Monkeypox-related ophthalmic disease (MPXROD): Monitoring the antiviral effect of tecovirimat with monkeypox virus detection in tear samples.

INTRODUCTION: Although monkeypox-related ophthalmic disease (MPXROD) is rare, visual impairing complications have been reported. At present, tecovirimat is the standard-of-care antiviral treatment. In this MPXROD case, the effect of tecovirimat was assessed with PCR analysis of tear samples and concurrent monitoring of inflammation with laser flare photometry (LFP). CASE DESCRIPTION: The patient presented with a palpebral lesion and a corneal ulcer in his right eye, with complete absence of the corneal epithelium, high intraocular pressure and anterior uveitis. MPXV-DNA was detected in tear samples with real-time PCR (RT-PCR). A total volume of 0.5 ml tear-wash was aspirated from the inferior fornix, following instillation of saline onto the ocular surface. In addition, LFP was used to quantify inflammation in both eyes. Viral load in tear samples was detected prior to treatment initiation. In the left eye, tear samples tested negative for MPXV-DNA one week post-treatment while MPXV-DNA was still detected in the right eye, before reaching undetectable levels four weeks post-treatment. Objective quantification of anterior chamber inflammation through LFP demonstrated gradual decrease that was more pronounced in the affected right eye and coincided with the clinical improvement of the corneal ulcer. CONCLUSIONS: This case of Mpox related corneal ulcer with associated uveitis manifests the feasibility of monitoring the antiviral effect of tecovirimat with virus detection in tear samples and LFP. Our observations indicate that tecovirimat resulted in viral load reduction in both eyes. RT-PCR MPXV detection in tear samples and LFP represent noninvasive tools that could assist with treatment response monitoring.

Characterization of the dominant strain (G-VII) of Newcastle disease viruses isolated from commercial chickens in Bangladesh during recent outbreaks.

Objective: Newcastle disease virus genotype VII (NDV-GVII), an extremely infectious pathogen, has been causing severe economic consequences for the chicken industry. The current study aimed to isolate and characterize NDV-GVII from commercial chickens in Bangladesh during a recent outbreak. Materials and Methods: From clinically suspected chickens from 70 commercial poultry farms, a total of 420 samples (trachea, lungs, and brain tissue) were collected. The samples were cultivated in 9-10 day-old seronegative embryonated chicken eggs (ECEs) after evaluating them using the rapid Newcastle disease virus (NDV) antigen detection kit. The hemagglutination (HA) inhibition test, agar gel immune diffusion (AGID) test, molecular detection by reverse transcription-polymerase chain reaction (RT-PCR), and phylogenetic studies using gene sequences of fusion (F) protein. The HA pattern of isolated NDV was determined using different avian and mammalian red blood cells (RBCs). The pathogenicity of the isolated virus was evaluated using mean death time (MDT), intravenous pathogenicity index (IVPI), and intracerebral pathogenicity index (ICPI). Results: The study found 87 NDV samples positive using the rapid NDV Ag detection kit and then 60 positives for virus isolation in ECEs. All 60 isolates were positive for NDV by HI, AGID, and RT-PCR. Phylogenetic tree analysis indicated that recent NDV isolates belong to genotype VII and exhibit a similarity of 99.7%-98.5% with isolates from Bangladesh, Iran, and India. The new isolates, identified as velogenic strains of NDV, possess an F protein cleavage site with 112-R-T-K-R-F-117 amino acid motifs. The isolated NDV showed diversified HA activity while using RBCs from birds and mammals. The results of ICPI, IVPI, and MDT indicated that the recent NDV isolates were very virulent. Conclusion: This study concluded that NDV-GVII is prevalent in commercial poultry farms in Bangladesh.

Spatiotemporal evolution of the distribution of Chronic bee paralysis virus (CBPV) in honey bee colonies.

Chronic bee paralysis virus (CBPV) is a Apis mellifera viral infectious disease, exhibiting dark and hairless abdomen in workers with tremors and ataxita. Clinical signs are also typically linked to adverse weather conditions and overcrowding in the hive. The disease occurs in spring but recently it has been observed cases increase and seasonality loss of the disease incidence. This study analyses the evolution of CBPV in Italy, through data collected from 2009 to 2023 within three monitoring projects comprising nationwide extended detection networks, aimed to investigate the evolution of the CBPV spatial distribution, identifying high-risk areas for the virus spread. This study highlights an increased risk over years. Prevalence increased from 4.3% during 2009-2010 to 84.7% during 2021-2023 monitoring years. CBPV outbreaks were irregular between investigated seasons, highlighting Spring and Autumn as the most susceptible seasons. Risk of CBPV infection has increased, reaching high-risk in last years of monitoring. Sequence analysis showed a high similarity to other isolated Italian CBPVs. The study offers an epidemiological insight into the aetiology of this disease. CBPV distribution is a prerequisite to predict its future spread and factors involved in its propagation not only in honey bees but also in other pollinators and environments.

Assessment of performance and comparison of three commercial HDV RNA detection assays: implications for diagnosis and treatment monitoring.

Objectives: Precise HDV-RNA detection and quantification are pivotal for diagnosis and monitoring of response to newly approved treatment. We evaluate the performance of three HDV RNA detection and quantification assays. Methods: Hepatitis Delta RT-PCR system kit, EurobioPlex HDV assay, and RoboGene HDV RNA Quantification kit 2.0 were used for testing 151 HBsAg-positive samples, 90 HDV-RNA negative and 61 HDV-RNA positive. We also evaluated serial dilutions of the WHO international standard for HDV, PEI 7657/12. All HDV-RNA positive samples were genotyped using a next-generation sequencing strategy. Results: Qualitative results indicated a 100% concordance between tests. Quantitative results correlated well, r2 = 0.703 (Vircell-vs-Eurobio), r2 = 0.833 (Vircell-vs-RoboGene), r2 = 0.835 (Robogene-vs-Eurobio). Bias index was 2.083 (Vircell-vs-Eurobio), -1.283 (Vircell-vs-RoboGene), and -3.36 (Robogene-vs-Eurobio). Using the WHO IS, Vircell overestimated the viral load by 0.98 log IU/mL, Eurobio by 1.46 log IU/mL, and RoboGene underestimated it by 0.98 log IU/mL. Fifty-nine samples were successfully genotyped (Genotype 1, n=52; Genotype 5, n=7; Genotype 6, n=1), with similar results for correlation and bias. Conclusion: This study underscores the necessity of using reliable HDV-RNA detection and quantification assays, as evidenced by the high concordance rates in qualitative detection and the observed variability in quantitative results. These findings highlight the importance of consistent assay use in clinical practice to ensure accurate diagnosis and effective treatment monitoring of HDV infection.

Development of reverse transcriptase-recombinase polymerase amplification (RT-RPA) assay for rapid detection of large cardamom chirke virus.

Large cardamom chirke virus (LCCV) causing chirke disease of large cardamom is a major production constraint of this crop. Rapid and accurate detection of LCCV is important for managing the disease. In the present study an isothermal assay namely, reverse transcriptase-recombinase polymerase amplification (RT-RPA) was developed for the detection of LCCV. Total RNA isolated by two different methods and crude extracts isolated using five different methods as templates were assessed for their ability to detect LCCV. Of these, only the total RNA isolated by both methods gave consistent and repeatable results while all the crude extracts used as templates gave non-specific amplification. RT-RPA was up to 1000 times more sensitive than conventional RT-PCR for the detection of LCCV. The detection limit of RPA was 10 fg when recombinant plasmid was used as the template. The RT-RPA assay was validated using field samples and found suitable for large-scale screening of large cardamom plants against LCCV for the selection of virus-free plants. Supplementary Information: The online version contains supplementary material available at 10.1007/s13337-024-00861-2.

Genotype classification and pathogenicity of infectious bursal disease virus circulating in vaccinated broiler chicken farms.

This study investigated the genotype classification and pathogenicity of infectious bursal disease virus (IBDV) circulating in vaccinated broiler chicken farms in Egypt. A total of 150 samples were collected from 30 vaccinated commercial broiler chicken farms and pooled into 30 working samples. IBDV was tested using reverse transcriptase polymerase chain reaction (RT-PCR) amplification of the hypervariable region of the viral protein 2 (hvVP2) and the VP1 gene 5' extremity. Both RT-PCR fragments were sequenced from six samples, and then the obtained nucleotide sequences were analyzed. The IBDV genotypes were identified using nucleotide sequences. Five sequences of the six strains examined were classified as genotype A3B2 for the highly virulent segments A and B (vv-A/vv-B IBDV). Interestingly, this study identified and classified a novel segment-reassortant strain as the A1B2 genotype. Specifically, it involved the segment reassortment of classical virulent segment A (cv-A) with vv-B producing cv-A/vv-B reassortant IBDV. Subsequently, we compared the pathogenicity of reassortant (cv-A/vv-B) IBDV and vvIBDV strains identified in this study. Both strains developed typical IBD clinical signs, postmortem lesions, histopathology, immunohistochemistry, and lesion scores, which were more severe in vvIBDV than reassortant IBDV. In conclusion, this is the first report of the genotype classification based on both genome segments (hvVP2 and VP1) with pathogenicity of IBDV circulating in vaccinated broiler chicken farms and this pathogenicity is more severe in vvIBDV strain than a novel reassortant IBDV strain.

Development of a CRISPR/SHERLOCK-Based Method for Rapid and Sensitive Detection of Selected Pospiviroids.

Pospiviroids infect a wide range of plant species, and many pospiviroids can be transmitted to potato and tomato. Pospiviroids continue to be a major production constraint as well as of quarantine concern for the movement of germplasm, and are regulated in several countries/regions. The USDA APHIS issued a federal order requiring all imported tomato and pepper seeds be certified free of six pospiviroids of quarantine significance. The six pospiviroids of quarantine interest include CLVd, PCFVd, PSTVd, TASVd, TCDVd, TPMVd. Currently, those six viroids are detected by real-time RT-PCR. CRISPR/Cas-based genome editing has been increasingly used for virus detection in the past five years. We used a rapid Cas13-based Specific High-sensitivity Enzymatic Reporter unLOCKing (SHERLOCK) platform for pospiviroid detection, determined the limits of detection and specificity of CRISPR-Cas13a assays. This platform combines recombinase polymerase amplification (RPA) with CRISPR and CRISPR-associated (CRISPR-Cas) RNA-guided endoribonuclease that is rapid and does not require expensive equipment, and can be adapted for on-site detection.

Biofilm Formation, Motility, and Virulence of Listeria monocytogenes Are Reduced by Deletion of the Gene lmo0159, a Novel Listerial LPXTG Surface Protein.

Listeria monocytogenes (L. monocytogenes) is a foodborne pathogen that causes listeriosis in humans and other animals. Surface proteins with the LPXTG motif have important roles in the virulence of L. monocytogenes. Lmo0159 is one such protein, but little is known about its role in L. monocytogenes virulence, motility, and biofilm formation. Here, we constructed and characterized a deletion mutant of lmo0159 (∆lmo0159). We analyzed not only the capacity of biofilm formation, motility, attachment, and intracellular growth in different cell types but also LD50; bacterial load in mice's liver, spleen, and brain; expression of virulence genes; and survival time of mice after challenge. The results showed that the cross-linking density of the biofilm of ∆lmo0159 strain was lower than that of WT by microscopic examination. The expression of biofilm-formation and virulence genes also decreased in the biofilm state. Subsequently, the growth and motility of ∆lmo0159 in the culture medium were enhanced. Conversely, the growth and motility of L. monocytogenes were attenuated by ∆lmo0159 at both the cellular and mouse levels. At the cellular level, ∆lmo0159 reduced plaque size; accelerated scratch healing; and attenuated the efficiency of adhesion, invasion, and intracellular proliferation in swine intestinal epithelial cells (SIEC), RAW264.7, mouse-brain microvascular endothelial cells (mBMEC), and human-brain microvascular endothelial cells (hCMEC/D3). The expression of virulence genes was also inhibited. At the mouse level, the LD50 of the ∆lmo0159 strain was 100.97 times higher than that of the WT strain. The bacterial load of the ∆lmo0159 strain in the liver and spleen was lower than that of the WT strain. In a mouse model of intraperitoneal infection, the deletion of the lmo0159 gene significantly prolonged the survival time of the mice, suggesting that the lmo0159 deletion mutant also exhibited reduced virulence. Thus, our study identified lmo0159 as a novel virulence factor among L. monocytogenes LPXTG proteins.

A high-throughput, polymerase-targeted RT-PCR for broad detection of mammalian filoviruses.

Filoviruses are some of the most lethal viruses in the modern world, and increasing numbers of filovirus species and genera have been discovered in recent years. Despite the potential severity of filovirus outbreaks in the human population, comparably few sensitive pan-filovirus RT-PCR assays have been described that might facilitate early detection and prevention. Here, we present a new pan-filovirus RT-PCR assay targeting the L polymerase gene for detection of all known mammalian filoviruses. We demonstrate the detection of 10 synthetic filovirus RNA templates with analytical sensitivity ranging from 178 to 3,354 copies/mL, without cross-reactivity on 10 non-filoviral human viral species. We verified assay performance on 10 inactivated filovirus isolates, yielding initial sensitivities of 0.012-44.17 TCID50/mL. We coupled this broadly reactive RT-PCR with a deep sequencing workflow that is amenable to high-throughput pooling to maximize detection and discovery potential. In summary, this pan-filovirus RT-PCR assay targets the most conserved filovirus gene, offers the widest breadth of coverage to date, and may help in the detection and discovery of novel filoviruses.IMPORTANCEFiloviruses remain some of the most mysterious viruses known to the world, with extremely high lethality rates and significant pandemic potential. Yet comparably few filovirus species and genera have been discovered to date and questions surround the definitive host species for zoonotic infections. Here, we describe a novel broadly reactive RT-PCR assay targeting the conserved L polymerase gene for high-throughput screening for filoviruses in a variety of clinical and environmental specimens. We demonstrate the assay can detect all known mammalian filoviruses and determine the sensitivity and specificity of the assay on synthetic RNA sequences, inactivated filovirus isolates, and non-filoviral species.

An outbreak of Akabane disease in a cattle herd on the Mughan plain, Iran.

In November 2021, an investigation was conducted into an outbreak of abortion, stillbirth, and the birth of calves with congenital abnormalities (arthrogryposis and hydranencephaly) at a dairy farm in Dasht-e-Mughan city, Ardabil province. A total of 70 cows experienced these issues. To determine the cause of the outbreak, post-mortem brain tissue samples were collected from two calves affected by hydranencephaly, which occurred shortly after their birth. Polymerase chain reaction (PCR) testing was conducted for multiple viruses, including bovine viral diarrhea (BVD), border disease, Akabane, Schmallenberg, and bluetongue viruses (BTVs). The samples were positive only for Akabane virus. Serum samples were collected from a group of 60 cattle, consisting of 45 adult cows and 15 younger calves aged between 8 to 10 months. These samples were analyzed to detect the presence of antibodies against the Akabane and Schmallenberg viruses. Both of these viruses are known to be responsible for causing abortion, stillbirth, and congenital abnormalities in calves. Among 45 cows that tested by competitive enzyme-linked immunosorbent assay (cELISA), 26.66% and 33.33% exhibited antibodies against Akabane and Schmallenberg viruses, respectively. Notably, 20.00% of cows co-exhibited antibodies for both viruses. Despite PCR evidence implicating Akabane virus as the principal etiology of clinical signs observed in the affected herd, the high co-seropositivity to Schmallenberg virus, warrants a thorough investigation into potential viral interactions. Further research is required to determine the source of the virus and their transmission routes. This information could facilitate the refinement of disease control strategies and improving the management of reproductive challenges in such affected herds.

Clinical and microbial evaluation of mouthwash containing Achyranthes aspera and Trachyspermum ammi: A randomized controlled non-inferiority trial.

Objectives: Achyranthes aspera (Apamarga) and Trachyspermum ammi (Ajwain) have been used in many clinical conditions, and it displays valuable properties as an alternative to Chlorhexidine (CHX) in the management of gingivitis. Therefore, this study aims to assess the effect of Achyranthes aspera and Trachyspermum ammi (AA + TA) based herbal mouthwash, 0.2 % CHX, and placebo mouthwash on gingival health, plaque control and antibacterial activity against specific periodontal pathogens (Porphyromonas gingivalis and Tannerella forsythia) using quantitative real-time PCR (RT-PCR). Methods: This was a randomized controlled non-inferiority trial involving 108 children with plaque-induced gingivitis who were randomly assigned to three groups of 36 children each: Group A, AA + TA mouthwash; Group B, CHX mouthwash; and Group C, placebo mouthwash. Gingival index and plaque index were recorded at baseline, 7th and 21st day. RT-PCR was employed to determine the bacterial counts of each plaque sample at baseline and after 21 days. Results: All three groups exhibited a gradual and significant reduction in both gingival and plaque scores from baseline to days 7 and 21. However, the placebo group did not demonstrate a significant difference in scores between days 7 and 21. Furthermore, a significant reduction in bacterial counts of P. gingivalis and T. forsythia was observed in the groups receiving CHX and AA + TA mouthwash after 21 days of intervention compared to the placebo group. Conclusion: AA + TA mouthwash demonstrated non-inferiority in anti-gingivitis and anti-plaque properties compared to CHX, suggesting its potential suitability as an alternative to CHX when used in conjunction with mechanical plaque control measures.

To evaluate the performance of simultaneous amplification and testing assay for group B Streptococcus detection: comparison with real-time PCR and ddPCR assays.

BACKGROUND: To evaluate the performance of simultaneous amplification and testing (SAT) assay for the detection of group B Streptococcus (GBS) in maternal vaginal and perianal swabs compared with real-time polymerase chain reaction (RT-PCR). METHODS: We obtained vaginal and perianal swabs from 1474 pregnant women at the Obstetrics and Gynecology Hospital of Fudan University (Shanghai, China) between April 2023 and June 2023. Vaginal and perianal swabs were collected at 35-37 weeks of gestation. Swabs were tested for GBS simultaneously by using the SAT assay and RT-PCR, and a comparative analysis (kappa coefficient) was performed. Furthermore, we conducted additional droplet digital PCR (ddPCR) tests to confirm the results when there were controversial results between SAT and RT-PCR. In addition, we compared the limit of detection, technical specificity, repeatability and reproducibility of SAT-GBS with those of routine RT-PCR assays. RESULTS: In our study, the detection rate of clinical GBS according to the SAT assay was 11.5% (169/1471). The SAT assay showed a sensitivity of 91.8%, a specificity of 99.9%, a diagnostic accuracy of 98.9%, a positive predictive value (PPV) of 99.4% and a negative predictive value (NPV) of 98.8%. The kappa value between RT-PCR and SAT was 0.917. CONCLUSIONS: This SAT assay for the detection of group B Streptococcus is not only easy to perform but can also detect GBS sensitively and specifically and may be used in the regular molecular diagnosis of GBS infection among pregnancies.

Efficacy and safety of oral ivermectin in the treatment of mild to moderate Covid-19 patients: a multi-centre double-blind randomized controlled clinical trial.

BACKGROUND: Evidence on ivermectin as a treatment for Covid-19 is controversial. A Cochrane review concluded that the efficacy and safety of ivermectin is uncertain (evidence up to April 2022) and WHO recommended its use only in the setting of clinical trials. This study aimed to assess the efficacy and safety of oral ivermectin in hospitalized patients with mild to moderate Covid-19. TRIAL DESIGN AND METHODS: A double-blind, randomized placebo-controlled clinical trial was conducted among RT-PCR-confirmed, adults, hospitalised within the first four days of symptoms. Patients received oral ivermectin 24 mg or placebo daily for five days. RT-PCR was repeated on days five and ten. Clinical progression was monitored using the World Health Organization Clinical Progression Scale. Serum ivermectin levels were measured on days three, five, and seven. The primary outcome was the difference in the viral load between day zero and ten in the two groups. RESULTS: Out of 1699 patients screened, 249 underwent randomization and 127 received ivermectin, and 122 placebo. D10 median viral load for E gene (IQR) was 2,000 copies/mL (100 - 20,500) with ivermectin (n = 80) and 4,100 copies/mL (1,000-65,600) with placebo (n = 81, p = 0.028), per protocol analysis. The difference in Log viral load between day zero and ten between ivermectin and placebo was 3.72 and 2.97 respectively (p = 0.022). There was no significant difference in the WHO clinical progression scale or the adverse effects. Ivermectin blood levels taken before or with meals were not significantly different. Only 7 and 17 patients achieved blood levels above 160ng/ML and 100ng/ML respectively and they did not achieve a significantly lower viral load. CONCLUSION: Although ivermectin resulted in statistically significant lower viral load in patients with mild to moderate Covid-19, it had no significant effect on clinical symptoms. TRIAL REGISTRATION NUMBER: SLCTR/2021/020, Sri Lanka Clinical Trials Registry. 19/07/2021.

Prevalence of SARS-CoV-2 virus in saliva, stool, and urine samples of COVID-19 patients in Bihar, India.

Introduction. The coronavirus illness caused by SARS-CoV-2 can cause multiple organ involvement, with varying degrees of severity. Besides inhalation as a route for transmission, feco-oral has also been proposed. Its transmission to sewage systems is a growing public health issue. Objective. To detect SARS-CoV-2 RNA in non-respiratory samples (saliva, urine, and stool) collected from COVID-19 cases, in Bihar. Methods. This cross-sectional observational study was conducted from January 2021 to March 2022 on human non-respiratory samples. A total of 345 samples including saliva (116), stool (97), and urine (132) were collected from 143 COVID-19 cases. Samples were analysed for SARS-CoV-2 by multiplex RT-PCR targeted against E, ORF 1ab, and RdRp genes. Results. In this study, out of 143 cases, a total of 107 (74.8 %) were positive for SARS-CoV-2 RNA in at least one of the non-respiratory samples. Conclusion. There is a high prevalence of SARS-CoV-2 virus in non-respiratory samples.

The Time to Negative Conversion among Adult COVID-19 Patients on Chronic Hemodialysis Admitted at the Philippine General Hospital - A Retrospective Cohort Study.

Objectives: In the Philippines, patients on chronic hemodialysis with COVID-19 remain admitted in hospitals despite clinical recovery because most free-standing dialysis units require proof of negative conversion via Reverse Transcriptase - Polymerase Chain Reaction (RT-PCR). This study aims to determine the time to negative conversion of COVID-19 RT-PCR testing among adult patients on chronic hemodialysis with COVID-19 admitted at the Philippine General Hospital (PGH) and bring insight in using the symptom or time-based procedure as recommended by local guideline, and ultimately, to ensure delivery of adequate hemodialysis despite being infected with COVID-19, shorten isolation period, and conserve resources especially in resource-limited settings. Methods: This is a retrospective cohort study on all adult patients on chronic hemodialysis who were admitted in PGH after the diagnosis of COVID-19 by RT-PCR between March 2020 and February 2021. Descriptive statistics was used in summarizing the data. Results: A total of 90 patients on chronic hemodialysis who tested positive for COVID-19 via RT-PCR admitted at PGH were included in the study. Most of these patients had moderate COVID-19 at 53.3%. The median number of days from onset of symptoms to clinical recovery was 14.5 days. The median time to first negative conversion was 18 days. Most of these patients had negative conversion at the second week. The correlation coefficient between time to clinical recovery and negative conversion was 0.214. Conclusion: Among adult patients on chronic hemodialysis who were admitted in PGH after the diagnosis of COVID-19, the time to negative conversion was longer compared to the time to clinical recovery with a very weak correlation between the two.

Assessing the performance of LumiraDx™ SARS-CoV-2 Ag test in detecting Omicron lineages: 2022-2023 study.

Background: The introduction of rapid antigen tests revolutionized the approach to SARS-CoV-2 diagnosis, offering prompt and accurate results with high sensitivity and specificity. Although it is more cost- and time-saving than the gold standard, real-time polymerase chain reaction (RT-PCR), the efficacy in general population screening in both hospital- and community-based settings remains unknown. Moreover, rapid antigen testing is limited by qualitative results. This study aims to evaluate the diagnostic reliability of the LumiraDx™ rapid antigen test during the Omicron era and to investigate its quantitative (analogue-to-digital converter (ADC)) results in comparison with RT-PCR Ct values. Methods: This prospective study included all adult patients with mild-to-moderate SARS-CoV-2 symptoms who were not hospitalised and did not require oxygen supplementation, consented to participate, and attended the Infectious and Tropical Diseases Unit of Padua University Hospital from July 14th, 2022 to January 3rd, 2023. The patients underwent two different tests simultaneously: a nasal LumiraDx™ swab and a real-time RT-PCR assay performed on a nasopharyngeal swab. Sampling was repeated several times for a subset of subjects. Results: We enrolled 266 consecutive participants and collected 601 pairs of LumiraDx™ and RT-PCR samples. The most prevalent variant was BA.4/BA.5 Omicron (60.2 %). The sensitivity and specificity of LumiraDx™ test when compared to real-time RT-PCR results as the reference standard were 93.1 % and 79.75 %, respectively. No significant differences in diagnostic reliability were found based on the available characteristics, age, sex, symptom status, or COVID-19 variant, except for the days from symptom onset. According to the multilevel logistic regression analysis, the only independent variable significantly associated with test concordance was the Ct value (adjusted odds ratio (OR) = 0.56, p < 0.001). Significant differences in quantitative ADC values were found between false negative (FN) versus true negative (TN), and false positive (FP) and true positive (TP) tests. Conclusions: This study showed that LumiraDx™ test is reliable for SARS-CoV-2 diagnosis in patients with mild-to-moderate SARS-CoV-2 symptoms. This finding confirms the efficacy of rapid antigen tests in monitoring vulnerable individuals during the current post-vaccination era. When compared with the RT-PCR, LumiraDx™ test effectively quantitatively distinguishes between FN and TN cases, as well as FP and true TP tests, despite inaccuracies in qualitative results.

Platelet Indices as Novel Surrogate Markers for the Prognosis of COVID-19 Infection: An Observational Study.

Background  The new severe acute respiratory syndromecoronavirus 2 (SARS-CoV-2) causes severe acute respiratory illness accountable for causing the coronavirus disease 2019 (COVID-19) illness. Thrombotic issues, acute respiratory distress syndrome (ARDS), and cytokine storm are significant contributors to morbidity and mortality in patients with COVID-19. Elevated D-dimer levels and prothrombin times are further indicators of abnormal coagulation parameters in COVID-19 patients. This study aimed to study the platelet indices as prognostic markers in COVID-19 infection. Methods In this prospective observational study, 150 real-time reverse transcription-polymerase chain reaction (RT-PCR)-positive COVID-19 patients were enrolled between October 2020 and September 2021. All the subjects were screened and explained the study procedure in their native language. Following enrolment, a detailed history and physical examination were performed. Subsequently, laboratory investigations were performed, and patients were subjected to high-resolution computed tomography (HRCT) examination to classify patients into mild, moderate, and severe according to the severity of the illness. The platelet indices taken into account were plateletcrit (PCT) in percentage, platelet count (PLT) in lakh per microlitre, mean platelet volume (MPV) in femtolitres, and platelet distribution width (PDW) in femtolitres. Results The mean PLT was significantly greater among survivors than non-survivors (2.03 ± 0.72 versus 1.76 ± 0.47; p-value = 0.018). The mean MPV (10.42 ± 0.53 versus 9.22 ± 0.64; p-value <0.0001) and PDW (17.99 ± 1.53 versus 16.54 ± 0.91 fl; p-value <0.0001) were significantly greater among non-survivors than survivors. However, the mean PCT was significantly greater among survivors than non-survivors (0.22 ± 0.03% versus 0.18 ± 0.33%; p-value <0.0001). At a cut-off of 0.213, the sensitivity and specificity of PCT in predicting death were found to be 79.2% and 74.5%, respectively. At a cut-off of 16.75, the sensitivity and specificity of PDW in predicting death were found to be 68.8% and 59.8%, respectively. The findings demonstrated a relationship between elevated MPV and PDW and mortality and severe COVID-19 infection. Increased PCT was connected to higher survival, with a specificity and sensitivity of 87.5% and 75.5%, respectively, and MPV >9.75 may predict death. PDW >16.75 exhibited a specificity and sensitivity of 68.8% and 59.8%, respectively, in predicting death. With comparable sensitivity and specificity of 79.2% and 74.5%, PCT >0.213 may predict death. Conclusion In severely sick COVID-19 patients, platelet indices should be routinely calculated and can be utilized as simple, low-cost prognostic indicators.

COVID-19 pandemic - Cocktail of variants, a study from Northern India.

Context: The aim of the study was to identify and monitor the circulating strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the samples received at our center and update the existing national and international genomic surveillance data. Introduction: SARS-CoV-2 is no exception to the basic nature of the viruses ability to change and evolve. Since its first report in December 2019 from Wuhan, China, multiple variants of the virus have emerged and been reported. Five variants of concern have been recognized and reported by the Centers for Disease Control and Prevention, which are associated with variable degrees of transmissibility and mortality. Materials and Methods: Nasopharyngeal and oropharyngeal swabs received in viral transport medium at the Viral Research Diagnostic Laboratory were processed for reverse transcription-polymerase chain reaction for SARS-CoV-2. Whole genome sequencing (WGS) was performed for selective positive samples using Oxford Nanopore sequencing technology, using MinKNOW software for data acquisition. Statistical Analysis: The clades were assigned using Nextclade v2.4.1 software. The statistical analysis was calculated using OpenEpi version 3, an open-source calculator, and two by two. Results: Variants reported over the study period included Alpha, Kappa, Delta, and Omicron. Delta dominated in the year 2021, while Omicron was the dominant variant in 2022. In both the dominant variants, asymptomatics contributed to around 30-40% of positives. Intensive care unit admissions and mortality were higher in the Delta variant, while vaccination history and travel history were higher in the patients with Omicron variant. Conclusion: The trend tracking of these variants has been important in view of public health, enabling early interventions to control the spread of the disease and foresight in preparation for the situation.

The epidemiology of intestinal protozoa in the Israeli population based on molecular stool test: a nationwide study.

Stool examination using microscopy was the traditional method for the diagnosis of intestinal parasites. Recently, the use of molecular tests to identify stool protozoa has become the main tool used in most clinical laboratories in Israel. This study aimed to evaluate the prevalence of intestinal parasites in Israel and to compare this prevalence in laboratories that use molecular tests vs a laboratory that uses microscopy. Samples collected from January to October 2021 at seven laboratories were analyzed by real-time PCR (RT-PCR) or by microscopy. The multiplex panel included the following pathogens: Giardia lamblia, Entamoeba histolytica, Cryptosporidium spp., Cyclospora, Dientamoeba fragilis, and Blastocystis spp. Overall, 138,415 stool samples were tested by RT-PCR and 6,444 by microscopy. At least one protozoa species was identified in 28.4% of the PCR-tested samples compared to 4.6% of the microscopy-tested samples. D. fragilis was the most common PCR-identified species (29%). D. fragilis, G. lamblia, and Cryptosporidium spp. were mainly found in pediatric population, while Blastocystis spp. was most prevalent among adults (P < 0.001). In a sub-cohort of 21,480 samples, co-infection was found in 4,113 (19.15%) samples, with Blastocystis spp. and D. fragilis being the most common (14.9%) pair. Molecular stool testing proved more sensitive compared to microscopy. D. fragilis was the most commonly detected pathogen. The above profile was identified during the COVID pandemic when traveling was highly restricted and most likely represents the locally circulating protozoa. IMPORTANCE: This study sheds light on the prevalence of stool parasites in Israel. Additionally, this study indicates that the shift from microscope analysis to molecular tests improved protozoa diagnosis.

Molecular Characterization of Lineage-IV Peste Des Petits Ruminants Virus and the Development of In-House Indirect Enzyme-Linked Immunosorbent Assay (IELISA) for its Rapid Detection".

Peste des petits ruminants (PPRV), a highly contagious viral disease, causes significant economic losses concerning sheep and goats. Recently, PPR viruses (PPRVs), have adopted new hosts and lineage IV of PPRVs represents genetic diversity within the same lineage. 350 samples, including blood, swabs, and tissues from sheep/goats, were collected during the 2020-2021 disease outbreaks in Pakistan. These samples were analysed through RT-PCR and three isolates of PPRV with accession numbers, MW600920, MW600921, and MW600922, were submitted to GenBank, based on the partial N-gene sequencing. This analysis provides a better understanding of genetic characterizations and a targeted RT-PCR approach for rapid PPRV diagnosis. An IELISA test was developed using the semi-purified antigen MW600922 isolate grown in Vero cells. The PPRV isolates currently present high divergence with the Turkish strain; conversely, similarities equivalent to 99.73% were observed for isolates collected from Pakistan. The developed indirect ELISA (IELISA) test demonstrated antibody detection rates at dilutions of 1:200 for antibodies (serum) and 1:32 for antigens. In comparison to cELISA, high specificity (85.23%) and sensitivity (90.60%) rates were observed. In contrast to the virus neutralization test (VNT), IELISA was observed to be 100% specific and 82.14% sensitive in its results. Based on these results, serological surveys conducted for PPR antibodies using IELISA can be a more effective strategy on a larger scale. Furthermore, our results demonstrate a significant breakthrough in the research in terms of cost-effectiveness and storage efficiency, and the developed IELISA test is highly recommended for use in developing countries.

Peste des petits ruminants (PPRV) is a transboundary, highly contagious, and economically significant viral disease affecting small ruminants and wildlife. PPRV, a disease that only targets animals, is the focus of the Global Eradication Programme (PPRV GEP), which aims to eradicate the disease by 2030. Following the completion of the first phase of the GEP (2017­2021), Pakistan has initiated the second phase: PPRV presence and the implementation of a control strategy. Rapid and accurate laboratory diagnosis is vital to the disease's effective control and eradication. In the present study, we have improved diagnosis by reverse transcriptase polymerase chain reaction (RT-PCR), which not only can detect low viral concentrations but also contributes to the genetic analysis of lineage-IV viruses. However, the development of cost-effective indirect ELISA (iELISA) may allow for the analysis of serum samples obtained from larger populations of small ruminants.