Effectiveness of a standardized quality control management procedure for COVID-19 RT-PCR testing: a large-scale diagnostic accuracy study in China.

BACKGROUND: The study aimed to construct a standardized quality control management procedure (QCMP) and access its accuracy in the quality control of COVID-19 reverse transcriptase-polymerase chain reaction (RT-PCR). METHODS: Considering the initial RT-PCR results without applying QCMP as the gold standard, a large-scale diagnostic accuracy study including 4,385,925 participants at three COVID-19 RT-PCR testing sites in China, Foshan (as a pilot test), Guangzhou and Shenyang (as validation sites), was conducted from May 21, 2021, to December 15, 2022. RESULTS: In the pilot test, the RT-PCR with QCMP had a high accuracy of 99.18% with 100% specificity, 100% positive predictive value (PPV), and 99.17% negative predictive value (NPV). The rate of retesting was reduced from 1.98% to 1.16%. Its accuracy was then consistently validated in Guangzhou and Shenyang. CONCLUSIONS: The RT-PCR with QCMP showed excellent accuracy in identifying true negative COVID-19 and relieved the labor and time spent on retesting.

L-Ergothioneine slows the progression of age-related hearing loss in CBA/CaJ mice.

The naturally occurring amino acid, l-ergothioneine (EGT), has immense potential as a therapeutic, having shown promise in the treatment of other disease models, including neurological disorders. EGT is naturally uptaken into cells via its specific receptor, OCTN1, to be utilized by cells as an antioxidant and anti-inflammatory. In our current study, EGT was administered over a period of 6 months to 25-26-month-old CBA/CaJ mice as a possible treatment for age-related hearing loss (ARHL), since presbycusis has been linked to higher levels of cochlear oxidative stress, apoptosis, and chronic inflammation. Results from the current study indicate that EGT can prevent aging declines of some key features of ARHL. However, we found a distinct sex difference for the response to the treatments, for hearing - Auditory Brainstem Responses (ABRs) and Distortion Product Otoacoustic Emissions (DPOAEs). Males exhibited lower threshold declines in both low dose (LD) and high dose (HD) test groups throughout the testing period and did not display some of the characteristic aging declines in hearing seen in Control animals. In contrast, female mice did not show any therapeutic effects with either treatment dose. Further confirming this sex difference, EGT levels in whole blood sampling throughout the testing period showed greater uptake of EGT in males compared to females. Additionally, RT-PCR results from three tissue types of the inner ear confirmed EGT activity in the cochlea in both males and females. Males and females exhibited significant differences in biomarkers related to apoptosis (Cas-3), inflammation (TNF-a), oxidative stress (SOD2), and mitochondrial health (PGC1a).These changes were more prominent in males as compared to females, especially in stria vascularis tissue. Taken together, these findings suggest that EGT has the potential to be a naturally derived therapeutic for slowing down the progression of ARHL, and possibly other neurodegenerative diseases. EGT, while effective in the treatment of some features of presbycusis in aging males, could also be modified into a general prophylaxis for other age-related disorders where treatment protocols would include eating a larger proportion of EGT-rich foods or supplements. Lastly, the sex difference discovered here, needs further investigation to see if therapeutic conditions can be developed where aging females show better responsiveness to EGT.

MOLECULAR DETECTION PROTOCOL OF SARS-COV-2 THROUGH SELF-COLLECTED SALIVA SPECIMENS VERSUS NASOPHARYNGEAL SWABS.

Background: Several reports have shown that saliva specimen is an excellent alternative biofluid sample for SARS-CoV-2 detection. We conducted this study, in order to assess the sensitivity and specificity of using saliva self-collected by adult and pediatric patients, as a biological sample for RT-PCR diagnosis. Aims: The present study was carried out to assess the sensitivity and specificity of using saliva self-collected from adult and pediatric patients, as a biological sample for RT-qPCR diagnosis. Methods: In this study, 50 symptomatic patients and 40 asymptomatic subjects (adult and pediatric) were enrolled between September 2020 and November 2020 at the Department of Infectious Diseases, Bejaia University Hospital (CHU), and tested simultaneously for the sensitivity and specificity of the SARS-CoV-2 viral genome by RT-PCR on both nasopharyngeal swabs NP swab and saliva samples. Results: Our RT-qPCR results revealed that saliva samples showed the highest sensitivity (95% CI [27.67, 29.82]) followed by a nasopharyngeal swab for symptomatic (95% CI [29.64, 31.49]) as well as for asymptomatic adult patients. Moreover, the saliva of symptomatic and asymptomatic patients was monitored, and the presence of viral RNA was detected in >95% of the asymptomatic patients as well as the symptomatic patients. Surprisingly, the Ct values of ORF1ab and N genes are highly lower in nasopharyngeal swabs compared to saliva. Indeed, the mean difference note that for the ORF1ab gene and N gene, the mean of difference in ΔCt value were respectively 3.683 and 3.578. Together, including symptomatic and asymptomatic subjects, the overall agreement between the saliva sample and the nasopharyngeal is about 84%. Conclusion: The sensitivity of saliva samples remains acceptable; it may still be a viable option in locations where laboratory facilities are lacking for diagnostic purposes in the early phase of the disease.

Epidemiological distribution of respiratory viral pathogens in marketable vaccinated broiler chickens in five governorates in the Nile Delta, Egypt, from January 2022 to October 2022.

Background and Aim: Respiratory viral infections significantly negatively impact animal welfare and have significant financial implications in the poultry industry. This study aimed to determine the frequency of the most economically relevant respiratory viruses that circulated in Egyptian chicken flocks in 2022. Materials and Methods: Chickens from 359 broiler flocks in five different Egyptian governorates in the Nile Delta (Beheira, Gharbia, Giza, Monufiya, and Qalyoubia) at marketing time (33-38 days of age) were used in this study. Combined oropharyngeal and cloacal swabs and tissue samples were collected from clinically diseased or freshly dead birds suffering from respiratory disease. Avian influenza (AI)-H5, AI-H9, Newcastle disease (ND), and infectious bronchitis virus (IBV) were analyzed by reverse transcriptase polymerase chain reaction. Results: Of the 359 flocks examined, 293 tested positive, whereas 66 were completely negative for the four viruses evaluated, with the highest positive results in Beheira. Out of 293 positive flocks, 211 were positive for a single virus, with Beheira having the highest rate, followed by Qalyoubia, Giza, and Monufiya. ND virus (NDV) was found to be the highest across all governorates, followed by IBV, AI-H9, and AI-H5. A double infection was detected in 73 flocks with either H9 or ND, or both H9 and IB could coinfect each other. The most common viral coinfections were H9 + IB, ND + IB, and ND + H9. Giza had the highest prevalence of ND + H9, H9 + IB, and ND + IB coinfection in the governorates, followed by Monufiya and Beheira. Only six out of 359 flocks were tribally infected with ND + H9 + IB in Giza, Monufiya, and Beheira governorates. On the basis of the number of flocks and the month of the year, July had the lowest number of flocks (23), while September and October had the highest number (48 flocks). Positive flock numbers were highest in October and lowest in January. Conclusion: From January to October 2022, prevalent respiratory viral infections (H5N1, NDV, H9N2, and IBV) were detected in broiler chickens across the Delta area governorate, according to the findings of the present study. In addition, IBV and H9, either alone or in combination, significantly contributed to the respiratory infection observed in broiler chickens. Regardless of the type and origin of the vaccine used, it is not possible to protect broiler chickens from the development of the infection and the subsequent dissemination of the virus into the poultry environment. In the presence of face-infectious field virus mutations, poultry vaccinations must be regularly reviewed and updated, and poultry farms must take further biosecurity measures.

Virulent systemic feline calicivirus infection: a case report and first description in Ireland.

BACKGROUND: Virulent systemic feline calicivirus (VS-FCV) infection is an emerging disease. It is distinct from classic oronasal calicivirus infection as it manifests with unique systemic signs including severe cutaneous ulcerations, limb oedema, and high mortality, even in adequately vaccinated cats. Devastating epizootic outbreaks with hospital-acquired infections have been described in the United States, the United Kingdom, continental Europe and Australia with up to 54 cats affected in one outbreak and a mortality rate of up to 86%. This highly contagious and potentially fatal disease has not yet been reported in Ireland. CASE PRESENTATION: An 11-month-old male neutered vaccinated domestic shorthair cat was presented with a 10-day history of lethargy, decreased appetite and progressively worsening pitting oedema in all four limbs. The signs were first noted after another kitten from a high-density cat shelter was introduced in to the household. Additional physical examination findings included marked pyrexia, and lingual and cutaneous ulcers. Virulent systemic feline calicivirus was diagnosed based on compatible history and clinical signs, exclusion of other causes, and calicivirus isolation by RT-PCR both in blood and oropharyngeal samples. Negative calicivirus RT-PCR in blood following resolution of the clinical signs further supported the diagnosis. CONCLUSION: This case represents the first known case of VS-FCV infection in Ireland. Given the severity of the clinical signs, and the high risk for epizootic outbreaks, Irish veterinarians should be aware of the disease to ensure prompt diagnosis and implementation of adequate preventive measures, in order to limit the threat that this disease represents for the wider cat population and particularly given the risk of hospital-acquired VS-FCV infection. Virulent systemic calicivirus should be suspected in cats with pyrexia of unknown origin, oedema or ulceration affecting the limbs or the face, and exposure to rescue cats from high-density households.

SARS-CoV-2 and the ocular surface: test accuracy and viral load / SARS-CoV-2 e a superfície ocular: acurácia dos testes e carga viral

ABSTRACT Purpose: This study aimed to evaluate the pre-sence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in the ocular surface of individuals clinically suspected of coronavirus disease 2019 (COVID-19) and determine the accuracy of different approaches of molecular testing on the ocular surface based on the nasopharyngeal positivity status for COVID-19. Methods: A total of 152 individuals with suspected COVID-19 symptoms who simultaneously underwent nasopharyngeal and two different tear film collection techniques for quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR) were included. Tears were collected and randomized: one eye had the filter strip for the Schirmer test and the contralateral eye had conjunctival swab/cytology in the inferior fornix. All patients underwent slit lamp biomicroscopy. The accuracy of various ocular surface collection techniques used for the detection of SARS-CoV-2 RNA was determined. Results: Of the 152 patients enrolled in the study, 86 (56.6%) had COVID-19 confirmed by nasopharyngeal PCR. Both tear film collection techniques detected viral particles: the Schirmer test was positive in 16.3% (14/86) and the conjunctival swab/cytology in 17.4% (15/86), with no statistically significant differences. No positive ocular tests were found among those with negative nasopharyngeal PCR tests. The overall agreement of the ocular tests was 92.7%, and in combination, the sensitivity would increase to 23.2%. The mean cycle threshold values in the nasopharyngeal, Schirmer, and conjunctival swab/cytology tests were 18.2 ± 5.3, 35.6 ± 1.4, and 36.4 ± 3.9, respectively. Compared with the nasopharyngeal test, the Schirmer (p=0.001) and conjunctival swab/cytology (p<0.001) tests had significantly different Ct values. Conclusion: The Schirmer (16.3%) and conjunctival swab (17.4%) tests were comparably capable of detecting SARS-CoV-2 RNA in the ocular surface by RT-PCR accurately based on nasopharyngeal status and demonstrated indistinct sensitivity and specificity. Simultaneous specimen sampling and processing from the nasopharyngeal, Schirmer, and conjunctival swab/cytology tests demonstrated significantly lower viral load in both ocular surface approaches than in the nasopharyngeal test. Ocular manifestations detected by slit lamp biomicroscopy were not associated with ocular RT-PCR positivity.

RESUMO Objetivo: Avaliar a presença de RNA de coronavírus 2 causador de síndrome respiratória aguda grave (SARS-CoV-2) na superfície ocular de indivíduos clinicamente suspeitos com COVID-19 e determinar a precisão de diferentes abordagens de testes moleculares na superfície ocular com base no status de positividade do RT-qPCR de nasofaringe para COVID-19. Métodos: 152 indivíduos com sintomas suspeitos para a COVID-19 foram submetidos a coleta de reação em cadeia da polimerase de nasofaringe simultaneamente a duas técnicas diferentes de coleta de filme lacrimal para RT-qPCR: aleatoriamente, um olho com a tira filtro do teste de Schirmer e, o olho contralateral, com citologia (swab) conjuntival no fórnice inferior. Todos os indivíduos foram submetidos à biomicroscopia com lâmpada de fenda. Resultados: Dos 152 pacientes, 86 (56,6%) tiveram a COVID-19 confirmada por PCR de nasofaringe. Ambas as técnicas de coleta detectaram partículas virais: o teste de Schirmer foi positivo em 16,3% (14/86) e a citologia conjuntival em 17,4% (15/86), sem diferenças estatisticamente significativas. Não houve testes oculares positivos entre aqueles com reação em cadeia da polimerase de nasofaringe negativo. A concordância geral dos testes oculares foi de 92,7% e, em combinação, a sensibilidade aumentaria para 23,2%. Os valores médios do limiar de ciclo nos testes de nasofaringe, Schirmer e citologia conjuntival foram 18,2 ± 5,3, 35,6 ± 1,4 e 36,4 ± 3,9, respectivamente. Conclusão: Os testes de Schirmer (16,3%) e swab conjuntival (17,4%) foram igualmente capazes de detectar RNA de SARS-CoV-2 na superfície ocular por RT-PCR e demonstraram sensibilidade e especificidade indistintas. A coleta simultânea de amostras ao processamento dos testes de RT-PCR de nasofaringe, Schirmer e citologia (swab) conjuntival demonstraram carga viral significativamente menor em ambas as abordagens da superfície ocular em comparação com o teste de nasofaringe. As manifestações oculares detectadas pela biomicroscopia com lâmpada de fenda não foram claramente associadas à positividade do RT-PCR ocular.

Genetic diversity of Potato virus M (PVM) in the major potato growing region in the Indo-Gangetic plain and characterization of a distinct strain of PVM occurring in India.

Potato virus M (PVM) is one of the most prevalent viruses infecting potatoes worldwide, showing a wide range of diversity in their populations; however, the diversity and genome information of PVM occurring in India is hardly known. The present study serologically detected the PVM in 22.8% of leaf samples collected from the potato fields, generated 13 coat protein (CP) genes and one complete genome sequence for the isolates from India, and identified four differential hosts confirming PVM-Del-144 as a distinct strain of PVM occurring in India. The phylogenetic analyses conducted based on the CP gene sequences (14 from India and 176 from other countries) suggested the existence of three evolutionary divergent lineages (PVM-o, PVM-d, and a new divergent group) in the PVM population, where isolates from India belong to only two clusters (PVM-o and PVM-d) within four sub-clusters. High levels of nucleotide diversity (0.124) and genetic distance (0.142) recorded among the isolates from India may be due to the deviation from the neutral evolution and experiencing population expansion in the past. The complete genome of the isolate Del-144 (KJ194171; 8,526 nucleotides) shared 92.2-93.9% nt sequence identity with the population of PVM-o, whereas it shared only 70.2-72.1% identity with PVM-d. In the phylogenetic analyses, Del-144 clustered with the isolates of PVM-o; however, it formed a separate branch away from all other isolates, indicating the diversity of the strain. Overall, this study revealed the diversity of the isolates of PVM from India and reported the first complete genome sequence of a distinct strain of PVM occurring in India.

SARS-CoV-2 RT-PCR as a universal screening on planned admission in asymptomatic patients.

Universal screening for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on admission is reportedly beneficial in preventing nosocomial infections. However, some issues remain, including low positivity rate, cost, and time required for testing. We describe SARS-CoV-2 reverse transcription polymerase chain reaction (PCR) for universal screening in asymptomatic patients on planned admissions. In total, 14,574 patients were included between October 12, 2020, and June 23, 2022. The PCR-positive rate for the period was 0.44 % (64/14,574). The PCR positivity for the epidemic period by strain was 0.28 % (95 % confidence interval [CI] 0.12-0.56 %), 0.16 % (95 % CI 0.05-0.37 %), 0.21 % (95 % CI 0.09-0.41 %), and 0.9 % (95 % CI 0.65-1.2 %) for the wild-type strain, Alpha, Delta, and Omicron variants, respectively. The proportion of Ct values < 30 was higher in the first half of the epidemic (first vs. second, 29.4 % [95 % CI 16.9-44.8 %] vs. 16.7 % [95 % CI 6.0-28.5 %]), whereas that of Ct values ≥ 35 increased significantly in the second half (first vs. second, 32.4 % [95 % CI 19.3-47.8 %] vs. 70.0 % [95 % CI 53.5-83.4 %]). Of all positives, 50 % (32/64) had a coronavirus disease (COVID-19) history before PCR screening, with a median of 28 days (10-105) from COVID-19 onset or positive to PCR screening. PCR screening may help detect positives with high viral loads early in the epidemic for each mutant strain, with an increasing proportion of positives with low viral loads later in the epidemic. PCR testing may be unnecessary for recently diagnosed cases and patients in whom reinfection is unlikely.

A Case Series of Scrub Meningoencephalitis from a Tertiary Care Center in North India.

Scrub typhus infection is reemerging leading cause of acute febrile illnesses in post-rainy or monsoon season in Southeast Asia. It is caused by Orientia tsutsugamushi and spread by the bite of chiggers, larval forms of trombiculid mites. The clinical picture can range from simple acute febrile illness to multiorgan dysfunction. Neurological manifestations also vary from aseptic meningitis, meningoencephalitis, cerebral infarction, acute disseminated encephalomyelitis, transverse myelitis, and psychiatric manifestations. Here, we present a case series of eight cases of scrub meningoencephalitis diagnosed based on clinical, laboratory, and radiological criteria.

Estimating the number of probable new SARS-CoV-2 infections among tested subjects from the number of confirmed cases.

OBJECTIVES: In most African countries, confirmed COVID-19 case counts underestimate the number of new SARS-CoV-2 infection cases. We propose a multiplying factor to approximate the number of biologically probable new infections from the number of confirmed cases. METHODS: Each of the first thousand suspect (or alert) cases recorded in South Kivu (DRC) between 29 March and 29 November 2020 underwent a RT-PCR test and an IgM and IgG serology. A latent class model and a Bayesian inference method were used to estimate (i) the incidence proportion of SARS-CoV-2 infection using RT-PCR and IgM test results, (ii) the prevalence using RT-PCR, IgM and IgG test results; and, (iii) the multiplying factor (ratio of the incidence proportion on the proportion of confirmed -RT-PCR+- cases). RESULTS: Among 933 alert cases with complete data, 218 (23%) were RT-PCR+; 434 (47%) IgM+; 464 (~ 50%) RT-PCR+, IgM+, or both; and 647 (69%) either IgG + or IgM+. The incidence proportion of SARS-CoV-2 infection was estimated at 58% (95% credibility interval: 51.8-64), its prevalence at 72.83% (65.68-77.89), and the multiplying factor at 2.42 (1.95-3.01). CONCLUSIONS: In monitoring the pandemic dynamics, the number of biologically probable cases is also useful. The multiplying factor helps approximating it.

Designing one-step reverse transcriptase loop-mediated isothermal amplification for serotype O foot-and-mouth disease virus detection during the 2022 outbreak in East Java, Indonesia.

Background and Aim: Various methods can detect foot-and-mouth disease (FMD) in cows, but they necessitate resources, time, costs, laboratory facilities, and specific clinical specimen submission, often leading to FMD virus (FMDV) diagnosis delays. The 2022 FMD outbreak in East Java, Indonesia, highlighted the need for an easy, inexpensive, rapid, and accurate detection approach. This study aims to devise a one-step reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) technique and phylogenetic analysis to detect the serotype O FMDV outbreak in East Java. Materials and Methods: Swab samples were collected from the foot vesicles, nasal secretions, and saliva of five suspected FMDV-infected cows in East Java between June and July 2022. The RT-LAMP design used hydroxy naphthol blue dye or SYBR Green I dye, with confirmatory analysis through reverse transcriptase polymerase chain reaction (RT-PCR) targeting 249 base pairs. PCR products underwent purification, sequencing, and nucleotide alignment, followed by phylogenetic analysis. Results: The RT-LAMP method using hydroxy naphthol blue dye displayed a positive reaction through a color shift from purple to blue in the tube. Naked-eye observation in standard light or ultraviolet (UV) light at 365 nm, with SYBR Green I stain, also revealed color change. Specifically, using SYBR Green I dye, UV light at 365 nm revealed a color shift from yellow to green, signifying a positive reaction. Nucleotide alignment revealed mutations and deletion at the 15th sequence in the JT-INDO-K3 isolate from the East Java FMDV outbreak. Despite differing branches, the phylogenetic tree placed it in the same cluster as serotype O FMDV from Malaysia and Mongolia. Conclusion: JT-INDO-K3 exhibited distinctions from Indonesian serotype O FMDV isolates and those documented in GenBank. Then, the RT-LAMP method used in this study has a detection limit 10 times higher latter than the conventional RT-PCR limit, without any cross-reactivity among strains.

Rapid response of a public health reference laboratory to the COVID-19 pandemic.

Introduction. Brazil was one of the most affected countries by the COVID-19 pandemic. Instituto Adolfo Lutz (IAL) is the reference laboratory for COVID-19 in São Paulo, the most populous state in Brazil. In April 2020, a secondary diagnostic pole named IAL-2 was created to enhance IAL's capacity for COVID-19 diagnosis.Hypothesis/Gap Statement. Public health laboratories must be prepared to rapidly respond to emerging epidemics or pandemics.Aim. To describe the design of IAL-2 and correlate the results of RT-qPCR tests for COVID-19 with secondary data on suspected cases of SARS-CoV-2 infection in the São Paulo state.Methodology. This is a retrospective study based on the analysis of secondary data from patients suspected of infection by SARS-CoV-2 whose clinical samples were submitted to real-time PCR after reverse transcription (RT-qPCR) at IAL-2, between 1 April 2020 and 8 March 2022. RT-qPCR Ct results of the different kits used were also analysed.Results. IAL-2 was implemented in April 2020, just over a month after the detection of the first COVID-19 case in Brazil. The laboratory performed 304,250 RT-qPCR tests during the study period, of which 98 319 (32.3 %) were positive, 205827 (67.7 %) negative, and 104 (0.03 %) inconclusive for SARS-CoV-2. RT-qPCR Ct values≤30 for E/N genes of SARS-CoV-2 were presented by 79.7 % of all the samples included in the study.Conclusion. IAL was able to rapidly implement a new laboratory structure to support the processing of an enormous number of samples for diagnosis of COVID-19, outlining strategies to carry out work with quality, using different RT-qPCR protocols.

Comparison between the accuracy of chest computerized tomography vs. reverse transcriptase polymerase chain reaction in a tertiary care center in Lebanon; along with their correlation to mortality, morbidity and symptoms in COVID-19 patients.

Objectives: Chest Computerized Tomography has been widely used in COVID patients' assessment. Hence the question arises as to whether there is any correlation between the Ct value and findings on Chest CT scan or clinical presentation of the patient. We wanted to test the hypothesis of whether low Ct values (≤30) in RT-PCR were associated with a high mortality rate, CT scan findings, or with comorbidities such as immunosuppression and lung disease. Methods: The radiographic records and RT-PCR Ct values of 371 COVID patents diagnosed at the American University of Beirut Medical Center were reviewed. Results: We found out that the sensitivity of chest CT scan compared to RT-PCR, the gold standard, turned out to be 74% (95% CI 69-79%). Specificity, on the other hand was 33% (95% CI 16-55%). The positive predictive value of CT was 94% (95% CI 91-97%) and the negative predictive value was 8% (95% CI 4-16%). low Ct values in RT-PCR were not associated with a higher mortality rate (p-value = 0.416). There was no significant positive association between low Ct value and suspicious CT scan findings (typical and indeterminate for COVID-19), with a p-value of 0.078. There was also no significant association between low Ct value and immunosuppression (p-value = 0.511), or lung disease (p-value =0.06). CT scan findings whether suspicious or not for COVID-19 infection, were not shown to be significantly associated with respiratory symptoms of any kind.No association was found between a history of lung disease, immunosuppression and suspicious CT scan findings for COVID-19. Conclusion: As long as this pandemic exists, nucleic acid testing was and remains the gold standard of COVID-19 diagnosis worldwide and in our community as it has a superior diagnostic accuracy to CT scan and higher sensitivity (94% vs 74%).

Computed Tomography Chest Findings in COVID-19 Patients.

BACKGROUND: COVID-19 which has caused significant morbidity and mortality around the world has been declared by the World Health Organization to be a global health emergency. Our objective was to find out the lung parenchymal patterns commonly evident in high resolution Computed Tomography in patients with COVID-19 pneumonia. METHODS: A retrospective cross-sectional study was conducted at a tertiary multi-specialty hospital in Kathmandu, Nepal. With ethical clearance from the institutional review board, a total of 235 patients with positive reverse transcriptase polymerase chain reaction for COVID-19 and having respiratory symptoms were included in the study. High Resolution Computed Tomography images of chest were retrieved from picture archiving and communication systems retrospectively and studied for the findings commonly attributed to COVID-19 pneumonia. The data was then analyzed using Stata version 14 (Stata Corp, College Station, TX, USA). Descriptive statistics were presented as mean and median while chi-square test was used to assess the association between socio-demographic characteristics and CT severity indices. RESULTS: Out of 235 patients, 174 (74.0%) were males and 61(26%) were females with a mean age of 54.8±14.5 years. The most commonly encountered pattern of pulmonary changes was bilateral involvement in 222 (94.5%) patients followed by ground-glass opacities in 218 (92.8%) patients and peripheral predominance of ground-glass opacities in 211 (89.8%) patients. CONCLUSIONS: Chest Computed Tomography abnormalities are common in COVID-19 positive patients with respiratory symptoms. These findings can guide in the assessment of the severity of the disease as well as patient management.

Prevalence of different virulence factors and their association with antimicrobial resistance among Pseudomonas aeruginosa clinical isolates from Egypt.

BACKGROUND: Emergence of multi-drug resistant Pseudomonas aeruginosa, coupled with the pathogen's versatile virulence factors, lead to high morbidity and mortality rates. The current study investigated the potential association between the antibiotic resistance and the production of virulence factors among P. aeruginosa clinical isolates collected from Alexandria Main University Hospital in Egypt. We also evaluated the potential of the phenotypic detection of virulence factors to reflect virulence as detected by virulence genes presence. The role of alginate in the formation of biofilms and the effect of ambroxol, a mucolytic agent, on the inhibition of biofilm formation were investigated. RESULTS: A multi-drug resistant phenotype was detected among 79.8% of the isolates. The most predominant virulence factor was biofilm formation (89.4%), while DNase was least detected (10.6%). Pigment production was significantly associated with ceftazidime susceptibility, phospholipase C production was significantly linked to sensitivity to cefepime, and DNase production was significantly associated with intermediate resistance to meropenem. Among the tested virulence genes, lasB and algD showed the highest prevalence rates (93.3% and 91.3%, respectively), while toxA and plcN were the least detected ones (46.2% and 53.8%, respectively). Significant association of toxA with ceftazidime susceptibility, exoS with ceftazidime and aztreonam susceptibility, and plcH with piperacillin-tazobactam susceptibility was observed. There was a significant correlation between alkaline protease production and the detection of algD, lasB, exoS, plcH and plcN; pigment production and the presence of algD, lasB, toxA and exoS; and gelatinase production and the existence of lasB, exoS and plcH. Ambroxol showed a high anti-biofilm activity (5% to 92%). Quantitative reverse transcriptase polymerase chain reaction showed that alginate was not an essential matrix component in P. aeruginosa biofilms. CONCLUSIONS: High virulence coupled with the isolates' multi-drug resistance to commonly used antimicrobials would increase morbidity and mortality rates among P. aeruginosa infections. Ambroxol that displayed anti-biofilm action could be suggested as an alternative treatment option, yet in vivo studies are required to confirm these findings. We recommend active surveillance of antimicrobial resistance and virulence determinant prevalence for better understanding of coregulatory mechanisms.

The first study on clinicopathological changes in cats with feline infectious peritonitis with and without retrovirus coinfection.

Background and Aim: Feline infectious peritonitis (FIP) is an infectious, immune-mediated, and fatal disease in cats caused by a mutant feline coronavirus (FCoV) infection. Feline immunodeficiency virus (FIV) and feline leukemia virus (FeLV) are two common retroviruses that play a role in reducing feline immune function with opportunistic retrovirus infection being a predisposing factor for the development of FIP. This study aimed to evaluate the clinicopathological parameters of FIP in cats with and without retrovirus coinfection. Materials and Methods: In total, 62 cats presenting with pleural and/or peritoneal effusion at the Kasetsart University Veterinary Teaching Hospital, Bangkok, Thailand, were selected for the study. Effusion samples were collected and a reverse transcriptase-polymerase chain reaction (RT-PCR) assay was performed on all samples using the 3' untranslated region primer. All FCoV-positive cats were tested for retrovirus infection using a commercial kit (Witness FeLV-FIV [Zoetis]; United States). Clinical signs, hematological, and biochemical parameters of these cats were investigated and grouped. Results: Of the 62 cats with pleural and/or peritoneal effusion, FCoV was detected in 32, of which 21 were highly suspicious for FIP. The cats suspected of FIP were divided into three subgroups following viral detection. A total of 14 had only FCoV infection (Group A), four had FCoV and FeLV infection (Group B), and three had FCoV, FeLV, and FIV infection (Group C). Of the rest, 11 had definitive diagnoses, which included three being FCoV and FeLV-positive (Group D), and eight were retrovirus-negative (Group E). Mild anemia and lymphopenia were found in cats infected with these three viruses. An albumin-to-globulin ratio lower than 0.5 was found in FIP cats with only FCoV infection. Conclusion: Typically, cats with clinical effusion and FIP, with and without retrovirus coinfection, had similar hematological findings. Clinical signs, blood parameters, fluid analysis with cytological assessment, and RT-PCR assays could identify better criteria to diagnose FIP with and without retrovirus coinfection.

First Round of External Quality Assessment Scheme for SARS-CoV-2 Laboratories During the COVID-19 Pandemic in Thailand.

The emergence of SARS-CoV-2 necessitated the rapid deployment of tests to diagnose COVID-19. To monitor the accuracy of testing across the COVID-19 laboratory network in Thailand, the Department of Medical Sciences under the Ministry of Public Health launched a national external quality assessment (EQA) scheme using samples containing inactivated SARS-CoV-2 culture supernatant from a predominant strain in the early phase of the Thailand outbreak. All 197 laboratories in the network participated; 93% (n=183) of which reported correct results for all 6 EQA samples. Ten laboratories reported false-negative results, mostly for samples with low viral concentrations, and 5 laboratories reported false-positive results (1 laboratory reported false positives and false negatives). An intralaboratory investigation of 14 laboratories reporting incorrect results revealed 2 main causes of error: (1) RNA contamination of the rRT-PCR reaction and (2) poor-quality RNA extraction. Specific reagent combinations were significantly associated with false-negative reports. Thailand's approach to national EQA for SARS-CoV-2 can serve as a roadmap for other countries interested in implementing a national EQA program to ensure laboratories provide accurate testing results, which is crucial in diagnosis, prevention, and control strategies. A national EQA program can be less costly and thus more sustainable than commercial EQA programs. National EQA is recommended to detect and correct testing errors and provide postmarket surveillance for diagnostic test performance.

Severe acute respiratory syndrome coronavirus-2 detection in domestic animals as a reservoir for the virus transmission to humans in Yogyakarta, Indonesia.

Background and Aim: The coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that attacks the respiratory and digestive tract. The SARS-CoV-2 showed systemic characteristics with various clinical symptoms from subclinical to fatal (causing death). Transmission of SARS-CoV-2 has been reported to occur from humans to pets (cats, dogs, tigers, ferrets, and poultry). Knowledge about the role of domestic animals in the transmission of SARS-CoV-2 to humans, and as reservoirs of this virus needs to be investigated further. This study aimed to detect the presence of SARS-CoV-2 in domestic animals such as dogs, cats, pigs, cows, birds, and bats that are often in contact with humans. Materials and Methods: A total of 157 samples, which included nasopharyngeal and oropharyngeal swabs, along with sera samples from domestic animals such as cats, pigs, cows, birds, and bats, were taken from Veterinary Hospitals, Veterinary Clinics, and farms around the Yogyakarta region. Detection of the virus was done using rapid detection of viral antigens, antibodies, and reverse transcriptase-polymerase chain reaction (RT-PCR) technique. Results: The results showed that 5/157 (3.1%) samples found positive against the COVID-19 virus using a rapid antibody test; however, the results were negative on the rapid antigen and RT-PCR tests. Antibody-positive samples came from animals that had a history of household COVID-19 human infection. Conclusion: Thus, findings of the present study conclude that there is a potential for transmission of the COVID-19 virus between animals and humans.

Genomic and proteomic characterization of Philadelphia-like B-lineage acute lymphoblastic leukemia: A report of Indian patients.

BACKGROUND: The gold standard for the identification of Philadelphia (Ph)-like acute lymphoblastic leukemia (ALL) patients is gene expression profiling. Because of its diverse nature, its identification is extremely difficult and expensive. On the genomic and proteomic landscape of Ph-like ALL patients, there is a paucity of published literature from developing countries. METHODS: The authors used digital barcoded nCounter NanoString gene expression profiling for its detection, followed by molecular and proteomic characterization using fluorescence in situ hybridization and liquid chromatography-tandem mass spectrometry (LC-MS/MS). RESULTS: The authors found 32.05% Ph-like ALL patients and their median age at presentation was considerably higher than Ph-negative ALL cases (p = .0306). Furthermore, we identified 20% CRLF2 overexpressed cases having 8.33% CRLF2-IGH translocation with concomitant R683S mutation and 8.33% CRLF2-P2RY8 translocation. In 80% of CRLF2 downregulated cases, we identified 10% as having JAK2 rearrangement. Minimal residual disease-positivity was more common in Ph-like ALL cases (55.55% vs. 25% in Ph-negative ALL cases). Immunoglobulin J chain (Jchain), small nuclear ribonucleoprotein SmD1 (SNRPD1), immunoglobulin κ constant (IGKC), NADH dehydrogenase (ubiquinone) 1 α subcomplex subunit 2 (NDUFA2), histone H2AX (H2AFX), charged multivesicular body protein 4b (CHMP4B), and carbonyl reductase (NADPH) (CBR1) proteins were identified to be substantially expressed in Ph-like ALL patients, using LC-MS/MS. Gene enrichment analysis indicated that involvement of spliceosomal mediated messenger RNA splicing pathway and four microRNAs was statistically significant in Ph-like ALL patients. CONCLUSIONS: For the first time, we have described incidence, molecular, and proteomic characterization of Ph-like ALL, in developing nations. PLAIN LANGUAGE SUMMARY: In developing countries, detecting Philadelphia (Ph)-like B-lineage acute lymphoblastic leukemia is complicated and challenging due to its diverse genetic landscape. There is no well-defined and cost-effective methodology for its detection. The incidence of this high-risk subtype is very high in adult cases, and there is an urgent need for its accurate detection. We have developed an online PHi-RACE classifier for its rapid detection, followed by delineating the genomic and proteomic landscape of Ph-like acute lymphoblastic leukemias for the first time in Indian patients.

Dengue Burden and Circulation of Dengue-2 Serotype Among Children Along With Clinical Profiling in Uttarakhand, India: A Cross-Sectional Study From 2018 to 2020.

BACKGROUND: The multiple serotypes of the dengue virus (DENV) are always a major public concern for dengue haemorrhagic fever (DHF) and dengue shock syndrome (DSS). OBJECTIVE: This study aimed to analyse the demographic characteristics and circulating serotypes of dengue among the paediatric age group. METHODOLOGY: One hundred forty-one clinically suspected children were enrolled in the study from 2018 to 2020 in a tertiary care hospital in Uttarakhand, India. Central tendency, frequency, and One-Way ANOVA were measured for continuous and categorical data. The Shapiro-Wilks test was used to calculate the normality assumption. Dengue NS1 Ag, IgM, and IgG antibodies ELISA were performed, and NS1-positive samples were further tested for molecular studies. RESULT: From one hundred forty-one suspected cases, 100 (70.92%) came positive for dengue NS1 antigen, 18 (12.76%), and three (2.12%) came positive for IgM and IgG antibodies respectively. Rest 20 (14.18%) samples came negative for dengue. Fever with chills (97.5%), headache (89%), and arthralgia (82%) were the most common clinical features. Molecular studies showed the dengue serotype-2 (DEN-2) was found in most cases, followed by the dengue-3 serotype (DEN-3). CONCLUSION: This is the preliminary study as the authors' best knowledge which demonstrate the burden of dengue in children with prevalent serotypes for consecutive three years in Uttarakhand. This study identifies that the serotype-2 (DEN-2) of the dengue virus was the primary cause of infection in children at the tertiary care hospital in northern India. These results will help further to understand the nature of the disease so that improved patient care management will imply. Further molecular studies on large sample sizes during the endemic would be helpful to gain knowledge of the actual load of the disease and the genetic characteristics of the virus.