RAPID IDENTIFICATION OF ETIOLOGICAL AGENTS OF RESPIRATORY TRACT INFECTIONS DURING THE COVID-19 PANDEMIC USING THE MULTIPLEX-PCR METHOD.

Objective. Most respiratory infections have similar symptoms, so it is clinically difficult to determine their etiology. This study aimed to show the importance of molecular diagnostics in identifying the etiological agent of respiratory infections, especially during the coronavirus disease 2019 (COVID-19) pandemic. Methods. A total of 849 samples from patients hospitalized at the University Clinical Center Kragujevac (from January 1 to August 1, 2022) were examined using automated multiplex-polymerase chain reaction (PCR) tests. The BioFire-FilmArray-Respiratory Panel 2.1 test was used for 742 nasopharyngeal swabs [identification of 19 viruses (including SARS-CoV-2) and four bacteria], while the BioFire-FilmArray-Pneumonia Panel was used [identification of 18 bacteria and nine viruses] (BioMerieux, Marcy l'Etoile, France) for 107 tracheal aspirates. The tests were performed according to the manufacturer's instructions, and the results were available within an hour. Results. In 582 (78.4%) samples, the BioFire-FilmArray-Respiratory Panel 2.1 plus test identified at least one pathogen. The rhinovirus (20.6%), SARS-CoV-2 (17.7%), influenza A (17.5%), respiratory syncytial virus (12.4%), and parainfluenza 3 (10.1%) were the most common. Other viruses were found less frequently, and Bordetella parapertussis was detected in one sample. In 85 (79.4%) samples, the BioFire-FilmArray-Pneumonia Panel test identified at least one bacterium or virus. The most prevalent bacteria were Staphylococcus aureus (42.4%), Haemophilus influenzae (41.2%), Streptococcus pneumoniae (36.5%), Moraxella catarrhalis (22.3%), and Legionella pneumophila (2.4%). Among viruses, rhinovirus (36.5%), adenovirus (23.5%), influenza A (11.8%), and the genus Coronavirus (4.7%), were detected. Conclusion. Multiplex-PCR tests improved the implementation of therapeutic and epidemiological measures, preventing the spread of the COVID-19 infection and Legionnaires' disease.Copyright © 2022, Serbian Medical Society. All rights reserved.

Bacterial Infectious Diseases in the Covid-19 Era

The outbreak of SARS-CoV-2 in December 2019 in China quickly spread to the rest of the world. By March 2020, the World Health Organization declared the COVID-19 pandemic, and several mitigation strategies were implemented worldwide, highlighting social distancing, quarantine and the use of face masks. Since then, many studies have reported the impact of these interventions on the occurrence of other infectious diseases, especially bacterial infectious diseases disseminated through airborne. Invasive infections with respiratory bacterial pathogens, such as Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, Bordetella pertussis, Chlamydia pneumoniae and Mycoplasma pneumoniae have had a marked decline in several countries of the world. Low- and middle-income (LMIC) and high-income countries (HIC) were at different seasons of the year when COVID-19 started and interventions were implemented, but long-lasting consequences of seasonal differences are yet to be elucidated. In this session, we aim to describe the impact of COVID-19 and related intervention strategies in bacterial infectious diseases between LMIC and HIC;determine whether and how the onset of COVID-19 pandemic has changed the broader scenario of infectious diseases;and envision future and emerging infectious diseases in the post-pandemic world.Copyright © 2023

RAPID IDENTIFICATION OF ETIOLOGICAL AGENTS OF RESPIRATORY TRACT INFECTIONS DURING THE COVID-19 PANDEMIC USING THE MULTIPLEX-PCR METHOD.

Objective. Most respiratory infections have similar symptoms, so it is clinically difficult to determine their etiology. This study aimed to show the importance of molecular diagnostics in identifying the etiological agent of respiratory infections, especially during the coronavirus disease 2019 (COVID-19) pandemic. Methods. A total of 849 samples from patients hospitalized at the University Clinical Center Kragujevac (from January 1 to August 1, 2022) were examined using automated multiplex-polymerase chain reaction (PCR) tests. The BioFire-FilmArray-Respiratory Panel 2.1 test was used for 742 nasopharyngeal swabs [identification of 19 viruses (including SARS-CoV-2) and four bacteria], while the BioFire-FilmArray-Pneumonia Panel was used [identification of 18 bacteria and nine viruses] (BioMerieux, Marcy l'Etoile, France) for 107 tracheal aspirates. The tests were performed according to the manufacturer's instructions, and the results were available within an hour. Results. In 582 (78.4%) samples, the BioFire-FilmArray-Respiratory Panel 2.1 plus test identified at least one pathogen. The rhinovirus (20.6%), SARS-CoV-2 (17.7%), influenza A (17.5%), respiratory syncytial virus (12.4%), and parainfluenza 3 (10.1%) were the most common. Other viruses were found less frequently, and Bordetella parapertussis was detected in one sample. In 85 (79.4%) samples, the BioFire-FilmArray-Pneumonia Panel test identified at least one bacterium or virus. The most prevalent bacteria were Staphylococcus aureus (42.4%), Haemophilus influenzae (41.2%), Streptococcus pneumoniae (36.5%), Moraxella catarrhalis (22.3%), and Legionella pneumophila (2.4%). Among viruses, rhinovirus (36.5%), adenovirus (23.5%), influenza A (11.8%), and the genus Coronavirus (4.7%), were detected. Conclusion. Multiplex-PCR tests improved the implementation of therapeutic and epidemiological measures, preventing the spread of the COVID-19 infection and Legionnaires' disease.Copyright © 2022, Serbian Medical Society. All rights reserved.

Evaluation of BioFire Respiratory Panel 2 plus for Detection of Bordetella pertussis in Nasopharyngeal Swab Specimens from Children with Clinically Suspected Pertussis.

The objective of this study was to compare the performances of BioFire Respiratory Panel 2 (RP2) plus, quantitative real-time PCR (qPCR), and culture for the detection of Bordetella pertussis in nasopharyngeal swab (NPS) specimens. Consecutive NPS specimens were collected from patients with clinically suspected pertussis from 1 March 1 to 31 July 2018 in Shenzhen Children's Hospital. All the specimens were tested in parallel by RP2 plus, qPCR, and culture methods. A total of 464 children were enrolled in this study. The positive pertussis rates of culture, RP2 plus, and qPCR were 23.1%, 39.0%, and 38.4%, respectively. Compared to the combined reference standard, the sensitivity, specificity, positive predictive value, and negative predictive values were, respectively, 56.6% (95% confidence interval [CI], 49.2 to 63.7%), 100% (98.3 to 100%), 100% (95.7 to 100%), and 77.0% (72.2 to 81.2%) for culture, 89.9% (84.5 to 93.7%), 96.0% (92.8 to 97.9%), 93.9% (89.1 to 96.8%), and 93.3% (89.5 to 95.8%) for RP2 plus, and 86.8% (80.9 to 91.1%), 94.9% (91.4 to 97.1%), 92.1% (86.9 to 95.5%), and 91.3% (87.2 to 94.2%) for qPCR. The most prevalent codetected pathogen was human rhinovirus/enterovirus (n = 99, 52.4%), followed by parainfluenza virus (n =32, 16.9%) and respiratory syncytial virus (n = 29, 15.3%), in children with B. pertussis present, which was consistent with the top three pathogens previously found in children with B. pertussis absent. Turnaround times for RP2 plus, qPCR, and culture were 2 h, 8 h, and 120 h, respectively. RP2 plus quickly and accurately detected B. pertussis, providing valuable information for an early clinical diagnosis and optimal choice of therapy. IMPORTANCE In recent years, there have been some epidemic or local outbreaks of pertussis in countries with high vaccination rates. One of the crucial factors in controlling pertussis is early diagnosis, which is based on specific laboratory measurements, including culture, serological tests, and PCR assays. Compared to culture and serological tests, PCR is more suitable for clinical application, with a fast detection speed of several hours independent of the disease stage and individual vaccination status. BioFire Respiratory Panel 2 plus, a multiplex PCR assay for simultaneously detecting 22 respiratory pathogens, facilitates the quick detection of Bordetella pertussis and coinfecting respiratory pathogens. It also provides valuable information for an early clinical diagnosis and optimal choice of therapy for children with clinically suspected pertussis.

Routine vaccination coverage - worldwide, 2021

This article discusses the worldwide routine vaccination coverage in 2021, as part of the Immunisation Agenda 2030, a global immunisation strategy to reduce morbidity and mortality from vaccine-preventable diseases. The report presents global, regional, and national estimates and trends in vaccination coverage through 2021, based on reviews of country-specific data, including administrative and survey-based coverage. Global estimates show that coverage with 3 doses of diphtheria, tetanus and pertussis-containing vaccine (DTPcv3) and the first dose of measles-containing vaccine (MCV1) decreased to their lowest levels since 2008. In 2021, 25.0 million infants were not vaccinated with DTPcv3, 2.1 million more than in 2020, and 5.9 million more than in 2019. The number of zero-dose children was 37% higher than in 2019, with 18.2 million infants not receiving any DTPcv dose by the age of 12 months. The report highlights that the full recovery from disruptions to immunisation programmes due to the COVID-19 pandemic will require context-specific strategies to find missed children, prioritise essential health services, and strengthen immunisation programmes to prevent outbreaks.

Vaccination against whooping cough in pregnancy: evaluation of an organizational proposal implemented between 2018 and 2022 in the health district of urban area of Pisa (italy) and a method for coverages calculation

Introduction: Vaccination against Bordetella pertussis is recommended by the Italian Ministry of Health starting from the 28th week of pregnancy. However, data about vaccine coverages are unknown and sharing good practices is necessary to increase adherence to vaccine programs implemented at local level. Here we present data on epidemiology and vaccine coverage of Pertussis in Tuscany from 2012 to 2021 and data on Pertussis vaccine coverage in pregnant women in the Health District of urban area of Pisa for the period 2017 to September 2022. Materials and methods: Data on pertussis cases and pertussis vaccine coverage were retrieved form the Regional Health Agency that made available data on Infectious Diseases Epidemiology in Tuscany on a public report. The diphteria, tetanus, pertussis (dTpa) vaccination in pregnant women were extracted from the vaccination registry from 2017 to 30 September 2022 and adjusted new births from 1st April to 30th March of the following year were considered as denominator. For the current year we assumed that the monthly trend of the absolute number of vaccinations is maintained (+45.3 vaccinations/month) and that the number of new-borns is the same as in 2021. Results: In Tuscany, a progressive increase in the number of cases has been observed since 2012, peaking in 2017 with 115 infections concentrated mainly in children under one year of age. After a significant reduction in the three-year period 2018-2020, with values between 25 and 39 infections per year, no cases of the disease were notified in 2021. Most likely due to the actions taken to counteract the transmission of SARS-CoV-2. Notably, from 2017 to 30 September 2022, a significant increase in vaccination coverage for dTpa in pregnant women was observed, with an average annual increase from 2018 onwards of 39% (range 18%-63%). Discussion and conclusions: Even if the vaccine coverage calculation has some limitations, the availability of a free access services for pregnant women and their contacts has improved adherence to the vaccination against pertussis. However, to achieve an active recruitment strategic to overcome cultural, linguistic and hesitancy barriers it is crucial to improve active call of the pregnant women.

Enhancing vaccination of key populations: lessons and actions

Vaccination is effective in preventing the increase of disease, especially emerging infectious diseases (EIDs), and it is particularly important for people in close contact with infected sources and susceptible populations who are at increased risk of getting infectious diseases due to behavior, occupation or health. Despite targeted vaccination guidelines, inadequate vaccination of the key populations fails to receive widespread attention, resulting in a high-risk transition of disease from key populations to general populations. Strengthening the vaccination of the susceptible groups can effectively block the spread of pathogens to general populations, and reduce the consumption of medical resources in universal vaccination, which has significant economic value. In this review, we describe the prevalence of EIDs, analyze the experience and lessons of infectious disease vaccination in key populations through several cases, and further explore the causes for the decline in vaccination rates of key populations. According to the trends of EIDs, a plan to strengthen the vaccination of key populations is proposed to effectively prevent the transition of EIDs from key populations to general populations.

Differentiating infectious from non-infectious respiratory disease in the cat and dog

This paper describes the clinical signs and use of differential laboratory diagnostic techniques (computed tomography, cytology, histopathology, antigen/antibody detection and polymerase chain reaction) for infectious (viral, bacterial, fungal and parasitic) and non-infectious (inflammatory/immune mediated, neoplastic, cardiac, malformation, foreign body, smoke inhalation, aspiration of caustic material, non-cardiogenic, pulmonary oedema, traumativ, pneumothorax, pulmonary contusions and idiopathic) causes of respiratory diseases in cats and dogs in Ontario, Canada.

Pathogenic characteristics of severe acute respiratory infection in adult inpatients in Yangpu District, Shanghai, 2019-2021

Objective: To understand the pathogenic spectrum and epidemiological characteristics of severe acute respiratory infection (SARI) in adult inpatients in Yangpu District, Shanghai, China, in order to explore strategies for the prevention and treatment of respiratory infectious diseases. Methods: Individual cases were from adult inpatients with SARI in Yangpu District, Shanghai, China from January 2019 to July 2021. Their respiratory samples were collected for etiological pathogen testing. Results: A total of 681 SARI cases were enrolled for sampling and lab testing. Among them, 79.00% were aged 60 years and older, and 75.48% had confirmed chronic disease history. A total of 163 infection inpatients (23.94%) were positive for at least one pathogen. The pathogens identified most frequently were influenza A virus (6.75%), followed by rhinovirus/enterovirus (3.23%), parainfluenza virus (PIV) (2.79%), Mycoplasma pneumoniae (2.35%), coronavirus (CoV) (2.06%). The positive rates of adenovirus (AdV), human metapneumovirus (hMPV), respiratory syncytial virus and bocavirus were all less than 2%. Bacterial strains were identified in eleven SARI cases, including Staphylococcus aureus and Pseudomonas aeruginosa (4 strains), Klebsiella pneumoniae (3 strains). Legionella pneumophila was detected in 9 cases (1.32%) and Bordetella pertussis in 5 cases (0.73%). Two pathogens were co-detected from 11 cases, accounting for 1.62% of 163 positive cases. The most common co-detected pathogens were influenza A virus and other pathogens, accounting for 54.55% of the mixed infection. The positive rates of pathogens were not significantly different between less than 60 years old and over 60 years old groups except for Bordetella pertussis, adenovirus and Mycoplasma pneumonia(P < 0.05). Influenza virus had epidemic peak in winter and spring, but not in summer from 2019 to 2021. Conclusion: Various respiratory pathogens are detected from adult SARI cases. It is mainly influenza virus, with co-detected pathogens and rare pathogens. This study provides helpful information for targeted prevention and control measures including vaccination.

A tale of three in symbiosis: TB-COVID-19-Bordetella coinfection.

Coinfections/mixed infections are common in the respiratory tract. Many times existing organisms have similar risk factors and clinical features that make the diagnosis difficult. Coronavirus diagnosed in 2019 (COVID-19) and tuberculosis (TB) are two such diseases. Patients with TB have lower cellular immunity and impaired pulmonary function. In such environment, atypical organisms, can infect and make the outcome unfavorable. A 21-year-old malnourished (body mass index- 15 kg/m2) girl presented with fever and cough for 10 days. Sputum for Cartridge Based Nucleic Acid Amplification Test demonstrated Mycobacterium tuberculosis with no rifampin resistance. Fever persisted (100-101°F) and saturation was dropping even after 10 days of antitubercular treatment. A repeat reverse transcription-polymerase chain reaction was done and was positive. In view of persistent symptoms after 20 days, bronchoscopy was done, and cultures showed Bordetella bronchiseptica. Fever and symptoms resolved completely after initiation of the sensitive drug. Diagnostic delay in coinfections can lead to increased morbidity and mortality.

A CASE OF BORDETELLA BRONCHISEPTICA AND PNEUMOCYSTIS JIROVECI PNEUMONIA IN A YOUNG PATIENT

SESSION TITLE: Procedures in Chest Infections Case Posters SESSION TYPE: Case Report Posters PRESENTED ON: 10/19/2022 12:45 pm - 01:45 pm INTRODUCTION: Pneumonia is a common condition that is seen in hospitals. Pneumocystis Jirovecii is an opportunist fungal pathogen. Bordetella bronchiseptica is a gram negative bacteria that causes infectious bronchitis in dogs and other animals, but rarely infects humans. CASE PRESENTATION: Patient is a 34 year old African American female with history of sickle cell trait, reported Lupus (not on treatment), asthma, COVID pneumonia who was admitted for worsening shortness of breath & productive cough with yellow sputum. She was previously hospitalized and discharged after being treated for Community-Acquired Pneumonia. In the ER, she was febrile, tachycardic, tachypneic, & hypoxic requiring BiPAP. CXR obtained showed findings concerning for multifocal pneumonia. Chest CT Angiogram was negative for PE. Patient was started on Vancomycin & Meropenem for treatment of her pneumonia. Blood cultures, Legionella, Strep pneumoniae, Aspergillus, Beta-D-glucan, Sputum culture, & MRSA screen were ordered for further evaluation of her infection. ANA screen reflex panel, lupus anticoagulant, anticardiolipin antibodies, beta-2 glycoprotein antibodies were also ordered given patient's reported history of SLE and the concern for SLE pneumonitis: ANA & Sjogren's Anti-SSA were positive;otherwise, autoimmune workup was unremarkable. During hospitalization, patient was eventually weaned down to nasal cannula and antibiotic was de-escalated to levaquin. However, sputum culture eventually grew Bordetella Bronchiseptica that was resistant to Levaquin so antibiotic regimen was switched to Doxycycline. In addition, Beta-D-glucan was noted to be elevated. Bronchoscopy was done for further evaluation;multiple transbronchial biopsies were positive Pneumocystis Jirovecii. Patient was then initiated on Bactrim for treatment of PJP Pneumonia along with a steroid taper. Patient was tested for HIV and it was negative. DISCUSSION: In this case, patient was found to have two rare pathogens, that are more common in immunocompromised patients such as those with HIV/AIDS, on high-dose corticosteroids or malignancy. This patient had a unconfirmed diagnosis of SLE and past COVID Pneumonia. Patient had Bordetella bronchiseptica pneumonia that is frequently isolated in the respiratory tract of animals but can cause severe respiratory infection in humans. This microorganism can cause upper respiratory tract infections, pneumonitis, endocarditis, peritonitis, meningitis, sepsis and recurrent bacteremia. Upon further discussion with the patient, she was found to have a recent pet dog. CONCLUSIONS: High level of clinical suspicious is needed in patient presenting with recurrent pneumonia with chest imaging findings suggestive of multifocal pneumonia. The mainstay of treatment for PJP is TMP-SMX and steroid. We recommend Fluoroquinolones or tetracycline for Bordetella bronchiseptica pneumonia. Reference #1: Benfield T, Atzori C, Miller RF, Helweg-Larsen J. Second-line salvage treatment of AIDS-associated Pneumocystis jirovecii pneumonia: a case series and systematic review. J Acquir Immune Defic Syndr. 2008 May 1;48(1):63-7. Reference #2: de la Fuente J, Albo C, Rodríguez A, Sopeña B, Martínez C. Bordetella bronchiseptica pneumonia in a patient with AIDS. Thorax. 1994 Jul;49(7):719-20. doi: 10.1136/thx.49.7.719. PMID: 8066571;PMCID: PMC475067. DISCLOSURES: No relevant relationships by Priya George No relevant relationships by ELINA MOMIN No relevant relationships by Mohammedumer Nagori

Routine vaccination coverage - worldwide, 2020

This report, which updates previous reports, presents estimates of global, regional, and national vaccination coverage and trends as of 2020. It describes the changes in vaccination coverage and the numbers of unvaccinated and undervaccinated children as measured by receipt of the first and third doses of diphtheria, tetanus, and pertussis-containing vaccine (DTP)in 2020, when the COVID-19 pandemic began, compared with 2019. Global coverage estimates with the third dose of DTP (DTP3) and a polio vaccine (Pol3) fell from 86% in 2019 to 83% in 2020. Similarly, MCV1 coverage fell from 86% in 2019 to 84% in 2020. The last year the coverage estimates were at 2020 levels was 2009 for DTP3 and 2014 for both MCV1 and the third dose of Pol (Pol3). Worldwide, 22.7 million children(17% of the target population) did not receive DTP in 2020, compared with 19.0 million (14%) in 2019. Children who did not receive the first DTP dose (DTP1) by age 12 months (zero-dose children) accounted for 95%of the increased number. Among those who did not receive DTP3 in 2020, approximately 17.1 million (75%)were zero-dose children. Global coverage decreased in 2020 compared with 2019 estimates for the completion of Haemophilus influenzae type b (Hib), hepatitis B vaccine (HepB), human papillomavirus vaccine (HPV),and rubella-containing vaccine (RCV). To reach full coverage with all recommended vaccines, tailored strategies will be needed, especially to reach communities with a lot of children who haven't had any or enough vaccines.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Bordetella bronchiseptica Co-Infection in a Stem Cell Transplant Patient.

Bordetella bronchiseptica infections may be overlooked by clinicians due to the uncommon encounter of this pathogen in humans and common isolation of co-pathogens. However, the isolation of B. bronchiseptica in immunocompromised individuals may represent a true infection. We report our experience with the fatal case of a stem cell transplant recipient, co-infected with SARS-CoV-2 and B. bronchiseptica, who was considered fully vaccinated (two doses) at the time of her case in spring 2021. Future studies are needed to evaluate the incidence of bacterial co-infections in immunosuppressed individuals with SARS-CoV-2 and clinicians should remain cognizant of the potential pathogenic role of uncommon pathogens isolated in these individuals.

Retrospective analysis of vaccine antibody titers in patients with different stages of monoclonal plasma cell disorders

Background: Infections occur with up to twofold increased risk in patients with monoclonal gammopathy of undetermined significance (MGUS) and tenfold increased risk in multiple myeloma (MM). To reduce risk, revaccination following autologous hematopoietic cell transplantation (AHCT) is recommended to restore humoral immunity. We have previously shown that vaccine titers after AHCT have prognostic significance. In the COVID era, reliable clinical data about antibody titers is relevant yet scarce. We investigated the significance of different vaccine titers in newly diagnosed patients in different stages of the disease. Methods: The study population comprised of 77 patients with MGUS, smoldering multiple myeloma (SMM) and MM who were seen at a tertiary cancer center from 2018- 2022. All patients had antibody titers (B. pertussis, Diptheria, H. Influenzae B, Hepatitis, Influenza, Meningitis, Mumps, Rubeola, Rubella, Poliovirus, S. pneumoniae, Varicella Zoster and Tetanus) tested at the time of diagnosis, prior to start of treatment if indicated. Titers were interpreted in accordance with the manufacturers' recommendations. Patient characteristics were compared using the Kruskal- Wallis and Fisher's exact tests. Associations with % titer positivity were evaluated using the Kruskal- Wallis test. Results: There was significant difference in antibody titer positivity between the different patient groups (51.4% in MGUS, 40.5% in SMM and 34.2% in MM) (p < 0.001). There was no difference in antibody titer positivity depending on age, sex or race. Among individual pathogens, there was a significant difference between the three groups in regards to titers for Diphtheria, Mumps, Poliovirus 3, Strep pneumoniae 19, Strep pneumoniae 56 and Varicella Zoster. Conclusions: Antibody titers for vaccine preventable diseases are significantly different between patients with MGUS, SMM and MM at the time of diagnosis, with MGUS having the highest and MM having the lowest positivity. Patient related factors such as age, sex or race were not associated with antibody titer positivity. Current guidelines for revaccination are not extended to patients with MGUS and SMM and can be considered in prospective trials.

Risk assessment of public health emergencies concerned in the mainland of China, April 2022

Objective To assess the risk of public health emergencies, both the indigenous ones and the imported ones, which might occur in the mainland of China in April 2022. Methods An internet based expert counsel was conducted to analyze the surveillance data of public health emergencies and priority communicable diseases in China reported through different channels, and the experts in all provincial centers for disease control and prevention attended this video conference. Results It is expected that number of domestically reported public health emergency events other than COVID-19 in April would remain unchanged from March. The risk of domestic COVID-19 outbreaks caused by the indigenous transmission and the foreign importation is high, making it more difficult to prevent and control the epidemic. Local governments need to strengthen epidemic prevention and control in accordance with national requirements and hold the bottom line of no large-scale rebound of the epidemic. The number of pertussis cases will maintain rising trend due to the improvement of laboratory testing technology, the weakening of vaccine protection and the strengthening of surveillance in some districts. Conclusion Special attention should be paid to COVID-19. General attentions should be paid to pertussis.

Bordetella pertussis, Chlamydia pneumoniae, and Mycoplasma pneumoniae Findings in Children During COVID-19 Pandemic in Finland.

Social restrictions effectively interrupted the typical respiratory virus circulation. The aim of this report is to describe how atypical pneumonia bacteria detections have changed during the COVID-19 pandemic in Finnish children. Bordetella pertussis, Chlamydia pneumoniae, and Mycoplasma pneumoniae findings were gathered from the National Infectious Diseases Register from 2015 to 2021 and stratified into three age groups (0-4, 5-9, and 10-14 years). Incidences per 100,000 children were calculated and 2020 and 2021 was compared to the mean incidence of reference years (2015-2019) by incidence rate ratios. B. pertussis incidence was 32% lower in 2020 and 88% lower in 2021 compared to reference years. C. pneumoniae detections decreased rapidly in 2020 and not a single detection of C. pneumoniae was reported to the register in 2021. M. pneumoniae incidence was 72% lower in 2020 and 89% lower in 2021 than in the reference years. All these findings were seen in all age groups. As the incidences of B. pertussis, C. pneumoniae, and M. pneumoniae detections have been low throughout the pandemic, it seems that the social restrictions have been effective in preventing the spreading of these respiratory bacteria in children. Supplementary Information: The online version contains supplementary material available at 10.1007/s42399-022-01251-9.

Exploring national COVID-19 variability across sub-Saharan Africa

Background: In early March 2020, coronavirus disease (COVID-19), an infectious disease caused by a novel coronavirus, was declared a pandemic by the World Health Organization. Since its emergence and global spread, the pandemic has been one of the greatest global crises in modern human history. Notably, in Sub-Saharan Africa (SSA), COVID-19-related burden and outcomes have been generally lower than many other parts of the world and substantially better than were initially feared. At the same time, there has been great heterogeneity in COVID-19 burden and outcomes between countries in the region, with some reporting particularly high incidence and death figures compared to others. What accounts for the significant cross-country variability apparent in SSA and why have some countries performed better than others? The present study investigates country-specific factors that may help to explain differences in COVID-19 outcomes across 48 countries in SSA.

Impact of fulfilling immunization coverage during the COVID-19 pandemic: a systematic review

Introduction: Indonesia reported the first case of COVID-19, the coverage of routine immunization to prevent diseases in children such as measles, rubella, and diphtheria is decreasing. For example, diphtheria, pertussis and tetanus (DPT3) and measles and rubella (MR1) immunization coverage rates were reduced by more than 35% in May 2020 compared to the same time period in the previous year.

An agile discovery method of drugs for infectious diseases and tentative exploration of its application in drug discovery for COVID-19

OBJECTIVE: To establish an agile discovery method of drugs or natural products for epidemics (aCODE) for the development of anti-infectious disease drugs. METHODS: Five infectious diseases (HIV infection, human influenza, Paramyxoviridae infections, bacterial infections and whooping cough) involving more than 40 drugs approved by the United States Food and Drug Administration (FDA) were selected. An experimental group and two negative control groups (A and B) for each disease were set up. The experimental group randomly selected (500 times) M FDA-approved indications as seed drugs for the disease, while negative control group A used all FDA-approved infectious drugs for non-current diseases instead of seed drugs, and negative control group B used all non-infectious disease drugs for non-infectious diseases instead of seed drugs. M ranged from 2 to 20, the target gene information of the seed drug was input, and the feature vector of the seed drug set was calculated. Candidate compounds were predicted through similarity search of drug feature vectors. The size of the inter- section between the predicted drug and the positive set of drugs approved by the FDA for the disease, and the significance of the intersection were calculated. After the establishment of the aCODE method, four drugs (lopinavir, ribavirin, ritonavir and chloroquine) were selected as seed drugs for COVlD-19 to predict the composition of natural products. Using natural products with known anti-coronavirus activities as the verification set, the significance of the prediction results was calculated. RESULTS: In the case of the five infectious diseases, the proportion of positive drugs in the results of prediction in the experimental group increased with the number of seed drugs, while the positive rate of the two negative control groups remained basically unchanged or somewhat trended down. The aCODE method, when applied to COVlD-19 drug screening, could effectively predict drugs with potential anti-SARS-Cov-2 activity (P=0.0046). CONCLUSION: With the aCODE method, the more the seed drugs, the more accu- rate the characteristics of the disease-related gene modules calculated from this group of seed drugs, and the higher the proportion of positive drugs in the prediction result. This method may contribute to the discovery of drugs for COVID-19.