Low incidence of severe bacterial infections in hospitalised patients with COVID-19: A population-based registry study.

BACKGROUND: Bacterial infections complicating COVID-19 are rare but present a challenging clinical entity. The aim of this study was to evaluate the incidence, aetiology and outcome of severe laboratory-verified bacterial infections in hospitalised patients with COVID-19. METHODS: All laboratory-confirmed patients with COVID-19 admitted to specialised healthcare hospitals in the Capital Province of Finland during the first wave of COVID-19 between 27 February and 21 June 2020 were retrospectively studied. We gathered the blood and respiratory tract culture reports of these patients and analysed their association with 90-day case-fatality using multivariable regression analysis. RESULTS: A severe bacterial infection was diagnosed in 40/585 (6.8%) patients with COVID-19. The range of bacteria was diverse, and the most common bacterial findings in respiratory samples were gram-negative, and in blood cultures gram-positive bacteria. Patients with severe bacterial infection had longer hospital stay (mean 31; SD 20 days) compared to patients without (mean 9; SD 9 days; p < 0.001). Case-fatality was higher with bacterial infection (15% vs 11%), but the difference was not statistically significant (OR 1.38 CI95% 0.56-3.41). CONCLUSIONS: Severe bacterial infection complicating COVID-19 was a rare occurrence in our cohort. Our results are in line with the current understanding that antibiotic treatment for hospitalised COVID-19 patients should only be reserved for situations where a bacterial infection is strongly suspected. The ever-evolving landscape of the pandemic and recent advances in immunomodulatory treatment of COVID-19 patients underline the need for continuous vigilance concerning the possibility and frequency of nosocomial bacterial infections.

Detection of SARS-CoV-2 nucleocapsid antigen from serum can aid in timing of COVID-19 infection.

SARS-CoV-2 RNA can be detected in respiratory samples for weeks after onset of COVID-19 disease. Therefore, one of the diagnostic challenges of PCR positive cases is differentiating between acute COVID-19 disease and convalescent phase. The presence of SARS-CoV-2 nucleocapsid antigen in serum and plasma samples of COVID-19 patients has been demonstrated previously. Our study aimed to characterize the analytical specificity and sensitivity of an enzyme-linked immunosorbent assay (Salocor SARS-CoV-2 Antigen Quantitative Assay Kit© (Salofa Ltd, Salo, Finland)) for the detection of SARS-CoV-2 nucleocapsid antigen in serum, and to characterize the kinetics of antigenemia. The evaluation material included a negative serum panel of 155 samples, and 126 serum samples from patients with PCR-confirmed COVID-19. The specificity of the Salocor SARS-CoV-2 serum nucleocapsid antigen test was 98.0 %. In comparison with simultaneous positive PCR from upper respiratory tract (URT) specimens, the test sensitivity was 91.7 %. In a serum panel in which the earliest serum sample was collected two days before the collection of positive URT specimen, and the latest 48 days after (median 1 day post URT sample collection), the serum N antigen test sensitivity was 95.6 % within 14 days post onset of symptoms. The antigenemia resolved approximately two weeks after the onset of disease and diagnostic PCR. The combination of simultaneous SARS-CoV-2 antigen and antibody testing appeared to provide useful information for timing of COVID-19. Our results suggest that SARS-CoV-2 N-antigenemia may be used as a diagnostic marker in acute COVID-19.

Isolation precautions cause minor delays in diagnostics and treatment of non-COVID patients.

BACKGROUND: Isolation precautions are essential prevent spread of COVID-19 infection but may have a negative impact on inpatient care. The impact of these measures on non-COVID-19 patients remains largely unexplored. AIM: This study aimed to investigate diagnostic and treatment delays related to isolation precautions, the associated patient outcome, and the predisposing risk factors for delays. METHODS: This observational study was conducted in seven Helsinki region hospitals during the first wave of the COVID-19 pandemic in Finland. The study used data on all non-COVID-19 inpatients, who were initially isolated due to suspected COVID-19, to estimate whether isolation precautions resulted in diagnostic or treatment delays. RESULTS: Out of 683 non-COVID-19 patients, 33 (4.8%) had delays related to isolation precautions. Clinical condition deteriorated non-fatally in seven (1.0%) patients. The following events were associated with an increased risk of treatment or a diagnostic delay: more than three ward transfers (P = 0.025); referral to an incorrect speciality in the emergency department (P = 0.004); more than three SARS-CoV-2 RT-PCR tests performed (P = 0.022); and where cancer was the final diagnosis (P = 0.018). In contrast, lower respiratory tract symptoms (P = 0.013) decreased the risk. CONCLUSIONS: The use of isolation precautions for patients who did not have COVID-19 had minor negative effects on patient outcomes. The present study underlines the importance of targeting diagnostic efforts to patients with unspecified symptoms and to those with a negative SARS-CoV-2 test result. Thorough investigations to achieve an accurate diagnosis improves the prognosis of patients and facilitates appropriate targeting of hospital resources.

Evaluation of three rapid lateral flow antigen detection tests for the diagnosis of SARS-CoV-2 infection.

INTRODUCTION: The COVID-19 pandemic has led to high demand of diagnostic tools. Rapid antigen detection tests have been developed and many have received regulatory acceptance such as CE IVD or FDA markings. Their performance needs to be carefully assessed. MATERIALS AND METHODS: 158 positive and 40 negative retrospective samples collected in saline and analyzed by a laboratory-developed RT-PCR test were used to evaluate Sofia (Quidel), Standard Q (SD Biosensor), and Panbio™ (Abbott) rapid antigen detection tests (RADTs). A subset of the specimens was subjected to virus culture. RESULTS: The specificity of all RADTs was 100 % and the sensitivity and percent agreement was 80 % and 85 % for Sofia, 81 % and 85 % for Standard Q, and 83 % and 86 % for Panbio™, respectively. All three RADTs evaluated in this study reached a more than 90 % sensitivity for samples with a high viral load as estimated from the low Ct (Cycle threshold) values in the reference RT-PCR. Virus culture was successful in 80 % of specimens with a Ct value <25. CONCLUSIONS: As expected, the RADTs were less sensitive than RT-PCR. However, they benefit from the speed and ease of testing, and lower price as compared to RT-PCR. Repeated testing in appropriate settings may improve the overall performance.

Laboratory-based surveillance of COVID-19 in the Greater Helsinki area, Finland, February-June 2020.

OBJECTIVES: The aim was to characterise age- and sex-specific severe acute respiratory syndrome coronavirus disease-2 (SARS-CoV-2) RT-PCR sampling frequency and positivity rate in Greater Helsinki area in Finland during February-June 2020. We also describe the laboratory capacity building for these diagnostics. METHODS: Laboratory registry data for altogether 80,791 specimens from 70,517 individuals was analysed. The data included the date of sampling, sex, age and the SARS-CoV-2 RT-PCR test result on specimens collected between 1 February and 15 June 2020. RESULTS: Altogether, 4057/80,791 (5.0%) of the specimens were positive and 3915/70,517 (5.6%) of the individuals were found positive. In all, 37% of specimens were from male and 67% from female subjects. While the number of positive cases was similar in male and female subjects, the positivity rate was significantly higher in male subjects: 7.5% of male and 4.4% of female subjects tested positive. The highest incidence/100,000 was observed in those aged ≥80 years. The proportion of young adults in positive cases increased in late May 2020. Large dips in testing frequency were observed during every weekend and also during public holidays. CONCLUSIONS: Our data suggest that men pursue SARS-CoV-2 testing less frequently than women. Consequently, a subset of coronavirus disease-2019 infections in men may have gone undetected. People sought testing less frequently on weekends and public holidays, and this may also lead to missing of positive cases. The proportion of young adults in positive cases increased towards the end of the study period, which may suggest their returning back to social behaviour with an increased risk of infection.

Performance of six SARS-CoV-2 immunoassays in comparison with microneutralisation.

There is an urgent need for reliable high-throughput serological assays for the management of the ongoing COVID-19 pandemic. Preferably, the performance of serological tests for a novel virus should be determined with clinical specimens against a gold standard, i.e. virus neutralisation. We compared the performance of six commercial immunoassays for the detection of SARS-COV-2 IgG, IgA and IgM antibodies, including four automated assays [Abbott SARS-COV-2 IgG (CE marked), Diasorin Liaison® SARS-COV-2 S1/S2 IgG (research use only, RUO), and Euroimmun SARS-COV-2 IgG and IgA (CE marked)], and two rapid lateral flow (immunocromatographic) tests [Acro Biotech 2019-nCoV IgG/IgM (CE marked) and Xiamen Biotime Biotechnology SARS-COV-2 IgG/IgM (CE marked)] with a microneutralisation test (MNT). Two specimen panels from serum samples sent to Helsinki University Hospital Laboratory (HUSLAB) were compiled: the patient panel (N=70) included sera from PCR confirmed COVID-19 patients, and the negative panel (N=81) included sera sent for screening of autoimmune diseases and respiratory virus antibodies in 2018 and 2019. The MNT was carried out for all COVID-19 samples (70 serum samples, 62 individuals) and for 53 samples from the negative panel. Forty-one out of 62 COVID-19 patients showed neutralising antibodies.The specificity and sensitivity values of the commercial tests against MNT, respectively, were as follows: 95.1 %/80.5 % (Abbott Architect SARS-CoV-2 IgG), 94.9 %/43.8 % (Diasorin Liaison SARS-CoV-2 IgG; RUO), 68.3 %/87.8 % (Euroimmun SARS-CoV-2 IgA), 86.6 %/70.7 % (Euroimmun SARS-CoV-2 IgG), 74.4 %/56.1 % (Acro 2019-nCoV IgG), 69.5 %/46.3 % (Acro 2019-nCoV IgM), 97.5 %/71.9 % (Xiamen Biotime SARS-CoV-2 IgG), and 88.8 %/81.3 % (Xiamen Biotime SARS-CoV-2 IgM). This study shows variable performance values. Laboratories should carefully consider their testing process, such as a two-tier approach, in order to optimize the overall performance of SARS- CoV-2 serodiagnostics.

Evaluation of two commercially available rapid diagnostic tests for Lyme borreliosis.

The diagnosis of Lyme disease is very complicated and a single diagnostic method cannot exclude infection. We assessed the performance of two commercially available Borrelia burgdorferi rapid diagnostic tests (RDT) in comparison to multiple laboratory-based diagnostic assays using specimens with a gradually increasing probability of Borrelia infection. Based on 200 specimens, the analytical sensitivities for IgG and IgM were 18 and 23% for the Lyme RDT and 24 and 32% for the Borreliose Complete RDT. The sensitivity for detecting diagnosed Lyme borreliosis cases was low (26% Lyme RDT and 32% with the Borreliose Complete RDT respectively), whereas the specificity was good (85% Lyme RDT and 88% Borreliose Complete). Based on this evaluation, the performance of RDTs in detecting Lyme borreliosis appeared to be below that of laboratory-based diagnostics.

Climatic, ecological and socioeconomic factors as predictors of Sindbis virus infections in Finland.

Mosquito-borne Sindbis virus (SINV) causes rash-arthritis syndrome in Finland. Major outbreaks with approximately 7-year cycles have caused substantial burden of illness. Forest dwelling grouse are suspected to be amplifying hosts, with the infection transmitted to humans by mosquito bites. SINV infection surveillance data for 1984­2010 were used to create a negative binomial hurdle model, with seasonality, long-term cycles, climatic, ecological and socioeconomic variables. Climatic factors during early summer and amount of snow in April described the occurrence and incidence of SINV infections. Regulated water shore and hatch-year black grouse density described the occurrence, while population working in agriculture, agricultural land(negative) and income (negative) described the incidence of the disease. The prediction for 2009 was 85 cases (95% prediction interval 2-1187), while the actual occurrence was 106. We identified novel and known risk factors. The prevention of SINV infections in regulated water areas by infected mosquito populations should be targeted.

Comparative hepatitis A seroepidemiology in 10 European countries.

The WHO recommends hepatitis A virus (HAV) immunization according to level of transmission and disease burden. We aimed to identify susceptible age groups by standardized serosurveys to inform HAV vaccination policy in participating countries: Belgium, Czech Republic, England, Finland, Germany, Italy, Lithuania, Malta, Romania, and Slovakia. Each country tested national serum banks (n = 1854-6748), collected during 1996-2004, for anti-HAV antibodies. Local laboratory results were standardized to common units. Forty-one per cent of those aged <30 years and 6% of those aged ≥30 years were susceptible to HAV in Romania; compared to 70-94% and 26-71%, respectively, elsewhere. Romania reported high HAV incidence in children and young adults. Other countries reported HAV disease primarily in older risk groups. The results suggest low level of HAV transmission in most of Europe. Romania, however, appeared as an area with intermediate transmission. Vaccination of risk groups in countries with high susceptibility of young and middle-aged adults needs to be continued.

Epidemiological analysis of mosquito-borne Pogosta disease in Finland, 2009.

Pogosta disease is a viral disease caused by a mosquito-borne alphavirus, Sindbis virus (SINV), and large human outbreaks of SINV infection have emerged in Finland every seven years. After a major outbreak in 2002 an epidemic was expected to take place in 2009. Data from the National Infectious Disease Registry showed a small outbreak in humans in 2009 with a total of 105 reported cases but the seven-year cycle did not recur as anticipated.

Pandemic (H1N1) 2009 virus outbreak in a school in London, April-May 2009: an observational study.

On 29 April 2009, an imported case of pandemic (H1N1) 2009 virus infection was detected in a London school. As further cases, pupils and staff members were identified, school closure and mass prophylaxis were implemented. An observational descriptive study was conducted to provide an insight into the clinical presentation and transmission dynamics in this setting. Between 15 April and 15 May 2009, 91 symptomatic cases were identified: 33 were confirmed positive for pandemic (H1N1) 2009 virus infection; 57 were tested negative; in one the results were unavailable. Transmission occurred first within the school, and subsequently outside. Attack rates were 2% in pupils (15% in the 11-12 years age group) and 17% in household contacts. The predominant symptoms were fever (97%), respiratory symptoms (91%), and sore throat (79%). Limited spread in the school may have been due to a combination of school closure and mass prophylaxis. However, transmission continued through household contacts to other schools.

Long-term effects of an early home-based intervention.

OBJECTIVE: To evaluate the long-term effects of an early home-based intervention on the quantity and quality of psychiatric symptoms in adolescents. METHOD: The material consisted of 160 families with a baby born in 1975-1976. First, the families were classified with a weighted risk index into low- and high-risk families. Eighty families attended a 5-year-long family counseling program (10 times/year). The other half of the families served as a control group for the effects of counseling. The mental state of the adolescents was assessed at age 14 to 15 years by the Child Behavior Checklist and the Youth Self-Report. RESULTS: The adolescents in the counseling families scored significantly fewer total symptoms on both the parent and the youth reports. The counseling reduced more effectively internalizing than externalizing symptoms. The counseling predicted better mental health in adolescence in both low- and high-risk families. CONCLUSIONS: Home-based early intervention can have positive long-term effects on the mental state of adolescents. These results can be used when programs for primary prevention in families with small children are planned.

Structure and expression of kin2, one of two cold- and ABA-induced genes of Arabidopsis thaliana.

We report the isolation of the second member, kin2, of a family of two cold-inducible genes of Arabidopsis thaliana. The proteins corresponding to the two genes have similarities to the small antifreeze proteins from Winter flounder. Kin1 and kin2 are organized in a close tandem array in the genome of A. thaliana. Both have three exons separated by introns with approximately the same length and location. The coding regions are highly conserved while the introns and especially the 3' flanking sequences of the mRNAs have diverged. The kin1 and kin2 genes are coordinately regulated in the cold. Unlike kin1, the kin2 mRNA has a detectable basal level, and accumulates to a higher level during acclimation. Both mRNAs are induced by 10 microM ABA but only kin2 responds strongly to drought and salinity stresses.

Cloning and characterization of a cold- and ABA-inducible Arabidopsis gene.

We have identified by differential screening a novel Arabidopsis thaliana gene, called kin1, which is induced at +4 degrees C. The nucleotide sequences of both the genomic clone and the corresponding cDNA were determined. The deduced 6.5 kDa polypeptide has an unusual amino acid composition being rich in alanine, glycine and lysine. The gene belongs to a family of at least two genes. Northern blot analysis revealed that the level of kin1 mRNA is increased 20-fold in cold-treated plants. In addition to being expressed in cold, kin1 is also induced by water stress and the plant hormone abscisic acid (ABA) which has been suggested to be a common mediator for osmotic stress responses and cold acclimation in plants. Sequence comparisons showed that the kin1 gene product has similarities to fish antifreeze proteins (AFPs).

Expression of dicistronic transcriptional units in transgenic tobacco.

We investigated whether the two cistrons of a dicistronic mRNA can be translated in plants to yield both gene products. The coding sequences of various reporter genes were combined in dicistronic units, and their expression was analyzed in stably transformed tobacco plants at the RNA and protein levels. The presence of an upstream cistron resulted in all cases in a drastically reduced expression of the downstream cistron. The translational efficiency of the gene located downstream in the dicistronic units was 500- to 1,500-fold lower than that in a monocistronic control; a 500-fold lower value was obtained with a dicistronic unit in which both cistrons were separated by 30 nucleotides, whereas a 1,500-fold lower value was obtained with a dicistronic unit in which the stop codon of the upstream cistron and the start codon of the downstream cistron overlapped. As a strategy to select indirectly for transformants with enhanced levels of expression of a gene which is by itself nonselectable, the gene of interest can be cloned upstream from a selectable marker in a dicistronic configuration. This strategy can be used provided that the amount of dicistronic mRNA is high. If, on the other hand, the expression of the dicistronic unit is too low, selection of the downstream cistron will primarily give clones with rearranged dicistronic units.

Cloning, nucleotide sequence and characterization of genes encoding naphthalene dioxygenase of Pseudomonas putida strain NCIB9816.

We have cloned the naphthalene dioxygenase(ND)-coding genes from Pseudomonas putida strain NCIB9816 based on their ability to convert indole to indigo. The region coding for this enzyme activity was sequenced and three successive open reading frames were found. The corresponding gene products were identified using the T7 polymerase/promoter system. All of them are necessary for the ND activity. A comparison of the ND-coding genes with the ones coding for benzene dioxygenase revealed significant homology which was more pronounced at the nucleotide level than at the amino acid level.

Cold induced gene expression in Arabidopsis thaliana L.

Exposure of Arabidopsis thaliana L. to an acclimation temperature (+4°C) results in a rapid increase of frost tolerance from -3°C to -7°C. This increase could be correlated to changes in soluble protein pattern. Analysis of in vitro translation products from isolated mRNA suggests that induction acts at the transcriptional level.

In vivo cloning ad characterization of mutations of the regulatory locus ompR of Escherichia coli K12.

The product of the ompR gene of E. coli K12 is a positive regulatory protein, which is needed for the expression of the major outer membrane proteins OmpC and OmpF in E. coli K12. A simple in vivo technique was used to transfer three ompR mutations (ompR101, ompR472, ompR4) onto a multicopy plasmid carrying the wild-type ompR gene. The resulting clones were transformed into wild type and corresponding mutant backgrounds to analyze their effects on ompC and ompF expression. All of the cloned ompR mutant alleles exhibited a dominant OmpC- phenotype in an ompR+ background. In addition negative complementation of ompF expression was observed between chromosomal ompR4 and multicopy ompR101 alleles. The results suggest an interaction between different OmpR molecules and thereby support the idea that OmpR can exist as a multimeric protein.