G189T); three of the H1N1pdm09 viruses also showed a small number of point mutations. None of the mutations appeared to affect either the sensitivity or efficiency of the RT-PCR when compared to the re-designed primers. Although the mutations we found agreed with those in the publications cited we did not encounter any problems with our routine diagnostic assay and no improvements were found when the primers were modified to suit those mutations. However, it is likely that the influenza A virus M1 gene will accumulate further mutations that could impact RT-PCR assays and, therefore, it would be prudent to implement routine sequencing of samples during the influenza seasons to ensure no loss in assay performance.

Effectiveness of Annual Flu Vaccination Until Week Four of the 2019–2020 Season

Background: Annual flu vaccination is the most effective way to prevent the disease and its complications. Vaccine effectiveness (EV) varies from season to season, requiring annual re-evaluation. The objective of this study was to estimate the preliminary effectiveness of the influenza vaccine until epidemiological week 4 of the 2019–2020 season, in patients admitted to a tertiary-level hospital. Method: We conducted a case-control study at University General Hospital, Alicante, Spain, during the 2019–2020 season. We included all patients hospitalized with influenza confirmed by laboratory test (ie, PCR positive for influenza) during the period between epidemiological week 40 of 2019 and epidemiological week 4 of 2020. These were considered cases, and those with clinical suspicion of influenza and negative RT-PCR were considered controls. Vaccination coverage was calculated in cases and in controls, determining the odds ratio. We calculated the vaccine effectiveness (VE) and its 95% confidence interval using the following formula: VE = (1 − odds ratio) ×100. Result: We included 545 patients: 61 cases and 484 controls. The overall EV for influenza cases prevention was 40.7% (95% CI, −17.1 to 70.1), and for those >1 year of age, the overall EV was 56.9% (95% CI, 13.9–78.5). Conclusion: The 2019–2020 Influenza vaccine was effective in preventing influenza cases in patients admitted up to week 4 of the 2019–2020 season. These results are preliminary and may vary; they should be re-evaluated at the end of the season.Funding: NoneDisclosures: None

Assessment of indirect protection from maternal influenza immunization among non-vaccinated household family members in a randomized controlled trial in Sarlahi, Nepal

Influenza is a significant cause of morbidity and mortality worldwide, and the World Health Organization highly recommends maternal vaccination during pregnancy. The indirect effect of maternal vaccination on other close contacts other than newborns is unknown. To evaluate this, we conducted a nested substudy between 2011 and 2012 of influenza and acute respiratory illness (ARI) among household members of pregnant women enrolled in a randomized placebo-controlled trial of antenatal influenza vaccination in the rural district of Sarlahi, Nepal. Women were assigned to receive influenza vaccination or placebo during pregnancy and then they and their household members were followed up to 6months postpartum with weekly symptom surveillance and nasal swab collection. Swabs were tested by RT-PCR for influenza. Rates of laboratory-confirmed influenza and of ARI were compared between vaccine and placebo groups using generalized estimating equations with a Poisson link function. Overall, 1752 individuals in 520 households were eligible for inclusion. There were 82 laboratory-confirmed influenza illness episodes, for a rate of 7.0 per 100 person-years overall. Of the influenza strains able to be typed, 29 were influenza A, 40 were influenza B, and 6 were coinfections with influenza A and B. The rate did not differ significantly whether the household was in the vaccine or placebo group (rate ratio (RR) 1.37, 95% confidence interval (CI) 0.83-2.26). The rate of ARI was 28.5 per 100 person-years overall and did not differ by household group (RR 0.99, 95% CI 0.72-1.36). Influenza vaccination of pregnant women did not provide indirect protection of unvaccinated household members.

Outcomes of patients with Severe Acute Respiratory Infections (SARI) admitted to the intensive care unit: results from the Egyptian Surveillance Study 2010-2014.

BackgroundFew data exist about respiratory viral infections in Egyptian patients. Hereby we describe the outcomes of hospitalized Egyptian patients with severe acute respiratory infections (SARI) admitted to the ICU.MethodsA prospective study in which all hospitalized patients meeting the WHO case definition for SARI and admitted to the ICU, during the period 2010–2014, were enrolled. Samples were tested using RT-PCR for influenza A, B, respiratory syncytial virus (RSV), human metapneumovirus (hMPV), parainfluenza virus, adenovirus, bocavirus, enterovirus, and rhinovirus. Data were analyzed to study the clinical features of SARI-ICU patients and which pathogens are related to severe outcomes. Associated comorbidities were evaluated using Charlson Age-Comorbidity Index (CACI).ResultsOut of 1,075 patients with SARI, 219 (20.3%) were admitted to the ICU. The highest rates were reported for RSV (37%). SARI-ICU patients had higher rates of hospital stay, pneumonia, respiratory failure, ARDS, and mortality. Multivariate logistic regression analysis identified associated respiratory disorders (p=0.001), radiological abnormalities (p=0.023), and longer hospital stay (p=0.005) as risk factors for severe outcomes.ConclusionsThis surveillance study showed that 20% of hospitalized Egyptian patients with viral SARI needed ICU admission. SARI-ICU patients had higher rates of hospital stay, pneumonia, respiratory failure, ARDS, and mortality. Higher comorbidity index scores, radiological abnormalities, and longer hospital stay are risk factors for severe outcomes in SARI-ICU patients in our locality.