Oropharyngeal Swabs Research Articles

Longitudinal observation of viral load in patients infected with Omicron variant and its relationship with clinical symptoms.

In 2022, a new coronavirus variant (Omicron) infection epidemic broke out in Shanghai, China. However, it is unclear whether the duration of this omicron variant is different from that of the prototype strain. We retrospectively analyzed 157 cases of Omicron variant infection in Taizhou Public Health Center from March 29, 2022, to April 18, 2022, and observed the dynamics of nucleic acid Ct values during the admission and discharge of patients. Clinical and laboratory indicators of these patients were also obtained. Compared to the prototype strain, the Omicron variant showed a broad population susceptibility in infected individuals (regardless of age and presence of underlying disease) and had slight damage to the immune system and renal function; the viral loads peaked was 2-3 days from disease onset; the median duration of omicron variant was 15-18 days; the nucleic acid Ct value of nasopharyngeal swabs of infected patients is lower than that of throat swabs, and the Ct value of oropharyngeal swabs is unstable during the recovery period. Therefore, we found that the time to peak viral load of this Omicron variant was 2-3 days after the onset of the disease, and the duration was 15-18 days; symptomatic patients had higher viral load and longer hospitalization time. This finding will provide a basis for understanding omicron variants and formulating the national prevention and control strategy.

Head-to-Head Comparison of Nasopharyngeal, Oropharyngeal and Nasal Swabs for SARS-CoV-2 Molecular Testing.

Nasopharyngeal swabs (NPS) are considered the gold standard for SARS-CoV-2 testing but are technically challenging to perform and associated with discomfort. Alternative specimens for viral testing, such as oropharyngeal swabs (OPS) and nasal swabs, may be preferable, but strong evidence regarding their diagnostic sensitivity for SARS-CoV-2 testing is still missing. We conducted a head-to-head prospective study to compare the sensitivity of NPS, OPS and nasal swabs specimens for SARS-CoV-2 molecular testing. Adults with an initial positive SARS-CoV-2 test were invited to participate. All participants had OPS, NPS and nasal swab performed by an otorhinolaryngologist. We included 51 confirmed SARS-CoV-2-positive participants in the study. The sensitivity was highest for OPS at 94.1% (95% CI, 87 to 100%) compared to NPS at 92.5% (95% CI, 85 to 99%) (p = 1.00) and lowest for nasal swabs at 82.4% (95% CI, 72 to 93%) (p = 0.07). Combined OPS/NPS was detected in 100% of cases, while the combined OPS/nasal swab increased the sensitivity significantly to 96.1% (95% CI, 90 to 100%) compared to that of the nasal swab alone (p = 0.03). The mean Ct value for NPS was 24.98 compared to 26.63 for OPS (p = 0.084) and 30.60 for nasal swab (p = 0.002). OPS achieved a sensitivity comparable to NPS and should be considered an equivalent alternative for SARS-CoV-2 testing.

Ultrasensitive detection of SARS-CoV-2 S protein with aptamers biosensor based on surface-enhanced Raman scattering.

A rapid and accurate diagnostic modality is essential to prevent the spread of SARS-CoV-2. In this study, we proposed a SARS-CoV-2 detection sensor based on surface-enhanced Raman scattering (SERS) to achieve rapid and ultrasensitive detection. The sensor utilized spike protein deoxyribonucleic acid aptamers with strong affinity as the recognition entity to achieve high specificity. The spherical cocktail aptamers-gold nanoparticles (SCAP) SERS substrate was used as the base and Au nanoparticles modified with the Raman reporter molecule that resonates with the excitation light and spike protein aptamers were used as the SERS nanoprobe. The SCAP substrate and SERS nanoprobes were used to target and capture the SARS-CoV-2 S protein to form a sandwich structure on the Au film substrate, which can generate ultra-strong "hot spots" to achieve ultrasensitive detection. Analysis of SARS-CoV-2 S protein was performed by monitoring changes in SERS peak intensity on a SCAP SERS substrate-based detection platform. This assay detects S protein with a LOD of less than 0.7 fg mL-1 and pseudovirus as low as 0.8 TU mL-1 in about 12min. The results of the simulated oropharyngeal swab system in this study indicated the possibility of it being used for clinical detection, providing a potential option for rapid and accurate diagnosis and more effective control of SARS-CoV-2 transmission.

Better design leads to better results - Importance of virological outcome design in clinical trials for antiviral treatment of coronavirus disease 2019.

Better design leads to better results - Importance of virological outcome design in clinical trials for antiviral treatment of coronavirus disease 2019.

HIV viral load monitoring during monkeypox virus infection among people with HIV.

Aims of this study were to assess the characteristics of Mpox among people with HIV (PWH) and describe the change of some immune-virological parameters during Mpox virus infection. Case series of PWH diagnosed with Mpox between May and July 2022 at the Infectious Diseases Unit of San Raffaele Scientific Institute, Milan, Italy. Real-time PCR was used to detect Mpox virus on oropharyngeal, cutaneous, genital and rectal swabs, plasma, seminal fluids, and urines. The values of the CD4 + lymphocytes and HIV-RNA were assessed both at Mpox diagnosis and after Mpox virological clearance and were compared to those prior to Mpox. The relationship between the symptoms clinical duration of Mpox and the CD4 + cell count at diagnosis was assessed with Spearman's correlation coefficient. Overall, 28 PWH on antiretroviral therapy with Mpox were evaluated. HIV-RNA did not substantially change at Mpox infection with respect to previous virological profile ( P = 0.721). However, at time of Mpox diagnosis, we observed a detectable HIV-RNA (196 copies/ml) in one individual previously undetectable (HIV-RNA < 20 copies/ml) and an increase to 1.220 copies/ml in a previously viremic subject (HIV-RNA = 263 copies/ml). No significant differences in CD4 + cell count were found before and at time of Mpox diagnosis ( P = 0.151) and a higher CD4 + cell count at Mpox diagnosis was marginally related to a lower duration of Mpox symptoms ( r = -0.341, P = 0.068). Among PWH, we advise monitoring HIV viral load at Mpox diagnosis and during follow-up, as well as providing counseling on the results, due to the important individual and community implications.

Monkeypox Outbreak 2022: Clinical and Virological Features of 30 Patients at the Sexually Transmitted Diseases Centre of Sant' Orsola Hospital, Bologna, Northeastern Italy.

Monkeypox infection is a zoonosis first described in humans in 1970 in Congo. While previously manifesting in small, confined outbreaks, the disease is rapidly spreading globally. The aim of this study was to investigate microbiological samples (skin, rectal, and oropharyngeal swab samples and plasma and urine samples) that can help in adequate diagnostic, therapeutic, and prognostic management. We present 30 laboratory-confirmed monkeypox patients with peculiar clinical and virological features admitted to the Sexually Transmitted Diseases Centre of Sant' Orsola Hospital, University of Bologna, in the period between 20 June and 10 August 2022. Demographic, anamnestic, and clinical data were obtained, and microbiological samples were collected and analyzed by real-time PCR to detect the presence of monkeypox virus (MPXV) DNA. All monkeypox patients were adult men who have sex with men (MSM) (mean age, 37.5 years). Nonskin samples were collected from 29 patients during the acute phase of the infection. The detection rates of MPXV DNA in plasma, urine, and oropharyngeal swab samples (82.3%, 64.7%, and 75.0%, respectively) were highest in samples collected 4 to 6 days after symptom onset. The presence of MPXV in plasma and urine samples was analyzed 11 to 38 days after symptom onset to monitor viral shedding duration. Interestingly, MPXV DNA was detected in a urine sample collected on day 21 in one patient. Prolonged positivity in urine after the clinical recovery suggests a potential source of infection by contamination of wastewater and sewage and transmission to possible animal reservoirs and highlights the need for further investigations on nonskin samples to extend and more adequately standardize the patient isolation period.

Saliva as a Viable and Simple Alternative to Nasopharyngeal and Oropharyngeal Swabs for COVID-19 Real-Time Reverse Transcriptase Polymerase Chain Reaction

Introduction: Attributable to the difficulties in specimen collection, discomfort and symptoms caused on by Nasopharyngeal (NPS) and Oropharyngeal Swab (OPS) collection, and significant risk to Healthcare Workers (HCW), evaluation of an alternative specimen for the diagnosis of Coronavirus Disease 2019 (COVID-19) is required. Saliva specimen could be an alternative specimen with many advantages over NPS and OPS, however little is known about how well it performs this purpose. Aim: The present study was conducted to assess the efficacy of saliva as a viable and simple alternative specimen to NPS and OPS for COVID-19 Real-Time reverse transcriptase Polymerase Chain Reaction (rRT-PCR). Materials and Methods: The present cross-sectional study was conducted in the Department of Microbiology, SGT Medical College Hospital and Research Institute, Haryana, India, from July 2020 to December 2020. A total of 60 symptomatic and 20 asymptomatic COVID-19 patients were recruited for the study and specimen viz., saliva, NPS and OPS were collected at four different sampling points i.e., on day 1, 5, 7 and 14 after confirmation of COVID-19 rRT-PCR test positivity. Data obtained from the study was analysed and expressed as median, frequency, interquartile range and Chi-square test was done for comparison of categorical variables. Results: Majority of the patients in symptomatic hospitalised COVID-19 patients were males (n=49, 81.7%) and remaining were females (n=11, 18.3%) and in asymptomatic group 8 (40%) were males and 12 (60%) were females. Saliva was the most sensitive specimen (74.2%), followed by NPS, Naso Oropharyngeal Swab (NOPS) with 70.8% each and OPS (65.8%) for detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in symptomatic patients at four different sampling points. Comparable findings were also observed in specimens obtained from asymptomatic individuals as well. In addition, the viral load was also highest in saliva sample, as measured by Cycle Threshold (CT)-value. Across all specimen types, high viral load (lower CT-values) was observed during the early period of infection. Majority of the study participants reported discomfort during NPS and OPS collection (90% and 85%, respectively), lacrimation, sneezing and gag reflex being the most commonly reported induced symptoms. Conclusion: In the present study, saliva could be a viable and alternate specimen for COVID-19 diagnosis due to its ease in sample collection, specimen stability and reduced risk of transmission of infection due to droplets.

Comparison of Two Molecular Diagnostic Tests for COVID-19: Abbott RealTime SARS-CoV-2 and Allplex&amp;amp;#8482; 2019-nCoV, in the Epidemic Context in Senegal

Background: The persistence of the rapid spread of the COVID-19 pandemic is linked to the appearance of several variants of SARS-CoV2 with an impact on biological diagnosis, treatment and vaccination. The United States Food and Drug Administration (FDA) has granted several SARS-CoV-2 detection tests Emergency Use Authorization (EUA) for diagnosis and better epidemiological surveillance. Thus, multiple RT-PCR tests have been developed and brought to market in order to meet the urgent need for the diagnosis of COVID-19. However, comparative data between these tests in clinical laboratories are scarcely available to assess their performance. Objective: To compare two molecular methods for detecting SARS-CoV-2: the RT-PCR, Allplex™ 2019-nCoV tests on CFX96 Bio-Rad and the Abbott m2000sp/rt RealTime SARS-CoV-2. Materials and Methods: Nasopharyngeal and oropharyngeal swabs were taken from patients to diagnose SARS-CoV-2 infection. For each sample, we searched for the virus with two different RT-PCR tests: 1) first on Abbott m2000 SARS-CoV-2 targeting the N and RdRp genes, 2) then on Allplex™ 2019-nCoV Assay looking for the E, N and RdRp genes. Results: Percentages of the agreement were calculated. A total of 100 samples that tested negative and 90 positives on Abbott m2000 SARS-CoV-2 were retested on Allplex™ 2019-nCoV. Overall agreement was 74.74% on all samples. The specific agreement was 84% and 64.4% respectively for negative and positive samples with the RealTime SARS-CoV-2 test. A positive correlation (r2 = 0.63; p ™ 2019-nCoV and Abbott RealTime SARS-CoV-2 tests in the diagnosis of COVID-19. As the concordance is low for small viremias, the RT-PCR Allplex™ 2019-nCoV Assay would be better indicated during the acute and symptomatic phase of the disease.

An Epidemiological Analysis of Severe Acute Repiratory Syndrome Coronavirus 2 Genome Sequencing: A Hospital-based Retrospective Study

Introduction: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a positive-sense enveloped single-stranded Ribonucleic Acid (RNA) virus. Structural proteins help the virus package its RNA, while other proteins enable viral replication by facilitating host entry. Through constant mutation, the virus changes its emergence profile, and combinations of mutations can lead to increased transmissibility and receptor binding capacity, altering its surface structure. Whole genome sequencing is an important tool for studying these changes. In this study, the authors report on the genome sequencing of patients who tested positive for SARS-CoV-2 using real-time Reverse TranscriptasePolymerase Chain Reaction (RT-PCR) tests. Aim: To identify the different lineages circulating in specific districts of West Bengal, India, and perform an epidemiological analysis of the patients to control disease severity during the second wave of Coronavirus Disease-2019 (COVID-19). Materials and Methods: This retrospective hospital-based study was conducted at the Virus Research and Diagnostic Laboratory (VRDL) at RG Kar Medical College and Hospital, West Bengal, India from January 2021 to October 2021. Data collection started in January 2021 and was analysed in October 2021. Nasopharyngeal and oropharyngeal swabs were taken from patients with SARS-CoV-2, and the samples were tested using RT-PCR. Positive samples were sent to the Regional Virus Research and Diagnostic Laboratory-National Institute of Cholera and Enteric Diseases (NICED) for sequencing. Samples were collected from patients in different districts of West Bengal who were reported to the VRDL of RG Kar Medical College and Hospital. A total of 172,550 samples were tested for SARSCoV-2, and out of 13,764 positive samples, 230 were sent for genome sequencing. The primary inclusion criteria were SARSCoV-2 positive patients with CT values between 25 and 30 who were vaccinated. Patient information, address, gene variant, and gene mutation of the samples were analysed. Statistical analysis was performed using t-test with Statistical Package for Social Sciences (SPSS) software. Results: Whole-genome sequencing helped identify new trends and their prevalence in specific areas, aiding in prevention efforts. The most common type of mutation observed after double vaccination was the delta variant (B.1.617.2), followed by the kappa variant (B.1.617.1) and the alpha variant (B.1.1.7). Conclusion: Epidemiological genome sequencing studies help to identify emerging and changing viral trends, contributing to the mitigation of the spread of new variants. The delta, kappa, and alpha variants were the three primary sequences discovered in this study. The identification of these lineages facilitates the design of novel vaccines and diagnostic medications. Continuous monitoring and analysis of sequences from new cases in India and other affected countries are crucial for understanding the genetic evolution and substitution rates of SARS-CoV-2.

Method Validation Study for SARS-CoV-2 Viral RNA Detection in Cervical, Rectal, Amniotic Fluid, Placental, Umbilical Cord Blood, and Breastmilk Specimens in a Cohort of Unvaccinated Women in Manila, Philippines.

To validate a method in detecting SARS-CoV-2 via RT-qPCR in pregnant and non-pregnant samples other than nasopharyngeal swabs and/or oropharyngeal swabs such as cervical, rectal, amniotic fluid, placental, umbilical cord blood, and breastmilk. We performed a validation experiment using MGI easy extraction kits and BGI PCR kits on non-conventional specimens, including cervical, rectal, amniotic fluid, placental, umbilical cord blood, and breastmilk to detect and confirm the presence of SARS-CoV-2. In addition, we tested the validated method on 572 purposively sampled field-collected non-conventional specimens from a cohort of 109 unvaccinated pregnant and 47 unvaccinated non-pregnant women to assess which candidate non-conventional maternal- and fetal-associated specimens may contribute to maternal-fetal viral vertical transmission. Positive detection of SARS-CoV-2 viral RNA in non-conventional specimens was demonstrated and verified. Of the 572 non-conventional samples tested, 1.8% (10/572) were positively validated by RT-qPCR for SARS-CoV-2 in the maternal-associated specimens particularly the rectal (5), placental (1), and cervical (4) swabs among six pregnant and four non-pregnant individuals. In contrast, no SARS-CoV-2 viral RNA was detected in fetal-associated specimens. The results of the validation study may serve as an additional diagnostic screening layer to support maternal-child care. Furthermore, viral detection in these non-conventional maternal specimens may also be utilized to provide guidance in the clinical management of neonates, and pregnant women during delivery.

Evento tromboembólico em neonato de mãe com COVID-19

INTRODUCTION: Premature birth is one of the main perinatal complications of maternal SARS-CoV-2 infection. CASE REPORT: Premature newborn, the daughter of a mother with a severe condition of COVID-19, who presented a thromboembolic event on the first day of life and evolved with hypoxic-ischemic encephalopathy. DISCUSSION: Investigation was carried out on the cause of the framework, management with enoxaparin and curative with collagenase, even though it was not possible to avoid the loss of the auricular region. Immunohistochemical evidence of Spike-19 protein was found in the fetal placental part. RT-PCR tests for SARS-CoV-2 without oropharyngeal swab were negative. A maternal coronavirus infection should be included in any differential diagnosis as a cause of a thromboembolic event in the neonatal period.

Frequency of feline herpesvirus 1 (FHV-1) in domestic cats from Campo Grande, MS, Brazil.

Feline herpesvirus type 1 (HVF-1) is the infectious agent of feline viral rhinotracheitis. The main clinical signs are cough, nasal and eye discharge, fever, conjunctivitis and sneezing. Although the occurrence of the virus is known in some regions of Brazil, in Campo Grande, Mato Grosso do Sul (MS), there is no epidemiological information about its frequency. Thus, this study aimed to determine the frequency of feline herpesvirus type 1 in the region, and to evaluate its possible association with clinical and epidemiological factors. Ocular, nasal and oropharyngeal swabs, and blood were collected from 152 animals and analyzed through PCR and sequencing. In addition, epidemiological and clinical data were obtained through clinical examination and anamnesis. FHV-1 was detected in samples from 84 (55.26%) animals. There was no association between infection and age or sex. However, there was a significant association between infection and nasal (p < 0.0001) and ocular (p = 0.014) discharge and sneezing (p = 0.001). The results demonstrate the occurrence of the virus in domestic cats in the region with a high frequency of infection. Thus, FHV-1 should be considered as a potential causal agent of upper respiratory tract disease in domestic cats from Campo Grande, MS, Brazil.

Gastrointestinal Manifestations and Liver Abnormalities in COVID-19: A Real-World Experience and a Novel COVID-19 Prognostic Index

Introduction: Gastrointestinal (GI) manifestations and liver function abnormalities have been reported in Coronavirus Disease-2019 (COVID-19). However, data is variable and lacking from the Indian Population. Moreover, the prognostic implication of these manifestations has not been well-defined. Aim: To determine the impact of COVID-19, on the gastrointestinal tract and Liver Function Test (LFT) and develop a prognostic model for mortality. Materials and Methods: An observational descriptive study was conducted in the Department of Internal Medicine at a temporary dedicated COVID-19 centre in a Tertiary Care Cardiothoracic Centre, Western Maharashtra, India. The hospital records of all the patients admitted from July 2020 to September 2020 were analysed. Clinical details and laboratory details were obtained from 589 Reverse Transcription– Polymerase Chain Reaction (RT-PCR) confirmed patients. The data was analysed and a prognostic scoring system was developed. Patients with positive Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RT-PCR on nasopharyngeal or oropharyngeal swabs. The data was entered in Microsoft Excel 2010 worksheet and t-test or Mann-Whitney test was also applied to compare the mean of variables being studied by separation of living and deceased patients based on the normality of the quantitative data. Results: The mean age±SD of the study participants was 44.74±19.61 years. The majority {127/589 (21.56 %)} of the patients were in the age group of 51-60 years. A total of 5 (0.84%) out of 589 patients had diarrhoea, and 3 (0.51%) had vomiting at the time of admission. Elevated Aspartate Aminotransferase (AST), Alanine Transaminase (AST), Alkaline Phosphatase (ALP), Gamma-glutamyl Transferase (GGT), Lactate Dehydrogenase (LDH), Creatine Kinase Myocardial Band (CK-MB) was reported in non survivors in 45 (90%), 39 (78%), 15 (30%), 28 (56%), 48 (96%) and 49 (98%) out of 50 cases, respectively. The prognostic scoring system was developed with the following variables: age, Diabetes Mellitus (DM), symptomatic, breathlessness, albumin, AST, ALP, LDH, Prothrombin Time (PT), D-Dimer. The area under the curve, came out to be 0.91 and a cut-off value of three in the scoring system was able to predict death at a sensitivity of 85.5% and specificity of 79.6%. Conclusion: Gastrointestinal manifestations and abnormalities in LFTs are important extrapulmonary manifestations of COVID19. Patients with abnormal liver tests had higher risks of progressing to severe disease. Hence, LFT should be monitored and evaluated frequently during hospitalisation for COVID-19.

Phylogenetic Changes in SARS-CoV-2 Virus in Bosnian-Herzegovinian Population Over the Period of Two Years.

All viral genomes, including the SARS-CoV-2 virus, mutate over time, and some of these mutations can affect the characteristics of the virus, such as the ease of spread, the severity of the patient's clinical picture, or the effect of vaccines, therapeutic drugs, diagnostic tools or other measures of public health and social protection. Because of all the above, it is imperative to carry out continuous sequencing of this pathogen. The main goal of this research was to obtain the highest quality genomic sequences of the SARS-CoV-2 virus, to compare the obtained sequences with the reference Wuhan-Hu-1 sequence and to obtain a high-quality genomic alignment in order to reconstruct the appropriate phylogenetic tree. For the purposes of this research, a next-generation semiconductor sequencing method was chosen. In this research, a total of 47 samples of nasopharyngeal and oropharyngeal swabs from patients from the human population of Bosnia and Herzegovina with a clinical diagnosis of COVID-19 were collected. In the processed 47 samples, there are several monophyletic groups on the constructed phylogenetic tree, of which one sample belongs to the same monophyletic group as the Wuhan-Hu-1 reference sequence. The greater number of samples is needed for a more comprehensive approach. Therefore, the results of this research can act as a guideline for the design of effective measures and strategies in order to solve problems regarding future pandemics as efficiently as possible.

The outcome of pulmonary function tests and high-resolution computed tomography of chest in post-coronavirus disease 2019-confirmed cases after 3 months of recovery

Background Coronavirus disease (COVID-19) is a recently prevalent infectious disease that is caused by a virus from the coronavirus family and causes acute respiratory syndrome. It is a pandemic catastrophe that has affected more than 60 million people around the world and has caused about 1.5 million deaths, as reported by the WHO. This disease affects the respiratory system and leads to different forms of symptoms and signs. Pneumonia is a common cause for hospitalization, with most patients treated in hospital wards and others requiring ICU. Although the number of complete recoveries from COVID-19 has increased, there is still concern about complications associated with the disease that appear after recovery. The studies that have looked at past types and other forms of coronavirus epidemics, such as SARS have shown that some cases had respiratory complications from the infection after being full recovered, as 36 and 30% of the entire study population had clinical and high-resolution computed tomography (HRCT) changes at 3 and 6 months after recovery, respectively. Mostly, the abnormalities seen in pulmonary function test (PFT) results are sequelae of diffusion capacity defect. In recovered cases of Middle East respiratory syndrome, 36% of patients showed HRCT sequelae at follow-up of 6 weeks, because of fibrosis. Data on COVID-19 indicate that prolonged disease and persistent symptoms show post-PFT affection and follow-up radiographic changes after recovery from COVID-19 as interstitial pulmonary changes and a degree of pulmonary vasculopathy. In recovered cases of COVID-19, capacity of diffusion is the commonest defect in lung function, followed by the restrictive pattern defects on spirometry; both are related to the degree of severity of pneumonic COVID-19. PFTs (involving spirometry as well as diffusion capacity) are considered as routine follow-up examinations for some of the recovered cases, especially severe cases. Rehabilitation programs of the respiratory system are an option strategy that might be considered. This study aims to show changes in pulmonary function and HRCT of chest in post-COVID-19-infected patients to detect long-term effects on the lungs after 3 months as obstructive or restrictive, or both, lung diseases. Patients and methods The study was conducted on 100 confirmed PCR-positive COVID-19 cases that were admitted to Ain Shams University Isolation Hospitals, and the follow-up was performed in the outpatient clinic. PCR samples (Combined nasopharyngeal and oropharyngeal swab) were taken after 3 months from discharge of patients above the age of 18 years who become negative with clinical improvement. PFT [spirometry and diffusion for carbon monoxide (DLCO)] and chest HRCT were done. All patients’ clinical data were recorded, and CT chest imaging data of these patients were correlated with the clinical data. Results A total of 100 patients were included in this study, where males represented 58% and female represented 42%. The mean±SD age of cases in this study was 45.05 ± 11.80 years and ranged from 20 to 79 years. CT chest severity score (SS) of abnormality in COVID-19-infectedd patients based on HRCT chest findings before and after 3 months from treatment showed a highly significant correlation (P=0.000). The results of PFT in the studied group after 3 months of discharge showed restrictive pattern in 14.9%, obstructive pattern in 17.8%, and both obstructive and restrictive patterns in 5.9% of the total number of cases. There was a significant correlation between DLCO abnormality findings and age of studied group (P=0.032), a significant correlation between abnormality findings on PFT and HRCT chest SS after discharge of the studied group (P&lt;0.001). There was a significant correlation between abnormality findings of DLCO and HRCT chest SS after 3 months of the studied group (P=0.000) and before treatment (P=0.001), whereas there was no significant correlation between other findings of PFT and HRCT chest SS after 3 months and before. There was a significant correlation between HRCT chest SS of the studied group and their age after (P=0.003) and before treatment (P=0.000). This cohort study provided the long-term dynamic sequelae and variations of lung function after hospital discharge. Conclusion DLCO-predicted value detected at 3 months is the most important factor associated with severe respiratory COVID-19, which is identified as the cause of impairment of any ordinary basic activity of patients in the stage of postrecovery from COVID-19. The radiological chest findings must be analyzed in conjunction with other functional parameters to provide accurate assessment of the disease. These findings highlight the significance of a comprehensive follow-up after severe and critical COVID-19 infection, with appropriate management of pulmonary consequences. Patients after discharge and on follow-up in outpatient clinics in the post-COVID-19 stage should be strictly followed up with PFTs. Further studies with longer follow-up periods might be needed.

SPECIFIC FEATURES OF THE ORAL MICROBIOME IN YOUNG CHILDREN WITH ARYNGOPHARYNGEAL REFLUX AND ITS ROLE THE DEVELOPMENT OF RECURRENT RESPIRATORY DISEASES.

The aim: To examine the composition of the oral microbiome in young children with laryngopharyngeal reflux (LPR) and its role the development of recurrent respiratory diseases. Materials and methods: There were examined 38 children with physiological gastroesophageal reflux (GER), 18 children with LPR who had a medical history of recurrent bronchitis and 17 healthy children (control group). The study included the collection of anamnesis, objective examination. The qualitative and quantitative microbial composition of the upper respiratory tract was performed obtained by oropharyngeal deep swab. Salivary pepsin level and IL-8 were determined by enzyme-linked immunosorbent assay. Results: This research showed significant alterations in the oral microbiome of patients with GER and LPR as compared to healthy control. We found that gram-negative microbiota such as Klebsiella pneumoniae, Escherichia coli, Proteus vulgaris, Proteus spp. and Candida albicans were identified in children with GER and LPR compared to the healthy control. At the same time, the amount of such a representative of the normal microbiome as Streptococcus viridans in children with LPR was sharply reduced. There were established a much higher mean salivary pepsin level of the patients with LPR than in the GER and control group. We found the association between high pepsin levels, saliva IL-8 levels and frequency of respiratory pathology in children with LPR. Conclusions: Our study confirms that increased levels of pepsin in saliva are a risk factor for recurrent respiratory diseases in children with LPR.

Prevalence of Neisseria gonorrhoeae and Chlamydia trachomatis infections among adolescent men who have sex with men and transgender women in Salvador, Northeast Brazil.

Adolescent men who have sex with men (AMSM) and transgender women (ATGW) enrolled as part of the PrEP1519 study between April 2019 and February 2021 in Salvador were tested for Neisseria gonorrhoeae (NG) and Chlamydia trachomatis (CT) infections.We performed real-time polymerase chain reaction using oropharyngeal, anal, and urethral swabs; assessed factors associated with NG and CT infections using multivariable Poisson regression analysis with robust variance; and estimated the prevalence ratios (PRs) and 95% confidence intervals (95% CIs). In total, 246 participants were included in the analyses (median age: 18.8; IQR: 18.2-19.4 years). The overall oropharyngeal, anal, and urethral prevalence rates of NG were 17.9%, 9.4%, 7.6%, and 1.9%, respectively. For CT, the overall, oropharyngeal, anal, and urethral prevalence rates were 5.9%, 1.2%, 2.4%, and 1.9%, respectively. A low level of education, clinical suspicion of STI (and coinfection with Mycoplasma hominis were associated with NG infection. The prevalence of NG and CT, especially extragenital infections, was high in AMSM and ATGW. These findings highlight the need for testing samples from multiple anatomical sites among adolescents at a higher risk of STI acquisition, implementation of school-based strategies, provision of sexual health education, and reduction in barriers to care.

Colonization Rate and Associated Factors of Non-Pathogenic Neisseria Species, and Moraxella catarrhalis Among Healthy School Children in Gondar, Northwest Ethiopia.

Although commensal Neisseria species inhabiting mucosal surfaces in the upper respiratory tract (URT) are rarely associated with infections, their presence in the area has been linked to the development of immunity against N. meningitidis and the source of antibiotic resistance determinants in pathogenic species. M. catarrhalis in the oropharynx of children is also a predisposing factor for otitis media. As a result, determining the oropharyngeal carriage rate of these commensal species and associated factors among healthy schoolchildren is substantial. This community-based cross-sectional study was conducted in Gondar, Northwest Ethiopia, from January to April 2019. A multi-stage and simple random sampling technique were used to select schools and participants, respectively. A total of 524 oropharyngeal swabs were collected using cotton swabs. Modified Thayer-Martin media was used for primary bacterial isolation, and battery of biochemical tests was performed to identify species. For frequencies, descriptive statistics were computed and the logistic regression model was used to see the relationship between dependent and independent variables. A total of 524 healthy schoolchildren with a mean age of 12.2 ± 2.74 years participated in this study. The overall oropharyngeal carriage rate was 21.8% (114/524). Of these, N. meningitidis, N. lactamica, N. sicca, and M. catarrhalis were identified in 53 (46.5%), 14 (12.3%), 11 (9.6%), and 36 (31.6%) children, respectively. The culture positivity rate was higher at a younger age, which was 8.1%, 11.3%, and 14.9% in ages between 15-18, 11-14, and 7-10, respectively. The oropharyngeal carriage was significantly associated with the number of students per class (>40). There is a higher proportion of carriers of commensal N. lactamica and M. catarrhalis in Gondar town schoolchildren. The oropharyngeal carriage rate was associated with a crowded classroom. The characterization of non-pathogenic Neisseria species and M. catarrhalis in the study area can support the diagnosis of patients suspected of having N. meningitis infections.

Dynamic Changes of ORF1ab and N Gene Ct Values in COVID-19 Omicron Inpatients of Different Age Groups - Beijing Municipality, China, November-December 2022.

In November 2021, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant was identified as the variant of concern and has since spread globally, replacing other cocirculating variants. To better understand the dynamic changes in viral load over time and the natural history of the virus infection, we analyzed the expression of the open reading frames 1ab (ORF1ab) and nucleocapsid (N) genes in patients infected with Omicron. We included patients initially admitted to the hospital for SARS-CoV-2 infection between November 5 and December 25, 2022. We collected daily oropharyngeal swabs for quantitative reverse transcriptase-polymerase chain reaction tests using commercial kits. We depicted the cycle threshold (Ct) values for amplification of ORF1ab and N genes from individual patients in age-specific groups in a time series. A total of 480 inpatients were included in the study, with a median age of 59 years (interquartile range, 42 to 78; range, 16 to 106). In the <45-year-old age group, the Ct values for ORF1ab and N gene amplification remained below 35 for 9.0 and 11.5 days, respectively. In the ≥80-year-old age group, the Ct values for ORF1ab and N genes stayed below 35 for 11.5 and 15.0 days, respectively, which was the longest among all age groups. The Ct values for N gene amplification took longer to rise above 35 than those for ORF1ab gene amplification. The time to test negative varied among different age groups, with viral nucleic acid shedding taking longer in older age groups compared to younger age groups. As a result, the time to resolution of Omicron infection increased with increasing age.

An inexpensive and rapid diagnostic method for detection of SARS-CoV-2 RNA by loop-mediated isothermal amplification (LAMP)

SARS-CoV-2 is a public pandemic health concern globally. Nasopharyngeal and oropharyngeal swab samples are used for Covid-19 viral detection. Sample collection procedure was tedious and uncomfortable and unsuitable for biochemical and CBC analysis in swab samples. Biochemistry and CBC tests are key determinant in management of Covid-19 patients. We developed a LAMP test to detect viral RNA in blood samples. LAMP is required four specific primers targeting the internal transcribed S-region and loop primers for viral RNA amplification. RNA was extracted from blood samples by TRIzol method. LAMP reaction was performed at 60 °C for 1 hour and amplicons were visualized in HNB dye. No cross-reactivity was seen with HBV, HCV, and HIV infected sample. Out of 40 blood samples, 33 samples were positive for LAMP and Q-PCR analysis, one sample was positive for LAMP and negative for Q-PCR, two samples were negative for LAMP but positive for Q-PCR, and four blood samples were negative for LAMP and Q-PCR. LAMP method has an accuracy of 92.50%, with sensitivity and specificity of 94.28% and 80%, respectively. Thus, LAMP diagnostic test has proved reliable, fast, inexpensive and can be useful for detection where the limited resources available.•LAMP method is a potential tool for detection of SARS-CoV-2.•Blood samples are the key determinant for routine diagnostics as well as molecular diagnostics.•LAMP assay is an appropriate diagnostics method which offers greater simplicity, low cost, sensitivity, and specificity than other methods in molecular diagnostics.