The laboratory diagnostic strategy for human immunodeficiency virus (HIV) is a process to accurately detect HIV patients through a combination of available HIV tests. Laboratory tests for HIV infection are mainly serological antibody and antigen testing and HIV RNA testing. With the update of testing reagents, the sensitivity and specificity have improved substantially and the window period of detection has shortened, but there is a risk of false positives. Various guidelines have recommended different diagnostic strategies for different target populations and different prevalence regions to guide patients to confirm the diagnosis and receive standardized antiretroviral therapy as early as possible. How to refer to the diagnostic strategies, reduce false positives and shorten the window period while increasing the detection rate is an urgent issue for laboratories to address. This article describes the characteristics and advantages and disadvantages of testing methods related to HIV infection from the perspective of laboratory diagnostic strategies, as well as the impact of the development of treatments on diagnostic strategies, in order to provide theoretical support for the practical application of HIV diagnostic strategies.
Humans ; HIV ; HIV Infections/diagnosis* ; Sensitivity and Specificity ; Clinical Laboratory Techniques/methods* ; Quality Control

Hepatitis type E virus (HEV) infection is a common cause of acute viral hepatitis in China, and its etiological diagnosis relies on laboratory detection. Therefore, this article introduces the HEV RNA, HEV antigen, anti-HEV IgM, and IgG detection methods and their diagnostic application value. In addition, it also discusses the current international diagnostic standard and HEV infection presentation.
Humans ; RNA, Viral ; Hepatitis Antibodies ; Clinical Laboratory Techniques/methods* ; Hepatitis E virus ; Immunoglobulin M ; Hepatitis

In Taiwan, high-risk patients have been identified and tested for preventing community spread of COVID-19. Most sample collection was performed in emergency departments (EDs). Traditional sample collection requires substantial personal protective equipment (PPE), healthcare professionals, sanitation workers, and isolation space. To solve this problem, we established a multifunctional sample collection station (MSCS) for COVID-19 testing in front of our ED. The station is composed of a thick and clear acrylic board (2 cm), which completely separates the patient and medical personnel. Three pairs of gloves (length, 45 cm) are attached and fixed on the outside wall of the MSCS. The gloves are used to conduct sampling of throat/nasal swabs, sputum, and blood from patients. The gap between the board and the building is only 0.2 cm (sealed with silicone sealant). ED personnel communicate with patients using a small two-way broadcast system. Medical waste is put in specific trashcans installed in the table outside the MSCS. With full physical protection, the personnel conducting the sampling procedure need to wear only their N95 mask and gloves. After we activated the station, our PPE, sampling time, and sanitization resources were considerably conserved during the 4-week observation period. The MSCS obviously saved time and PPE. It elevated the efficiency and capacity of the ED for handling potential community infections of COVID-19.
Betacoronavirus ; Clinical Laboratory Techniques ; Coronavirus Infections ; diagnosis ; epidemiology ; Emergency Service, Hospital ; organization & administration ; Humans ; Mass Screening ; methods ; Pandemics ; Personal Protective Equipment ; supply & distribution ; Pneumonia, Viral ; diagnosis ; epidemiology ; Taiwan ; epidemiology

Aged ; Cholecystectomy, Laparoscopic ; methods ; Cholelithiasis ; complications ; diagnosis ; surgery ; Clinical Laboratory Techniques ; Coronavirus Infections ; complications ; diagnosis ; Elective Surgical Procedures ; methods ; Follow-Up Studies ; Humans ; Infection Control ; methods ; Male ; Pandemics ; Patient Safety ; Pneumonia, Viral ; complications ; diagnosis ; Postoperative Care ; methods ; Risk Assessment ; Singapore ; Treatment Outcome

Clinical Laboratory Techniques ; Coronavirus Infections ; diagnosis ; Hospitals, General ; Humans ; Pandemics ; Pneumonia, Viral ; diagnosis ; Singapore ; Virology ; methods

OBJECTIVE: To analyze the CT findings of patients with different clinical types of coronavirus disease 2019 (COVID-19). METHODS: A total of 67 patients diagnosed as COVID-19 by nucleic acid testing were included and divided into 4 groups according to the clinical staging based on . The CT imaging characteristics were analyzed among patients with different clinical types. RESULTS: Among 67 patients, 3 (4.5%) were mild cases, 35 (52.2%) were ordinary cases, 22 (32.8%) were severe cases, and 7 (10.4%) were critically ill. There were no abnormal CT findings in mild cases. In 35 ordinary cases, there were single lesions in 3 cases (8.6%) and multiple lesions in 33 cases (91.4%), while in severe case 1 case had single lesion (4.5%) and 21 had multiple lesions (95.5%). CT images of ordinary patients were mainly manifested as solid plaque shadow and halo sign (18/35, 51.4%); while fibrous strip shadow with ground glass shadow was more frequent in severe cases (7/22, 31.8%). Consolidation shadow as the main lesion was observed in 7 cases, and all of them were severe or critical ill patients. CONCLUSIONS CT images in patients with different clinical types of COVID-19 have characteristic manifestations, and solid shadow may predict severe and critical illness.
Betacoronavirus ; Clinical Laboratory Techniques ; Coronavirus Infections ; diagnosis ; diagnostic imaging ; Humans ; Lung ; diagnostic imaging ; pathology ; Pneumonia, Viral ; diagnostic imaging ; pathology ; Severity of Illness Index ; Tomography, X-Ray Computed ; methods

COVID-19 Nucleic Acid Testing/methods* ; Clinical Laboratory Techniques ; Containment of Biohazards ; Disinfection ; Environmental Monitoring ; Humans ; Nucleic Acids/isolation & purification* ; SARS-CoV-2/isolation & purification* ; Specimen Handling

OBJECTIVETo provide a feasible and cost-effective next-generation sequencing (NGS) method for accurate identification of viral pathogens in clinical specimens, because enormous limitations impede the clinical use of common NGS, such as high cost, complicated procedures, tremendous data analysis, and high background noise in clinical samples.

METHODSViruses from cell culture materials or clinical specimens were identified following an improved NGS procedure: reduction of background noise by sample preprocessing, viral enrichment by barcoded oligonucleotide (random hexamer or non-ribosomal hexanucleotide) primer-based amplification, fragmentation-free library construction and sequencing of one-tube mixtures, as well as rapid data analysis using an in-house pipeline.

RESULTSNGS data demonstrated that both barcoded primer sets were useful to simultaneously capture multiple viral pathogens in cell culture materials or clinical specimens and verified that hexanucleotide primers captured as many viral sequences as hexamers did. Moreover, direct testing of clinical specimens using this improved hexanucleotide primer-based NGS approach provided further detailed genotypes of enteroviruses causing hand, foot, and mouth disease (HFMD) and identified other potential viruses or differentiated misdiagnosis events.

CONCLUSIONThe improved barcoded oligonucleotide primer-based NGS approach is simplified, time saving, cost effective, and appropriate for direct identification of viral pathogens in clinical practice.

Clinical Laboratory Techniques ; DNA Barcoding, Taxonomic ; DNA Primers ; Enterovirus ; classification ; genetics ; isolation & purification ; Herpesvirus 4, Human ; genetics ; isolation & purification ; Humans ; Influenza B virus ; genetics ; isolation & purification ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; methods ; Sequence Analysis, RNA ; methods

BACKGROUNDThe accuracy of nasopharyngeal aspirate (NPA) specimens in detecting lower respiratory pathogens remains controversial. The objective of this study was to evaluate the diagnostic accuracy of aspirates (NPAs) specimen in lower respiratory tract infections (LRTIs) in children.

METHODSThe prospective study was designed to collect the data of paired NPAs and bronchoalveolar lavage fluids from children with acute LRTIs from January 2013 to December 2015. All specimens were subjected to pathogen detection: bacterial detection by culture, Mycoplasma pneumoniae (Mp) detection by polymerase chain reaction assay and virus (influenza A and B viruses, parainfluenza virus [PIV] Types 1 and 3, respiratory syncytial virus, and adenovirus) detection by immunofluorescence assay. The diagnostic accuracy analysis of NPAs was stratified by age ≤3 years (n = 194) and >3 years (n = 294).

RESULTSWe collected paired specimens from 488 children. The positive rate of pathogen was 61.6%. For Streptococcus pneumoniae, NPA culture had the specificity of 89.9% and negative predictive value of 100% in age ≤3 years, the specificity of 97.2% and negative predictive value of 98.9% in age >3 years. For Mp, the positive predictive values of NPA was 77.4% in children ≤3 years, and 89.1% in children >3 years. For PIV III, NPA specimen had the specificity of 99.8% and negative predictive value of 96.5% in children ≤3 years. For adenovirus, NPA had the specificity of 97.8% and negative predictive value of 98.4% in age ≤3 years, the specificity of 98.9% and negative predictive value of 99.3% in age >3 years.

CONCLUSIONSNPAs are less invasive diagnostic respiratory specimens, a negative NPA result is helpful in "rule out" lower airway infection; however, a positive result does not reliably "rule in" the presence of pathogens.

Acinetobacter baumannii ; isolation & purification ; pathogenicity ; Adolescent ; Child ; Child, Preschool ; Clinical Laboratory Techniques ; methods ; Enterobacter aerogenes ; isolation & purification ; pathogenicity ; Escherichia coli ; isolation & purification ; pathogenicity ; Female ; Haemophilus influenzae ; isolation & purification ; pathogenicity ; Humans ; Infant ; Male ; Nasopharynx ; microbiology ; Prospective Studies ; Pseudomonas aeruginosa ; isolation & purification ; pathogenicity ; Respiratory Tract Infections ; diagnosis ; microbiology ; Sensitivity and Specificity ; Staphylococcus aureus ; isolation & purification ; pathogenicity ; Streptococcus pneumoniae ; isolation & purification ; pathogenicity

BACKGROUND: It is crucial to understand the current status of clinical laboratory practices for the largest outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infections in the Republic of Korea to be well prepared for future emerging infectious diseases. METHODS: We conducted a survey of 49 clinical laboratories in medical institutions and referral medical laboratories. A short questionnaire to survey clinical laboratory practices relating to MERS-CoV diagnostic testing was sent by email to the directors and clinical pathologists in charge of the clinical laboratories performing MERS-CoV testing. The survey focused on testing volume, reporting of results, resources, and laboratory safety. RESULTS: A total of 40 clinical laboratories responded to the survey. A total of 27,009 MERS-CoV real-time reverse transcription PCR (rRT-PCR) tests were performed. Most of the specimens were sputum (73.5%). The median turnaround time (TAT) was 5.29 hr (first and third quartile, 4.11 and 7.48 hr) in 26 medical institutions. The median TAT of more than a half of the laboratories (57.7%) was less than 6 hr. Many laboratories were able to perform tests throughout the whole week. Laboratory biosafety preparedness included class II biosafety cabinets (100%); separated pre-PCR, PCR, and post-PCR rooms (88.6%); negative pressure pretreatment rooms (48.6%); and negative pressure sputum collection rooms (20.0%). CONCLUSIONS: Clinical laboratories were able to quickly expand their diagnostic capacity in response to the 2015 MERS-CoV outbreak. Our results show that clinical laboratories play an important role in the maintenance and enhancement of laboratory response in preparation for future emerging infections.
Clinical Laboratory Services/*standards ; Clinical Laboratory Techniques/instrumentation/methods ; Coronavirus Infections/*diagnosis/epidemiology/virology ; Disease Outbreaks ; Humans ; Middle East Respiratory Syndrome Coronavirus/genetics/isolation & purification ; RNA, Viral/analysis ; Real-Time Polymerase Chain Reaction ; Republic of Korea/epidemiology ; Sputum/virology ; Surveys and Questionnaires