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Introduction: This study aimed to perform mutation and phylogenetic analyses of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Delta variants and analyze the characteristic signs and symptoms of patients infected with SARS-CoV-2 Delta variant originated from Makassar during the Delta outbreak.Methods: We collected samples from patients who were infected with coronavirus disease 2019 (COVID-19) between June and October 2021. We selected the Quantitative Reverse Transcription-Polymerase Chain Reaction (PCR)-positive samples with a cycle threshold value of <30 for whole genome sequencing. Total viral ribonucleic acid (RNA) was isolated from 34 PCR-positive nasopharyngeal swab samples, and whole genome sequencing was performed using the Oxford Nanopore GridlON sequencer. Phylogenetic and maximum clade credibility analyses were performed using the Bayesian Markov chain Monte Carlo method. Results: It was found that 33 patients were infected with the SARS-CoV-2 Delta variant in this cohort study, among whom 63.6% (21) patients were female. According to the clinical data, 24 (72.7%), 7 (21.2%), and 2 (6.1%) patients had mild, moderate, and severe COVID-19 infections. Phylogenetic analysis based on the spike and RNA-dependent RNA polymerase (RdRp) genes showed that the collected samples were clustered in the main lineage of B.1.617.2 (Delta variant). The Delta variants had a high frequency of distinct mutations in the spike protein region, including T19R (94.12%), L452R (88.23%), T478K (91.17%), D614G (97%), P681R (97%), and D950 N (97%). Other unique mutations found in a smaller frequency in our samples were present in the N-terminal domain, including A27T (2.94%) and A222V (14.70%), and in the receptor-binding domain, including Q414K (5.88%), G446V (2.94%), and T470 N (2.94%). Conclusion: This study revealed the unique mutations in the S protein region of Delta variants. T19R, L452R, T478K/T478R, D614G, P681R, and D950 N were the most common substitutions in Makassar's Delta variant.
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Introduction: A global surge in SARS-CoV-2 cases is occurring due to the emergence of new disease variants, and requires continuous adjustment of public health measures. This study aims to continuously monitor and mitigate the impact of SARS-CoV-2 through genomic surveillance, to determine the emergence of variants and their impact on public health. Methods: Data were collected from 50 full-genome sequences of SARS-CoV-2 isolates from Makassar, South Sulawesi, Indonesia. Mutation and phylogenetic analysis was performed of SARS-CoV-2 from Makassar, South Sulawesi, Indonesia. Results: Phylogenetic analysis showed that two samples (4%) were of the B.1.319 lineage, while the others (96%) were of the B.1.466.2 lineage. Mutation analysis of the spike (S) protein region showed that the most common mutation was D614G (found in 100% of the sequenced isolates), followed by N439K (98%) and P681R (76%). Several mutations were also identified in other genomes with a high frequency, including P323L (nsp12), Q57H (ns3-orf3a), and T205I (nucleoprotein). Conclusion: Our findings highlight the importance of continuous genomic surveillance to identify new viral mutations and variants with possible impacts on public health.
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INTRODUCTION AND OBJECTIVES: Common laboratory parameters are crucial in aiding coronavirus disease 2019 (COVID-19) case detection. This study aimed to determine the differences between laboratory parameters in (1) COVID-19 versus non-COVID-19 pneumonia, and (2) severe versus non-severe COVID-19 cases. METHODS: Studies were collected until March 2020, and retrieved parameters include leukocyte, neutrophil, thrombocyte, and lymphocyte counts in addition to C-reactive protein (CRP), procalcitonin (PCT) and D-dimer levels. In the presence of heterogeneity, the random-effect model (REM) was used instead of the fixed-effect model (FEM). RESULTS: Seven studies in the first analysis showed significantly lower leukocyte, neutrophil and platelet counts in COVID-19 pneumonia (SMD = -0.42, 95%CI -0.60 to -0.25, p < 0.00001, SMD = -0.23, 95%CI -0.41 to -0.06, p = 0.01, SMD = -0.54, 95%CI -0.91 to -0.16, p = 0.0005) compared to non-COVID-19 pneumonia. Twenty-six studies in the second analysis showed significantly lower lymphocyte and thrombocyte counts (SMD = -0.56, 95%CI -0.71 to -0.40, p < 0.0001, SMD = -0.32, 95%CI -0.49 to -0.15, p = 0.0002) and significantly higher leukocyte, neutrophil, D-dimer, and CRP (SMD = 0.31, 95%CI 0.07-0.56, p = 0.01; SMD = 0.44, 95%CI 0.24-0.64, p < 0.0001; SMD = 0.53, 95%CI 0.31-0.75, p < 0.00001; SMD = 0.97, 95%CI 0.70-1.24, p < 0.00001) in severe COVID-19 compared to non-severe COVID-19. CONCLUSIONS: In conclusion, thrombocyte count is key in both diagnosis and prognosis. Low leukocyte and neutrophil counts are markers of COVID-19 infection, but contrastingly higher counts indicate progressive COVID-19. And although lymphocyte, D-dimer and CRP levels did not demonstrate diagnostic value, all indicate severity of COVID-19. Confirmation of these findings should be performed in future studies.
INTRODUCCIÓN Y OBJETIVOS: Los parámetros comunes de laboratorio son cruciales para ayudar a la detección de casos de enfermedad por coronavirus 2019 (COVID-19). Este estudio tuvo como objetivo determinar las diferencias entre los parámetros de laboratorio en: 1) COVID-19 versus neumonía no COVID-19, y 2) Casos severos versus no severos de COVID-19. MÉTODOS: Los estudios se recolectaron hasta marzo de 2020, y los parámetros recuperados incluyen recuentos de leucocitos, neutrófilos, trombocitos y linfocitos además de los niveles de proteína C reactiva (PCR), procalcitonina (PCT) y dímero-D. En presencia de heterogeneidad, se utilizó el modelo de efectos aleatorios en lugar del modelo de efectos fijos. RESULTADOS: Siete estudios en el primer análisis mostraron recuentos de leucocitos, neutrófilos y plaquetas significativamente más bajos en la neumonía por COVID-19 (SMD = −0,42; IC 95%: −0,60 a −0,25; p < 0,00001; SMD = −0,23; IC 95%: −0,41 a −0,06; p = 0,01; SMD = −0,54; IC 95%: −0,91 a −0,16; p = 0,0005) en comparación con la neumonía no COVID-19. Veintiséis estudios en el segundo análisis mostraron recuentos de linfocitos y trombocitos significativamente más bajos (SMD = −0,56; IC 95%: −0,71 a −0,40; p < 0,0001; SMD = −0,32; IC 95%: −0,49 a −0,15; p = 0,0002) y leucocitos, neutrófilos, dímero D y PCR significativamente más altos (SMD = 0,31; IC 95%: 0,07-0,56; p = 0,01; SMD = 0,44; IC 95%: 0,24-0,64; p < 0,0001; SMD = 0,53; IC 95%: 0,31-0,75; p < 0,00001; SMD = 0,97; IC 95%: 0,70-1,24; p < 0,00001) en COVID-19 severo en comparación con COVID-19 no severo. CONCLUSIONES: En conclusión, el recuento de trombocitos es clave tanto en el diagnóstico como en el pronóstico. Los recuentos bajos de leucocitos y neutrófilos son marcadores de infección por COVID-19, pero los recuentos contrastantemente más altos indican COVID-19 progresivo. Y aunque los niveles de linfocitos, dímero D y PCR no mostraron valor diagnóstico, todos indican la gravedad de COVID-19. La confirmación de estos hallazgos debe realizarse en futuros estudios.
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OBJECTIVE: To compare the accuracy parameters of seven commercial molecular in vitro diagnostic tests for detecting SARS-CoV-2. METHODS: Studies evaluating the accuracy of seven different commercial molecular diagnostic tests for detecting SARS-CoV-2 (Cepheid Xpert Xpress SARS-CoV-2 test, Simplexa COVID-19 Direct, Abbott ID NOW COVID-19, Cobas SARS-CoV-2, Allplex 2019-nCoV Assay, Panther Fusion SARS-CoV-2, and BioFire COVID-19 Test) were included. The quality of the included studies was assessed using the QUADAS-2 checklist. A bivariate random-effects regression model was implemented. RESULTS: Meta-analysis of 12 included studies showed that the performances of commercial COVID-19 molecular in vitro diagnostic tests were high, with a summary sensitivity of 95.9% (95% CI 93.9-97.2%, I2 = 60.22%) and specificity of 97.2% (95% CI 95.5-98.3%, I2 = 56.66%). Among seven evaluated tests, the Abbott ID NOW COVID-19 and Simplexa COVID-19 Direct displayed lower sensitivity (91.6%, 95% CI 80.5-96.6% and 92%, 95% CI 86.2-95.5, respectively). CONCLUSION: All evaluated tests showed good accuracy. However, the slightly lower sensitivity observed in the Abbott ID Now COVID-19 and Simplexa COVID-19 Direct should be considered when deciding on a test platform. Moreover, the diagnostic accuracy of COVID-19 commercial diagnostic tests should be weighed against their ease of use and speed.
Subject(s)
COVID-19 Testing , COVID-19/diagnosis , SARS-CoV-2 , Humans , Sensitivity and SpecificitySubject(s)
Antibodies, Monoclonal, Humanized/therapeutic use , COVID-19 Drug Treatment , COVID-19/therapy , Interleukin-6/genetics , Polymorphism, Single Nucleotide , Promoter Regions, Genetic/genetics , Receptors, Interleukin-6/antagonists & inhibitors , SARS-CoV-2 , Adult , Antiviral Agents/therapeutic use , C-Reactive Protein/analysis , Case-Control Studies , Clinical Trials as Topic , Combined Modality Therapy , Female , Humans , Interleukin-6/physiology , Male , Middle Aged , Polymorphism, Genetic , Respiration, ArtificialABSTRACT
INTRODUCTION AND OBJECTIVES: Common laboratory parameters are crucial in aiding coronavirus disease 2019 (COVID-19) case detection. This study aimed to determine the differences between laboratory parameters in (1) COVID-19 versus non-COVID-19 pneumonia, and (2) severe versus non-severe COVID-19 cases. METHODS: Studies were collected until March 2020, and retrieved parameters include leukocyte, neutrophil, thrombocyte, and lymphocyte counts in addition to C-reactive protein (CRP), procalcitonin (PCT) and D-dimer levels. In the presence of heterogeneity, the random-effect model (REM) was used instead of the fixed-effect model (FEM). RESULTS: Seven studies in the first analysis showed significantly lower leukocyte, neutrophil and platelet counts in COVID-19 pneumonia (SMD=-0.42, 95%CI -0.60 to -0.25, p<0.00001, SMD=-0.23, 95%CI -0.41 to -0.06, p=0.01, SMD=-0.54, 95%CI -0.91 to -0.16, p=0.0005) compared to non-COVID-19 pneumonia. Twenty-six studies in the second analysis showed significantly lower lymphocyte and thrombocyte counts (SMD=-0.56, 95%CI -0.71 to -0.40, p<0.0001, SMD=-0.32, 95%CI -0.49 to -0.15, p=0.0002) and significantly higher leukocyte, neutrophil, D-dimer, and CRP (SMD=0.31, 95%CI 0.07-0.56, p=0.01; SMD=0.44, 95%CI 0.24-0.64, p<0.0001; SMD=0.53, 95%CI 0.31-0.75, p<0.00001; SMD=0.97, 95%CI 0.70-1.24, p<0.00001) in severe COVID-19 compared to non-severe COVID-19. CONCLUSIONS: In conclusion, thrombocyte count is key in both diagnosis and prognosis. Low leukocyte and neutrophil counts are markers of COVID-19 infection, but contrastingly higher counts indicate progressive COVID-19. And although lymphocyte, D-dimer and CRP levels did not demonstrate diagnostic value, all indicate severity of COVID-19. Confirmation of these findings should be performed in future studies.