POLYMORPHISMS OF LEUKOCYTE GENES HUMAN AND CONGENITAL ANTIGEN IMMUNITY ASSOCIATED WITH DIFFERENT THE SEVERITY OF THE COURSE OF THE NEW CORONAVIRUS INFECTIONS

The most significant single nucleotide human leukocyte antigen genes polymorphisms and innate immunity genes associated with varying degrees of acute respiratory infection severity are considered–COVID-19 caused by the SARS-CoV-2 coronavirus. As data accumulated, it became clear that the SARS-CoV-2 virus exhibits significant regional, ethnic, and individual specificity. This is due to the population groups' genetic characteristics. This is necessary to reliably know the human genotype relationship with the COVID-19 course severity (asymptomatic, mild, moderate, severe, and extremely severe up to fatal outcomes) for more successful therapy and vaccination. At the same time, it was also known that the innate immunity system is on the first line of defense against the pathogenic penetration into the body, and the human leukocyte antigen system encodes molecules of the same name on the surface of cells that present various antigens, including viral infection pathogens, and determine the severity of the course of many diseases;therefore, these systems' genes. This approach makes it possible to assess the likelihood of a severe and extremely severe disease course in healthy and infected people, which in turn contributes to the correct therapy strategy, pharmacotherapy, and vaccination, as well as to create new antiviral therapeutic and preventive medicines. The genetically determined immune response heterogeneity to SARS-CoV-2 infection requires further study, since there is no unambiguous opinion about the leading mechanism that determines disease severity. The article can be used under the CC BY-NC-ND 4.0 license © Authors, 2022.

Continuous evolution and emerging lineage of seasonal human coronaviruses: A multicenter surveillance study.

The seasonal human coronaviruses (HCoVs) have zoonotic origins, repeated infections, and global transmission. The objectives of this study are to elaborate the epidemiological and evolutionary characteristics of HCoVs from patients with acute respiratory illness. We conducted a multicenter surveillance at 36 sentinel hospitals of Beijing Metropolis, China, during 2016-2019. Patients with influenza-like illness (ILI) and severe acute respiratory infection (SARI) were included, and submitted respiratory samples for screening HCoVs by multiplex real-time reverse transcription-polymerase chain reaction assays. All the positive samples were used for metatranscriptomic sequencing to get whole genomes of HCoVs for genetical and evolutionary analyses. Totally, 321 of 15 677 patients with ILI or SARI were found to be positive for HCoVs, with an infection rate of 2.0% (95% confidence interval, 1.8%-2.3%). HCoV-229E, HCoV-NL63, HCoV-OC43, and HCoV-HKU1 infections accounted for 18.7%, 38.3%, 40.5%, and 2.5%, respectively. In comparison to ILI cases, SARI cases were significantly older, more likely caused by HCoV-229E and HCoV-OC43, and more often co-infected with other respiratory pathogens. A total of 179 full genome sequences of HCoVs were obtained from 321 positive patients. The phylogenetical analyses revealed that HCoV-229E, HCoV-NL63 and HCoV-OC43 continuously yielded novel lineages, respectively. The nonsynonymous to synonymous ratio of all key genes in each HCoV was less than one, indicating that all four HCoVs were under negative selection pressure. Multiple substitution modes were observed in spike glycoprotein among the four HCoVs. Our findings highlight the importance of enhancing surveillance on HCoVs, and imply that more variants might occur in the future.

Resurgence of influenza and respiratory syncytial virus in Egypt following two years of decline during the COVID-19 pandemic: outpatient clinic survey of infants and children, October 2022.

INTRODUCTION: Two years after unprecedented low rates of circulation of most common respiratory viruses (SARS-CoV-2), the Egyptian ARI surveillance system detected an increase in acute respiratory infections (ARIs) with a reduced circulation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), especially among school children. A national survey was conducted to estimate the burden and identify the viral causes of ARIs among children < 16 years of age. METHODS: A one-day survey was carried out in 98 governmental outpatient clinics distributed all over Egypt 26 governorates. The four largest referral hospitals in each governorate where most influenza-like illness (ILI) patients seek care were selected. Using the WHO case definition, the first five patients < 16 years of age with ILI symptoms visiting the selected outpatient clinics on the survey day were enrolled. Basic demographic and clinical data of patients were collected using a linelist. Patients were swabbed and tested for SARS-CoV-2, influenza, and Respiratory Syncytial virus (RSV) by RT-PCR at the Central Laboratory in Cairo. RESULTS: Overall, 530 patients enrolled, their mean age was 5.8 ± 4.2, 57.1% were males, and 70.2% reside in rural or semi-rural areas. Of all patients, 134 (25.3%) had influenza, 111 (20.9%) RSV, and 14 (2.8%) coinfections. Influenza-positive children were older compared to RSV, (7.2 ± 4.1, 4.3 ± 4.1, p < 0.001), with more than half of them (53.0%) being school students. Dyspnea was reported in RSV more than in influenza (62.2% vs. 49.3%, p < 0.05). Among RSV patients, children < 2 years had a higher rate of dyspnea than others (86.7% vs. 53.1%, < 0.001). CONCLUSIONS: A resurgence of influenza and RSV was detected in Egypt in the 2022-2023 winter season. Influenza caused a higher rate of infection than RSV, while RSV caused more severe symptoms than influenza. Monitoring a broader range of respiratory pathogens is recommended to estimate the ARI burden and risky groups for severe disease in Egypt.

Establishing severe acute respiratory infection (SARI) surveillance in a sentinel hospital, Ireland, 2021 to 2022.

BackgroundIn 2020, due to the COVID-19 pandemic, the European Centre for Disease Prevention and Control (ECDC) accelerated development of European-level severe acute respiratory infection (SARI) surveillance.AimWe aimed to establish SARI surveillance in one Irish hospital as part of a European network E-SARI-NET.MethodsWe used routine emergency department records to identify cases in one adult acute hospital. The SARI case definition was adapted from the ECDC clinical criteria for a possible COVID-19 case. Clinical data were collected using an online questionnaire. Cases were tested for SARS-CoV-2, influenza and respiratory syncytial virus (RSV), including whole genome sequencing (WGS) on SARS-CoV-2 RNA-positive samples and viral characterisation/sequencing on influenza RNA-positive samples. Descriptive analysis was conducted for SARI cases hospitalised between July 2021 and April 2022.ResultsOverall, we identified 437 SARI cases, the incidence ranged from two to 28 cases per week (0.7-9.2/100,000 hospital catchment population). Of 431 cases tested for SARS-CoV-2 RNA, 226 (52%) were positive. Of 349 (80%) cases tested for influenza and RSV RNA, 15 (4.3%) were positive for influenza and eight (2.3%) for RSV. Using WGS, we identified Delta- and Omicron-dominant periods. The resource-intensive nature of manual clinical data collection, specimen management and laboratory supply shortages for influenza and RSV testing were challenging.ConclusionWe successfully established SARI surveillance as part of E-SARI-NET. Expansion to additional sentinel sites is planned following formal evaluation of the existing system. SARI surveillance requires multidisciplinary collaboration, automated data collection where possible, and dedicated personnel resources, including for specimen management.

Metagenomics characterization of respiratory viral RNA pathogens in children under five years with severe acute respiratory infection in the Free State, South Africa.

Prompt detection of viral respiratory pathogens is crucial in managing respiratory infection including severe acute respiratory infection (SARI). Metagenomics next-generation sequencing (mNGS) and bioinformatics analyses remain reliable strategies for diagnostic and surveillance purposes. This study evaluated the diagnostic utility of mNGS using multiple analysis tools compared with multiplex real-time PCR for the detection of viral respiratory pathogens in children under 5 years with SARI. Nasopharyngeal swabs collected in viral transport media from 84 children admitted with SARI as per the World Health Organization definition between December 2020 and August 2021 in the Free State Province, South Africa, were used in this study. The obtained specimens were subjected to mNGS using the Illumina MiSeq system, and bioinformatics analysis was performed using three web-based analysis tools; Genome Detective, One Codex and Twist Respiratory Viral Research Panel. With average reads of 211323, mNGS detected viral pathogens in 82 (97.6%) of the 84 patients. Viral aetiologies were established in nine previously undetected/missed cases with an additional bacterial aetiology (Neisseria meningitidis) detected in one patient. Furthermore, mNGS enabled the much needed viral genotypic and subtype differentiation and provided significant information on bacterial co-infection despite enrichment for RNA viruses. Sequences of nonhuman viruses, bacteriophages, and endogenous retrovirus K113 (constituting the respiratory virome) were also uncovered. Notably, mNGS had lower detectability rate for severe acute respiratory syndrome coronavirus 2 (missing 18/32 cases). This study suggests that mNGS, combined with multiple/improved bioinformatics tools, is practically feasible for increased viral and bacterial pathogen detection in SARI, especially in cases where no aetiological agent could be identified by available traditional methods.

Surveillance of Influenza and Other Airborne Transmission Viruses during the 2021/2022 Season in Hospitalized Subjects in Tuscany, Italy.

Winter in the northern hemisphere is characterized by the circulation of influenza viruses, which cause seasonal epidemics, generally from October to April. Each influenza season has its own pattern, which differs from one year to the next in terms of the first influenza case notification, the period of highest incidence, and the predominant influenza virus subtypes. After the total absence of influenza viruses in the 2020/2021 season, cases of influenza were again recorded in the 2021/2022 season, although they remained below the seasonal average. Moreover, the co-circulation of the influenza virus and the SARS-CoV-2 pandemic virus was also reported. In the context of the DRIVE study, oropharyngeal swabs were collected from 129 Tuscan adults hospitalized for severe acute respiratory infection (SARI) and analyzed by means of real-time polymerase chain reaction (RT-PCR) for SARS-CoV-2 and 21 different airborne pathogens, including influenza viruses. In total, 55 subjects tested positive for COVID-19, 9 tested positive for influenza, and 3 tested positive for both SARS-CoV-2 and the A/H3N2 influenza virus. The co-circulation of different viruses in the population requires strengthened surveillance that is no longer restricted to the winter months. Indeed, constant, year-long monitoring of the trends of these viruses is needed, especially in at-risk groups and elderly people.

MERS-CoV seroconversion amongst Malaysian Hajj pilgrims returning from the Middle East, 2016-2018: results from the MERCURIAL multiyear prospective cohort study.

Prospective cohort study to investigate the potential exposure to the Middle East Respiratory Syndrome-Coronavirus (MERS-CoV) following Hajj pilgrims is still very limited. Here, we report the antibody seroconversion study results obtained from successive three years cohort studies (2016-2018) involving the Malaysian Hajj pilgrims returning from the Middle East. A cohort study of Hajj pilgrims from Malaysia enrolled 2,863 participants from 2016-2018, all of whom consented to provide paired blood samples for both pre- and post-Hajj travel to the Middle East. ELISAs and micro-neutralization assays were performed to detect the presence of MERS-CoV IgG antibodies. Sociodemographic data, symptoms experienced during Hajj, and history of exposure to camels or camel products were recorded using structured pre- and post-Hajj questionnaires. A 4-fold increase in anti-MERS-CoV IgG between paired pre-Hajj and post-Hajj serum samples in twelve participants was observed. None of the twelve ELISA-positive sera had detectable levels of virus-neutralizing antibodies. All reportedly had mild symptoms of respiratory symptoms at a certain point during the pilgrimage, implying mild or asymptomatic infections. No association between post-Hajj serum positivity and a history of exposure to camels or camel products was obtained. Findings from the study suggest that serologic conversion to MERS-CoV occurred in at least 0.6% of the Hajj pilgrims returning from the Middle East. Since all the seroconvertants had mild to no symptoms during the sampling period, it highlights the likelihood of occurrence of only low infectivity spillover infections among the Hajj pilgrims.

The surge of RSV and other respiratory viruses among children during the second COVID-19 pandemic winter season.

Background: The non-pharmaceutical measures in the first Covid-19 winter season significantly impacted respiratory pathogens such as RSV, influenza, or metapneumovirus, which cause respiratory infections, especially in infants and young children. This longitudinal prospective study aimed to determine how less strict measures affect the pathogen profile in the second winter season. Methods: From September 2021 till the end of March 2022, 678 children (0-36 months) admitted to Vienna's largest pediatric center with an acute respiratory infection were enrolled in this study. The researchers performed nasal swabs and tested them by multiplex PCR for 23 respiratory pathogens, chronicled clinical features and treatment, and analyzed the effect of lockdown on the pathogen prevalence. Results: The 815 smears of 678 children revealed the most common pathogens to be rhino-/enterovirus (38.5%), RSV (26.7%), and metapneumovirus (7.2%). The lockdown interrupted the early RSV onset in September [RR 0.367, CI (0.184-0.767), p = 0.003], while no effects on the other pathogens were found. Metapneumovirus started circulating in January. Influenza was only sporadically detected. The hospitalization rate was significantly higher than last season due to RSV [OR 4.089, 95%CI (1.414-11.827), p-adj = 0.05]. Conclusion: With more flexible non-pharmaceutical measures, children aged 0-36 months started presenting again with viral pathogens, such as RSV and metapneumovirus. RSV, associated with a high hospitalization rate, had a very early onset with an abrupt interruption due to the only lockdown.

Change in departure time for a train trip to avoid crowding during the COVID-19 pandemic: A latent class study in the Netherlands.

After the outbreak of COVID-19 pandemic, crowding has been highlighted as a risk factor for contracting acute respiratory infections (ARIs) such as COVID-19, which has affected the demand for public transport. Although several countries, including the Netherlands, have implemented differential fare systems for peak and off-peak travel to reduce crowding during the rush hours, the problem of overcrowding on trains has remained prevalent and is expected to cause more disutility than even before the pandemic. A stated choice experiment in the Netherlands is conducted to understand the extent to which people can be motivated to change their departure time to avoid crowded trains during rush hours by offering them real-time information on on-board crowding levels and a discount on the train fare. To gain further insights into how travelers respond to crowding and capture unobserved heterogeneity in the data, latent class models have been estimated. Unlike the previous studies, the respondents were segregated into two groups before the start of the choice experiment based on their indicated preference to schedule a delay earlier or later than their desired departure. To study the change in travel behavior during the pandemic, the context of different vaccination stages was also provided in the choice experiment. Background information collected in the experiment was broadly categorized as socio-demographic, travel and work-related factors, and attitudes towards health and COVID-19. It was found that the coefficients obtained for the main attributes which were presented in the choice experiment (on-board crowd levels, scheduled delay and discount offered on full fare) were found statistically significant, and in line with previous research. It was concluded that when most of the people are vaccinated in the Netherlands, the travelers become less averse to on-board crowding. The research also indicates that certain groups of respondents, such as those who are highly crowd averse, and are not students, can be motivated to change their departure time if real-time crowding information was provided. Other groups of respondents who were found to value fare discounts can also be motivated to change their departure by similar incentives.

Effectiveness of influenza vaccination in preventing influenza in primary care, Navarre, Spain, 2021/22.

Compared with individuals unvaccinated in the current and three previous influenza seasons, in 2021/22, influenza vaccine effectiveness at primary care level was 37% (95% CI: 16 to 52) for current season vaccination, regardless of previous doses, and 35% (95% CI: -3 to 45) for only previous seasons vaccination. Against influenza A(H3N2), estimates were 39% (95% CI: 16 to 55) and 24% (95% CI: -8 to 47) suggesting moderate effectiveness of current season vaccination and possible remaining effect of prior vaccinations.

Application of machine learning approaches to predict the impact of ambient air pollution on outpatient visits for acute respiratory infections

With a remarkable increase in industrialization among fast-developing countries, air pollution is rising at an alarming rate and has become a public health concern. The study aims to examine the effect of air pollution on patient's hospital visits for respiratory diseases, particularly Acute Respiratory Infections (ARI). Outpatient hospital visits, air pollution and meteorological parameters were collected from March 2018 to October 2021. Eight machine learning algorithms (Random Forest model, K-Nearest Neighbors regression model, Linear regression model, LASSO regression model, Decision Tree Regressor, Support Vector Regression, X.G. Boost and Deep Neural Network with 5-layers) were applied for the analysis of daily air pollutants and outpatient visits for ARI. The evaluation was done by using 5-cross-fold confirmations. The data was randomly divided into test and training data sets at a scale of 1:2, respectively. Results show that among the studied eight machine learning models, the Random Forest model has given the best performance with R2 = 0.606, 0.608 without lag and 1-day lag respectively on ARI patients and R2 = 0.872, 0.871 without lag and 1-day lag respectively on total patients. All eight models did not perform well with the lag effect on the ARI patient dataset but performed better on the total patient dataset. Thus, the study did not find any significant association between ARI patients and ambient air pollution due to the intermittent availability of data during the COVID-19 period. This study gives insight into developing machine learning programs for risk prediction that can be used to predict analytics for several other diseases apart from ARI, such as heart disease and other respiratory diseases. © 2022 Elsevier B.V.

Surveillance of Severe Acute Respiratory Infection and Influenza Vaccine Effectiveness among Hospitalized Italian Adults, 2021/22 Season.

Following an extremely low incidence of influenza during the first waves of the ongoing COVID-19 pandemic, the 2021/22 Northern Hemisphere winter season saw a resurgence of influenza virus circulation. The aim of this study was to describe epidemiology of severe acute respiratory infections (SARIs) among Italian adults and estimate the 2021/22 season influenza vaccine effectiveness. For this purpose, a test-negative case-control study was conducted in a geographically representative sample of Italian hospitals. Of 753 SARI patients analyzed, 2.5% (N = 19) tested positive for influenza, most of which belonged to the A(H3N2) subtype. Phylogenetic analysis showed that these belonged to the subclade 3C.2a1b.2a.2, which was antigenically different from the 2021/22 A(H3N2) vaccine component. Most (89.5%) cases were registered among non-vaccinated individuals, suggesting a protective effect of influenza vaccination. Due to a limited number of cases, vaccine effectiveness estimated through the Firth's penalized logistic regression was highly imprecise, being 83.4% (95% CI: 25.8-97.4%) and 83.1% (95% CI: 22.2-97.3%) against any influenza type A and A(H3N2), respectively. Exclusion of SARS-CoV-2-positive controls from the model did not significantly change the base-case estimates. Within the study limitations, influenza vaccination appeared to be effective against laboratory-confirmed SARI.

Outcomes of patients with end-stage kidney disease hospitalized with COVID-19: A single-center experience from Eastern India

Aim: This study aimed to describe the clinical characteristics, survival outcome, and its correlation with biochemical parameters in coronavirus disease-2019 (COVID-19)-infected patients with end-stage kidney disease (ESKD). Materials and Methods: A prospective observational study was on hospitalized patients with confirmed COVID-19 infection from September 1, 2020 to October 31, 2020. Data related to demographics, baseline history of comorbid conditions, dialysis-specific data, details on hospital admissions, COVID-19 treatment regimen, laboratory investigations, computed tomography (CT) severity score, COVID-19 Reporting and Data System score, and clinical outcomes (improved/death), duration of hospital stay, oxygen/vasopressor support were collected. Results: A total of 216 ESKD patients with COVID-19 infection were included in this study. The median age was 48.0 years (74.5% men, 25.5% women). Severe acute respiratory infection (44.7%), hypertension (28.2%), and type 2 diabetes mellitus (22.4%) were the most common comorbidities. Elevated levels of serum creatinine (9.3 mg/dL) and blood urea nitrogen (84.8 mg/dL) were observed in the patients with COVID-19 infection. The change in mean levels of serum creatinine and estimated glomerular filtration rate from baseline to post-treatment was significant (0.9 [95% CI: 0.7, 1.1;P < 0.001] and 3.4 [95% CI: 3.2, 3.6;P < 0.001], respectively). Approximately, 79.6% (n = 172) of patients improved post-treatment. Serum creatinine (1.786, 95% CI: 1.031, 3.095;0.039) and ferritin levels (51.959, 95% CI: 7.901, 341.685;P < 0.001) remained significantly and independently associated with survival. The median time to clinical survival was 17.0 days. Conclusion: Serum creatinine and ferritin levels were independently associated with survival.

Identification of viral agents in children with acute respiratory infection

Introduction: Acute respiratory infections represent a health problem in children, with high morbidity and high mortality rates. Objective(s): To determine the circulation of respiratory viruses in children admitted with a diagnosis of acute respiratory infection, negative to COVID-19. Method(s): Descriptive observational study in 119 children with acute respiratory infection, in the ages from 0 to 6, and with hospital admission in the period from October 2021 to April 2022. Nasopharyngeal exudate samples were taken for virological study (real-time polymerase chain reaction). The variables studied were: age, sex, clinical diagnosis, period of occurrence and isolation of respiratory viruses. Result(s): The female sex predominated with 51% and the age corresponding to the neonatal period with 50 %, followed by infants between 1 and 11 months (40%), and only 10% in the ages from 1 to 6 years. 42 % of the samples with a predominance of CoV229E (78%) were positive;other viruses such as influenza A (6 %), respiratory syncytial (6 %), CoVOC43 (2%) and rhinovirus (2%) were isolated. CoV229E was common in patients with high acute respiratory infection (48.7%), followed by severe acute respiratory infection (20.5%) and bronchiolitis (28.2%). Viral co-infection was detected only in severe acute respiratory infection, specifically by IFA/CoV229E (4%) and CoV229E/bocavirus (2%). Conclusion(s): The importance of molecular biology for viral isolation is highlighted. The Coronavirus CoV229E has relevance in cases of acute high and severe respiratory infection mainly in children under 1 year old. Copyright © 2022, Editorial Ciencias Medicas. All rights reserved.

Severe Acute Respiratory Syndrome Coronavirus 2 Diagnostic Tests for Border Screening During the Very Early Phase of Coronavirus Disease 2019 Pandemic: A Systematic Review and Meta-Analysis.

Diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during border screening among returning residents and prioritized travelers during the early phase of a pandemic can reduce the risk of importation and transmission in the community. This study aimed to compare the accuracy of various SARS-CoV-2 diagnostics and assess their potential utility as border screening for infection and immunity. Systematic literature searches were conducted in six electronic databases for studies reporting SARS-CoV-2 diagnostics (up to April 30, 2020). Meta-analysis and methodological assessment were conducted for all included studies. The performance of the diagnostic tests was evaluated with pooled sensitivity, specificity, and their respective 95% confidence intervals. A total of 5,416 unique studies were identified and 95 studies (at least 29,785 patients/samples) were included. Nucleic acid amplification tests (NAAT) consistently outperformed all other diagnostic methods regardless of the selected viral genes with a pooled sensitivity of 98% and a pooled specificity of 99%. Point-of-care (POC) serology tests had moderately high pooled sensitivity (69%), albeit lower than laboratory-based serology tests (89%), but both had high pooled specificity (96-98%). Serology tests were more sensitive for sampling collected at ≥ 7 days than ≤ 7 days from the disease symptoms onset. POC NAAT and POC serology tests are suitable for detecting infection and immunity against the virus, respectively as border screening. Independent validation in each country is highly encouraged with the preferred choice of diagnostic tool/s.

Viruses responsible for acute respiratory infections before (2016-2019) and during (2021) circulation of the SARS-CoV-2 virus in pediatric patients in a reference center at Barranquilla Colombia: A pattern analysis.

OBJECTIVE: To evaluate the behavior of the viruses responsible for acute respiratory infections before (2016-2019) and after (2020-2021) the start of the circulation of the SARS-CoV-2 virus in pediatric patients treated at a reference center from Barranquilla, Colombia. MATERIALS AND METHODS: A descriptive observational study was carried out, and data were obtained by reviewing the influenza-like illness and severe acute respiratory infection database in the pediatric population of the sentinel surveillance reference center in the district of Barranquilla during the years 2016-2021, applying inclusion and exclusion criteria. RESULTS: During 2016-2019, the average age of individuals was 1.3 (±1.7) years, during 2021, it was 2.3 (±3.5) years. The distribution by sex was similar, predominantly male. August and February were the months with the highest record of symptoms for 2016-2019 and 2021, respectively, the most frequent being cough, fever, shortness of breath, and diarrhea. By 2021 there was a higher use of antibiotics and antivirals reported than in 2016-2019. Most patients tested negative for viral detection. When comparing the percentage of viruses detected by age group and years of detection, positivity was lower in 2021 by every age group, and respiratory syncytial virus (RSV) was the most frequently detected. CONCLUSIONS: There was less virus positivity in viral detection tests in the pediatric population in 2021. RSV persists as the main etiology affecting this population, especially infants. The use of antibiotic therapy in viral infections continues to be a problematic practice in their management. Sentinel surveillance can be strengthened throughout the country.

Clinical, Biochemical, and Radiological Presentation of RT-PCR-Positive vs RT-PCR-Negative SARS-CoV-2 Pneumonia Requiring ICU Care: An Observational, Cross-Sectional, Single-Center Study in Kalaburagi, Kalyana Karnataka.

Introduction Studies have reported similar clinical, biochemical, and radiological features between real-time polymerase chain reaction (RT-PCR)-positive and RT-PCR-negative patients. Therefore, the present study aims to assess differences in RT-PCR-positive versus RT-PCR-negative patients' characteristics. Methods We prospectively included 70 consecutive patients with typical coronavirus disease 2019 (COVID-19)-like clinical features who were either RT-PCR-positive or negative, requiring admission to the intensive care unit. The patients were classified into positive and negative RT-PCR groups and evaluated for clinical features, comorbidities, laboratory findings, and radiologic features. Results Fifty-seven point one percent (57.1%; 40/70) were RT-PCR positive, and 42.9% (30/70) were RT-PCR negative patients. The respiratory rate was higher among negative patients (P = 0.02), whereas the mean duration of fever was longer (3.34 vs 2.5; P = 0.022) among positive patients. At presentation, RT-PCR-negative patients had lower saturation of peripheral oxygen (SpO2) (near significant P = 0.058). Evaluation of co-morbidities revealed no differences. The neutrophil/lymphocyte ratio (NLR) (4.57 vs 6.52; P = 0.048), C-reactive protein (CRP) (9.97 vs 22.7; P = 0.007), and serum ferritin (158 vs 248.52; P = 0.010) were higher in patients who tested negative for RT-PCR. Thrombocytopenia (2.42 vs 1.76; P = 0.009), D-dimer levels (408.91 vs 123.06; P = 0.03), and interleukin (IL-6) levels (219.3 vs 80.81; P = 0.04) were significantly elevated among RT-PCR positive patients. The percentage of lung involvement in negative cases was 42.29+/-22.78 vs 36.21+/-21.8 in positive cases (P=0.23). The CT severity score was similar in both cohorts. Conclusion Both RT-PCR-positive and negative patients have similar clinical, biochemical, and radiological features. Considering that we are amidst a pandemic, it is advisable to have a similar approach irrespective of the RT-PCR report and triage and isolate accordingly. We recommend an RT-PCR-negative intensive care unit (ICU) ward and that the treating physician take a call on the management with a holistic approach driven clinically by the laboratory findings and helped by radiological findings. Stressing only on the RT-PCR report for management can be counterproductive.

Clinical features and viral etiology of acute respiratory infection in an outpatient fever clinic during COVID-19 pandemic in a tertiary hospital in Nanjing, China.

BACKGROUND: Clinical feature and viral etiology for acute respiratory infection (ARI) in the community was unknown during coronavirus disease 2019 (COVID-19) pandemic. OBJECTIVE: In a retrospective study, we aimed to characterize the clinical feature and etiology for the ARI patients admitted to the outpatient fever clinic in Nanjing Drum Tower Hospital between November 2020 and March 2021. METHODS: Fifteen common respiratory pathogens were tested using pharyngeal swabs by multiplex reverse transcriptase-polymerase chain reaction assays. RESULTS: Of the 242 patients, 56 (23%) were tested positive for at least one viral agent. The predominant viruses included human rhinovirus (HRV) (5.4%), parainfluenza virus type III (PIV-III) (5.0%), and human coronavirus-NL63 (HCoV-NL63) (3.7%). Cough, sputum, nasal obstruction, and rhinorrhea were the most prevalent symptoms in patients with viral infection. Elderly and the patients with underlying diseases were susceptible to pneumonia accompanied with sputum and chest oppression. Three (5.4%) patients in virus infection group, whereas 31 (16.7%) in non-viral infection group (p = 0.033), were empirically prescribed with antiviral agents. Among 149 patients who received antibiotic therapy, 30 (20.1%) patients were later identified with viral infection. CONCLUSION: Our study indicated the importance of accurate diagnosis of ARI, especially during the COVID-19 pandemic, which might facilitate appropriate clinical treatment.