Analysis of COVID-19-Related RT-qPCR Test Results in Hungary: Epidemiology, Diagnostics, and Clinical Outcome

Signs and symptoms to determine if a patient presenting in primary care or hospital outpatient settings has COVID-19

BACKGROUND

COVID-19 illness is highly variable, ranging from infection with no symptoms through to pneumonia and life-threatening consequences. Symptoms such as fever, cough, or loss of sense of smell (anosmia) or taste (ageusia), can help flag early on if the disease is present. Such information could be used either to rule out COVID-19 disease, or to identify people who need to go for COVID-19 diagnostic tests. This is the second update of this review, which was first published in 2020.

OBJECTIVES

To assess the diagnostic accuracy of signs and symptoms to determine if a person presenting in primary care or to hospital outpatient settings, such as the emergency department or dedicated COVID-19 clinics, has COVID-19.

SEARCH METHODS

We undertook electronic searches up to 10 June 2021 in the University of Bern living search database. In addition, we checked repositories of COVID-19 publications. We used artificial intelligence text analysis to conduct an initial classification of documents. We did not apply any language restrictions.

SELECTION CRITERIA

Studies were eligible if they included people with clinically suspected COVID-19, or recruited known cases with COVID-19 and also controls without COVID-19 from a single-gate cohort. Studies were eligible when they recruited people presenting to primary care or hospital outpatient settings. Studies that included people who contracted SARS-CoV-2 infection while admitted to hospital were not eligible. The minimum eligible sample size of studies was 10 participants. All signs and symptoms were eligible for this review, including individual signs and symptoms or combinations. We accepted a range of reference standards.

DATA COLLECTION AND ANALYSIS

Pairs of review authors independently selected all studies, at both title and abstract, and full-text stage. They resolved any disagreements by discussion with a third review author. Two review authors independently extracted data and assessed risk of bias using the QUADAS-2 checklist, and resolved disagreements by discussion with a third review author. Analyses were restricted to prospective studies only. We presented sensitivity and specificity in paired forest plots, in receiver operating characteristic (ROC) space and in dumbbell plots. We estimated summary parameters using a bivariate random-effects meta-analysis whenever five or more primary prospective studies were available, and whenever heterogeneity across studies was deemed acceptable.

MAIN RESULTS

We identified 90 studies; for this update we focused on the results of 42 prospective studies with 52,608 participants. Prevalence of COVID-19 disease varied from 3.7% to 60.6% with a median of 27.4%. Thirty-five studies were set in emergency departments or outpatient test centres (46,878 participants), three in primary care settings (1230 participants), two in a mixed population of in- and outpatients in a paediatric hospital setting (493 participants), and two overlapping studies in nursing homes (4007 participants). The studies did not clearly distinguish mild COVID-19 disease from COVID-19 pneumonia, so we present the results for both conditions together. Twelve studies had a high risk of bias for selection of participants because they used a high level of preselection to decide whether reverse transcription polymerase chain reaction (RT-PCR) testing was needed, or because they enrolled a non-consecutive sample, or because they excluded individuals while they were part of the study base. We rated 36 of the 42 studies as high risk of bias for the index tests because there was little or no detail on how, by whom and when, the symptoms were measured. For most studies, eligibility for testing was dependent on the local case definition and testing criteria that were in effect at the time of the study, meaning most people who were included in studies had already been referred to health services based on the symptoms that we are evaluating in this review. The applicability of the results of this review iteration improved in comparison with the previous reviews. This version has more studies of people presenting to ambulatory settings, which is where the majority of assessments for COVID-19 take place. Only three studies presented any data on children separately, and only one focused specifically on older adults. We found data on 96 symptoms or combinations of signs and symptoms. Evidence on individual signs as diagnostic tests was rarely reported, so this review reports mainly on the diagnostic value of symptoms. Results were highly variable across studies. Most had very low sensitivity and high specificity. RT-PCR was the most often used reference standard (40/42 studies). Only cough (11 studies) had a summary sensitivity above 50% (62.4%, 95% CI 50.6% to 72.9%)); its specificity was low (45.4%, 95% CI 33.5% to 57.9%)). Presence of fever had a sensitivity of 37.6% (95% CI 23.4% to 54.3%) and a specificity of 75.2% (95% CI 56.3% to 87.8%). The summary positive likelihood ratio of cough was 1.14 (95% CI 1.04 to 1.25) and that of fever 1.52 (95% CI 1.10 to 2.10). Sore throat had a summary positive likelihood ratio of 0.814 (95% CI 0.714 to 0.929), which means that its presence increases the probability of having an infectious disease other than COVID-19. Dyspnoea (12 studies) and fatigue (8 studies) had a sensitivity of 23.3% (95% CI 16.4% to 31.9%) and 40.2% (95% CI 19.4% to 65.1%) respectively. Their specificity was 75.7% (95% CI 65.2% to 83.9%) and 73.6% (95% CI 48.4% to 89.3%). The summary positive likelihood ratio of dyspnoea was 0.96 (95% CI 0.83 to 1.11) and that of fatigue 1.52 (95% CI 1.21 to 1.91), which means that the presence of fatigue slightly increases the probability of having COVID-19. Anosmia alone (7 studies), ageusia alone (5 studies), and anosmia or ageusia (6 studies) had summary sensitivities below 50% but summary specificities over 90%. Anosmia had a summary sensitivity of 26.4% (95% CI 13.8% to 44.6%) and a specificity of 94.2% (95% CI 90.6% to 96.5%). Ageusia had a summary sensitivity of 23.2% (95% CI 10.6% to 43.3%) and a specificity of 92.6% (95% CI 83.1% to 97.0%). Anosmia or ageusia had a summary sensitivity of 39.2% (95% CI 26.5% to 53.6%) and a specificity of 92.1% (95% CI 84.5% to 96.2%). The summary positive likelihood ratios of anosmia alone and anosmia or ageusia were 4.55 (95% CI 3.46 to 5.97) and 4.99 (95% CI 3.22 to 7.75) respectively, which is just below our arbitrary definition of a 'red flag', that is, a positive likelihood ratio of at least 5. The summary positive likelihood ratio of ageusia alone was 3.14 (95% CI 1.79 to 5.51). Twenty-four studies assessed combinations of different signs and symptoms, mostly combining olfactory symptoms. By combining symptoms with other information such as contact or travel history, age, gender, and a local recent case detection rate, some multivariable prediction scores reached a sensitivity as high as 90%.

AUTHORS' CONCLUSIONS

Most individual symptoms included in this review have poor diagnostic accuracy. Neither absence nor presence of symptoms are accurate enough to rule in or rule out the disease. The presence of anosmia or ageusia may be useful as a red flag for the presence of COVID-19. The presence of cough also supports further testing. There is currently no evidence to support further testing with PCR in any individuals presenting only with upper respiratory symptoms such as sore throat, coryza or rhinorrhoea. Combinations of symptoms with other readily available information such as contact or travel history, or the local recent case detection rate may prove more useful and should be further investigated in an unselected population presenting to primary care or hospital outpatient settings. The diagnostic accuracy of symptoms for COVID-19 is moderate to low and any testing strategy using symptoms as selection mechanism will result in both large numbers of missed cases and large numbers of people requiring testing. Which one of these is minimised, is determined by the goal of COVID-19 testing strategies, that is, controlling the epidemic by isolating every possible case versus identifying those with clinically important disease so that they can be monitored or treated to optimise their prognosis. The former will require a testing strategy that uses very few symptoms as entry criterion for testing, the latter could focus on more specific symptoms such as fever and anosmia.

The Value of Early Positive Nucleic Acid Test and Negative Conversion Time of SARS-CoV-2 RNA in the Clinical Outcome of COVID-19 Patients

Background

The outbreak of coronavirus disease (COVID-19) poses a great threat to global public health. At present, the number of newly confirmed COVID-19 cases and deaths is increasing worldwide. The strategy of comprehensive and scientific detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through quantitative real-time polymerase chain reaction (qRT-PCR) for special populations and environments provides great support for the prevention and control of this pandemic in China. Our study focused on determining the factors associated with the length of time from symptom onset to the first positive nucleic acid test of throat swabs in COVID-19 patients, evaluating the effect of early positive nucleic acid detection on the disease severity and its significance in prognosis, and predicting the factors associated with the time from positive SARS-CoV-2 RNA test to negative conversion (negative conversion of SARS-CoV-2 virus) in COVID-19 patients.

Methods

This study included 116 hospitalized patients with COVID-19 from January 30, 2020 to March 4, 2020 in Wuhan, China. Throat swab samples were collected for qRT-PCR testing of SARS-CoV-2 RNA, and all patients included in this study were positive for this test.

Results

The multivariate Cox proportional hazards model showed that disease severity (HR = 0.572; 95% CI 0.348–0.942; p = 0.028) was a protective factor for the time from symptom onset to positive nucleic acid detection. Meanwhile, the time from symptom onset to positive nucleic acid detection (HR = 1.010; 95% CI 1.005–1.020; p = 0.0282) was an independent risk factor for the delay in negative conversion time of SARS-CoV-2 virus. However, the severity of the disease (HR=1.120; 95% CI 0.771–1.640; p = 0.544) had no correlation with the negative conversion time of SARS-CoV-2 virus.

Conclusions

Patients with more severe disease had a shorter time from symptom onset to a positive nucleic acid test. Prolonged time from symptom onset to positive nucleic acid test was an independent risk factor for the delay in negative conversion time of SARS-CoV-2 virus, and the severity of the disease had no correlation with negative conversion time of SARS-CoV-2 virus.

Monitoring of anti-SARS-CoV-2 IgG antibody immune responses in two cohorts of Hungarian healthcare workers following infection or immunization

Összefoglaló. Bevezetés: A SARS-CoV-2-fertőzések és az anti-SARS-CoV-2-vakcinák által kiváltott immunvédelem tartóssága, nagysága és különbségeinek háttere nem teljesen tisztázott, az oltási protokollok optimális időzítése vitatott. Célkitűzés: A humorális immunválaszok nagyságát, időbeli változását, a reinfekciók gyakoriságát, demográfiai és klinikai paraméterekkel való összefüggését vizsgáltuk magyarországi egészségügyi dolgozóknál. Módszerek: Megyei egyetemi oktató kórházunkban prospektív, longitudinális vizsgálatot végeztünk egészségügyi dolgozók két csoportjában. 1. kohorsz: SARS-CoV-2-fertőzésen átesett, oltatlan 42 dolgozó (nő: 100%) antinukleokapszid-IgG-szintjét mértük 8 hónapon keresztül (2020. június-2021. február). Az immunválasznak a változását és az életkorral, a krónikus betegségekkel, a vércsoporttal és a tünetek súlyosságával való összefüggését vizsgáltuk. 2. kohorsz: két dózis mRNS-vakcinával (Pfizer-BioNTech) végzett immunizálást követően, fertőzésnaiv 49 dolgozó (nő: 73%) anti-spike-RBD-protein-IgG-szintjét monitoroztuk 8 hónapig (2020. december-2021. augusztus). Medián analízis, lineáris regresszió, ANCOVA, Kruskal-Wallis- és Skillings-Mack-teszt-elemzéseket végeztünk. Eredmények: 1. kohorsz: az IgG-szintek átlagosan a betegség 4-es súlyossági kategóriájában voltak a legmagasabbak, a negatív tartományba csökkenés medián ideje 6 hónap volt. 2. kohorsz: a második vakcina hatására az IgG-szint a 25-szörösére nőtt, majd 210 nap után a csúcsszint 6%-ra csökkent. Az ellenanyagtiter negatív összefüggést mutatott az idősebb életkorral és a férfinemmel. Tünetmentes (újra)fertőződést valószínűsítettünk a fertőzésen átesettek 17%-ánál és az immunizált kohorsz 14%-ánál. Az érintettek magas kockázatú osztályokon dolgoztak. Következtetés: 6 hónap után mind a fertőzésen átesettek, mind az immunizáltak jelentősen csökkenő IgG-védelmet mutattak. A (re)infekciók átlagosan 15%-ban, tünetmentesen zajlottak. Az eredmények megerősítik az oltás hatékonyságát a betegség megelőzésében, a harmadik emlékeztető vakcina fontosságát 6 hónap után és az anti-SARS-CoV-2-IgG-monitorozás potenciális értékét. Orv Hetil. 2022; 163(12): 455-462.

SUMMARY

INTRODUCTION

The length, level and variation of immune responses to infection with SARS-CoV-2 or following anti-SARS-CoV-2 vaccination remains unclear, optimal (re)vaccination protocols remain debated.

OBJECTIVE

We investigated the magnitude of humoral immune responses, their over-time changes, the frequency of (re)infections and the association with demographic and clinical parameters in Hungarian healthcare workers.

METHODS

We conducted a prospective, longitudinal study in two groups of healthcare workers of a public, county-level teaching hospital. Cohort 1: The anti-nucleocapsid IgG levels of 42 workers (female: 100%) were followed up over 8 months after SARS-CoV-2 infection (June 2020-February 2021). The change in humoral immune response and its associations with age, existing chronic conditions, blood type and severity of symptoms were investigated. Cohort 2: The anti-spike-RBD protein IgG levels of 49 workers (female: 73%) with no prior COVID-19 infection were monitored over 8 months (December 2020-August 2021) following immunisation with two doses of mRNA vaccine (Pfizer-BioNTech). Analyses included median analysis, linear regression, ANCOVA, Kruskal-Wallis and Skilling-Mack tests.

RESULTS

Cohort 1: IgG levels were on average the highest among those in illness severity category 4, the median time of IgG level reduction below the positive test cut-off was 6 months. Cohort 2: The IgG levels increased 25-fold between the first and second immunisations, but decreased to 6% of the peak level after 210 days. They showed an overall negative association with older age and male sex. The suspected levels of (re)infections were 17% and 14% within the infected and the immunised cohorts, respectively, all symptomless. Those affected all worked on high-risk wards.

CONCLUSION

Both the infected and the immunised cohorts showed significantly declining IgG protections beyond 6 months. The average observed rate of (re)infections was 15%, all asymptomatic. Our findings are confirmative of the effectiveness of vaccination to prevent illness, the importance of booster vaccination due to declining humoral immune protection beyond 6 months, and the potential value of anti-SARS-CoV-2 IgG monitoring. Orv Hetil. 2022; 163(12): 455-462.

SARS-CoV-2 in Egypt: epidemiology, clinical characterization and bioinformatics analysis

COVID-19 is an infectious disease caused by SARS-CoV-2 and has spread globally, resulting in the ongoing coronavirus pandemic. The current study aimed to analyze the clinical and epidemiological features of COVID-19 in Egypt. Oropharyngeal swabs were collected from 197 suspected patients who were admitted to the Army Hospital and confirmation of the positivity was performed by rRT-PCR assay. Whole genomic sequencing was conducted using Illumina iSeq 100® System. The average age of the participants was 48 years, of which 132 (67%) were male. The main clinical symptoms were pneumonia (98%), fever (92%), and dry cough (66%). The results of the laboratory showed that lymphocytopenia (79.2%), decreased levels of haemoglobin (77.7%), increased levels of interleukin 6, C-reactive protein, serum ferritin, and D-dimer (77.2%, 55.3%, 55.3%, and 25.9%, respectively), and leukocytopenia (25.9%) were more common. The CT findings showed that scattered opacities (55.8%) and ground-glass appearance (27.9%) were frequently reported. The recovered validated sequences (n = 144) were submitted to NCBI Virus GenBank. All sequenced viruses have at least 99% identity to Wuhan-Hu-1. All variants were GH clade, B.1 PANGO lineage, and L.GP.YP.HT haplotype. The most predominant subclade was D614G/Q57H/V5F/G823S. Our findings have aided in a deep understanding of COVID-19 evolution and identifying strains with unique mutational patterns in Egypt.

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Isolation and clinical characterization of SARS-CoV-2 from Egyptian patients.

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Whole Genome Sequencing of recovered isolates revealed unique sequences.

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Egyptian SARS-CoV-2 variants in 2020 with at least 99% identity to Wuhan-Hu-1.

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Egyptian SARS-CoV-2 variants were GH clade and L.GP.YP.HT haplotype.

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A unique mutation (D614G/Q57H/V5F/G823S) pattern was predominant among SARS-CoV-2.

Evaluation of Anti-SARS-CoV-2 IgG Antibody in Healthcare Professionals Infected with COVID-19

Background: The knowledge of antibody’s significance and frequency in patients cured of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is extremely limited. Objectives: This study aimed to evaluate anti-SARS-CoV-2 IgG antibodies in patients exposed to SARS-CoV-2. Methods: Healthcare professionals infected with SARS-CoV-2 were enrolled in this study. The levels of anti-SARS-CoV-2 IgG antibodies were detected 15 days after the onset of symptoms and five months later. Results: A total of 167 patients with coronavirus disease 2019 (COVID-19) were evaluated, including 119 (71.3%) females and 48 (28.7%) males. Of the 88 polymerase chain reaction (PCR)-positive patients, 55 (62.5%) had IgG-positive antibodies, and of the 79 reverse transcriptase (RT)-PCR-negative patients, 12 (16.9%) had IgG-positive antibodies. Out of 23 anosmia cases, 19 (82.6%) had positive antibodies. There was a significant relationship between anosmia and positive antibody (P  =  0.001), but there was no correlation between antibody titers and gender and other disease symptoms. Immortally, 63 (94%) cases demonstrated high levels of anti-SARS-CoV-2 IgG antibodies after five months of infection. Moreover, 6.5% (N  =  11) of the total population were re-infected with COVID-19 six months later. Conclusions: Overall, anti-SARS-CoV-2 IgG antibodies detection may be an appropriate method to identify suspected patients with a negative RT-PCR test. Antibodies can remain high in most infected patients for up to five months after infection. Moreover, anosmia seems to be a valuable diagnostic factor, and the healthcare system should implement isolation measures for patients with anosmia.