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1.
Viruses ; 14(9)2022 09 13.
Article in English | MEDLINE | ID: covidwho-2033143

ABSTRACT

In late November 2021, the World Health Organization declared the SARS-CoV-2 lineage B.1.1.529 the fifth variant of concern, Omicron. This variant has acquired over 30 mutations in the spike protein (with 15 in the receptor-binding domain), raising concerns that Omicron could evade naturally acquired and vaccine-derived immunity. We utilized an authentic virus, multicycle neutralisation assay to demonstrate that sera collected one, three, and six months post-two doses of Pfizer-BioNTech BNT162b2 had a limited ability to neutralise SARS-CoV-2. However, four weeks after a third dose, neutralising antibody titres were boosted. Despite this increase, neutralising antibody titres were reduced fourfold for Omicron compared to lineage A.2.2 SARS-CoV-2.


Subject(s)
COVID-19 , Vaccines , Antibodies, Neutralizing , Antibodies, Viral , BNT162 Vaccine , COVID-19/prevention & control , COVID-19 Vaccines , Humans , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Viral Envelope Proteins/genetics
2.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-329890

ABSTRACT

Background: SARS-CoV-2 infection is associated with a significant risk of hospitalisation, death, and prolonged impact on quality of life. Evaluation of new treatment options and optimising therapeutic management of people hospitalised with SARS-CoV-2 infection remains essential, but rapid changes in pandemic conditions and potential therapies have limited the utility of traditional approaches to randomised controlled trials. Methods ASCOT ADAPT is an international, investigator-initiated, adaptive platform, randomised controlled trial of therapeutics for non-critically ill patients hospitalised with COVID-19. The study design is open label and pragmatic. Potential participants are hospitalised adults with PCR confirmed, symptomatic, SARS-CoV-2 infection, within 14 days of symptom onset. Domains include antiviral, antibody and anticoagulant interventions, with a composite primary outcome of 28-day mortality or progression to intensive-care level respiratory or haemodynamic support. Initial interventions include intravenous nafamostat and variable dose anticoagulation. A range of secondary endpoints, and substudies for specific domains and interventions are outlined. Discussion This paper presents the trial protocol and management structure, including international governance, remote site monitoring and biobanking activities, and provides commentary on ethical and pragmatic considerations in establishing the ASCOT ADAPT trial under pandemic conditions.

4.
Open Forum Infect Dis ; 9(3): ofac002, 2022 Mar.
Article in English | MEDLINE | ID: covidwho-1692167

ABSTRACT

BACKGROUND: As of mid-2021, Australia's only nationwide coronavirus disease 2019 (COVID-19) epidemic occurred in the first 6 months of the pandemic. Subsequently, there has been limited transmission in most states and territories. Understanding community spread during the first wave was hampered by initial limitations on testing and surveillance. To characterize the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific antibody seroprevalence generated during this time, we undertook Australia's largest national SARS-CoV-2 serosurvey. METHODS: Between June 19 and August 6, 2020, residual specimens were sampled from people undergoing general pathology testing (all ages), women attending antenatal screening (20-39 years), and blood donors (20-69 years) based on the Australian population's age and geographic distributions. Specimens were tested by Wantai total SARS-CoV-2-antibody assay. Seroprevalence estimates adjusted for test performance were produced. The SARS-CoV-2 antibody-positive specimens were characterized with microneutralization assays. RESULTS: Of 11 317 specimens (5132 general pathology; 2972 antenatal; 3213 blood-donors), 71 were positive for SARS-CoV-2-specific antibodies. Seroprevalence estimates were 0.47% (95% credible interval [CrI], 0.04%-0.89%), 0.25% (CrI, 0.03%-0.54%), and 0.23% (CrI, 0.04%-0.54%), respectively. No seropositive specimens had neutralizing antibodies. CONCLUSIONS: Australia's seroprevalence was extremely low (<0.5%) after the only national COVID-19 wave thus far. These data and the subsequent limited community transmission highlight the population's naivety to SARS-CoV-2 and the urgency of increasing vaccine-derived protection.

5.
Aust N Z J Public Health ; 45(6): 616-621, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1511266

ABSTRACT

INTRODUCTION: In May 2020, The Communicable Diseases Network of Australia (CDNA) case definition introduced serological criteria to support the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We present findings that support the utility of SARS-CoV-2-specific serology for public health investigations. METHODS: From 24 January to 31 July 2020, the following information was collected from individuals with positive SARS-CoV-2-specific immunofluorescence antibody tests: history of contact with COVID-19 cases; recent travel; symptoms consistent with COVID-19; and SARS-CoV-2 nucleic acid testing (NAT) results. Individuals were classified as confirmed or probable by CDNA criteria or additionally as possible (SARS-CoV-2-specific IgG positive with compatible symptoms or epidemiologic risk) or indeterminate (SARS-CoV-2-specific IgA/IgM positive only) cases. RESULTS: A total of 10,595 individuals were tested in the six-month period. Of these, 9.8% (1,037) individuals had positive SARS-CoV-2-specific serology of which 566 (53.6%) were NAT-confirmed COVID-19 cases and 286 (27.6%) were part of a cruise ship outbreak sero-survey. The remaining 185 individuals (NAT negative) were individually classified as serologically confirmed (4, 0.4%), probable (72, 6.9%) possible (66, 6.4%) and indeterminate (38, 3.7%) cases. Maternal antibody transfer was inferred in one infant and four were unclassified. CONCLUSION: SARS-CoV-2-specific serology is a key diagnostic tool for retrospective identification of COVID-19 infection. Implications for public health: SARS-CoV-2 specific serology can enhance the ability to find cases, link missing cases in clusters of infection and identify the epidemiological extent of SARS-CoV-2 outbreaks. A combination of epidemiological criteria, clinical criteria and a quantitative serological test can be used as an adjunct to classify SARS-CoV-2 cases. Our study confirms the low level of community transmission in NSW during the first year of the COVID-19 pandemic.


Subject(s)
COVID-19 , SARS-CoV-2 , Antibodies, Viral , COVID-19 Testing , Humans , Pandemics , Retrospective Studies
6.
Clin Infect Dis ; 73(9): e2952-e2959, 2021 11 02.
Article in English | MEDLINE | ID: covidwho-1501018

ABSTRACT

BACKGROUND: The detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA by reverse-transcription polymerase chain reaction (PCR) does not necessarily indicate shedding of infective virions. There are limited data on the correlation between the isolation of SARS-CoV-2, which likely indicates infectivity, and PCR. METHODS: A total of 195 patients with Coronavirus disease 2019 were tested (outpatients, n = 178; inpatients, n = 12; and critically unwell patients admitted to the intensive care unit [ICU] patients, n = 5). SARS-CoV-2 PCR-positive samples were cultured in Vero C1008 cells and inspected daily for cytopathic effect (CPE). SARS-CoV-2-induced CPE was confirmed by PCR of culture supernatant. Where no CPE was observed, PCR was performed on day 4 to confirm absence of virus replication. The cycle thresholds (Cts) of the day 4 PCR (Ctculture) and the PCR of the original clinical sample (Ctsample) were compared, and positive cultures were defined where Ctsample - Ctculture was ≥3. RESULTS: Of 234 samples collected, 228 (97%) were from the upper respiratory tract. SARS-CoV-2 was isolated from 56 (24%), including in 28 of 181 (15%), 19 of 42 (45%), and 9 of 11 samples (82%) collected from outpatients, inpatients, and ICU patients, respectively. All 56 samples had Ctsample ≤32; CPE was observed in 46 (20%). The mean duration from symptom onset to culture positivity was 4.5 days (range, 0-18). SARS-CoV-2 was significantly more likely to be isolated from samples collected from inpatients (P < .001) and ICU patients (P < .0001) compared with outpatients, and in samples with lower Ctsample. CONCLUSIONS: SARS-CoV-2 culture may be used as a surrogate marker for infectivity and inform de-isolation protocols.


Subject(s)
COVID-19 , Animals , Chlorocebus aethiops , Critical Care , Humans , Immunologic Tests , SARS-CoV-2 , Vero Cells
8.
Virus Evol ; 6(1): veaa027, 2020 Jan.
Article in English | MEDLINE | ID: covidwho-1388022

ABSTRACT

The SARS-CoV-2 epidemic has rapidly spread outside China with major outbreaks occurring in Italy, South Korea, and Iran. Phylogenetic analyses of whole-genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases.

9.
Open Forum Infect Dis ; 7(9): ofaa387, 2020 Sep.
Article in English | MEDLINE | ID: covidwho-1205747

ABSTRACT

BACKGROUND: Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific antibodies has become an important tool, complementing nucleic acid tests (NATs) for diagnosis and for determining the prevalence of coronavirus disease 2019 (COVID-19) in population serosurveys. The magnitude and persistence of antibody responses are critical for assessing the duration of immunity. METHODS: A SARS-CoV-2-specific immunofluorescent antibody (IFA) assay for immunoglobulin G (IgG), immunoglobulin A (IgA), and immunoglobulin M (IgM) was developed and prospectively evaluated by comparison to the reference standard of NAT on respiratory tract samples from individuals with suspected COVID-19. Neutralizing antibody responses were measured in a subset of samples using a standard microneutralization assay. RESULTS: A total of 2753 individuals were eligible for the study (126 NAT-positive; prevalence, 4.6%). The median "window period" from illness onset to appearance of antibodies (range) was 10.2 (5.8-14.4) days. The sensitivity and specificity of either SARS-CoV-2 IgG, IgA, or IgM when collected ≥14 days after symptom onset were 91.3% (95% CI, 84.9%-95.6%) and 98.9% (95% CI, 98.4%-99.3%), respectively. The negative predictive value was 99.6% (95% CI, 99.3%-99.8%). The positive predictive value of detecting any antibody class was 79.9% (95% CI, 73.3%-85.1%); this increased to 96.8% (95% CI, 90.7%-99.0%) for the combination of IgG and IgA. CONCLUSIONS: Measurement of SARS-CoV-2-specific antibody by IFA is an accurate method to diagnose COVID-19. Serological testing should be incorporated into diagnostic algorithms for SARS-CoV-2 infection to identify additional cases where NAT was not performed and resolve cases where false-negative and false-positive NATs are suspected. The majority of individuals develop robust antibody responses following infection, but the duration of these responses and implications for immunity remain to be established.

10.
J Clin Virol ; 138: 104797, 2021 05.
Article in English | MEDLINE | ID: covidwho-1152482

ABSTRACT

A total of 1080 individual patient samples (158 positive serology samples from confirmed, predominantly mildly symptomatic COVID-19 patients and 922 serology negative including 496 collected pre-COVID) from four states in Australia were analysed on four commercial SARS-CoV-2 serological assays targeting antibodies to different antigens (Roche Elecsys and Abbott Architect: nucleocapsid; Diasorin Liaison and Euroimmun: spike). A subset was compared to immunofluorescent antibody (IFA) and micro-neutralisation. Sensitivity and specificity of the Roche (n = 1033), Abbott (n = 806), Diasorin (n = 1034) and Euroimmun (n = 175) were 93.7 %/99.5 %, 90.2 %/99.4 %, 88.6 %/98.6 % and 91.3 %/98.8 %, respectively. ROC analysis with specificity held at 99 % increased the sensitivity for the Roche and Abbott assays from 93.7% to 98.7% (cut-off 0.21) and 90.2 % to 94.0 % (cut-off 0.91), respectively. Overall seropositivity of samples increased from a maximum of 23 % for samples 0-7 days-post-onset of symptoms (dpos), to 61 % from samples 8-14dpos and 93 % from those >14dpos. IFA and microneutralisation values correlated best with assays targeting antibodies to spike protein with values >80 AU/mL on the Diasorin assay associated with neutralising antibody. Detectable antibody was present in 22/23 (96 %), 20/23 (87 %), 15/23 (65 %) and 9/22 (41 %) patients with samples >180dpos on the Roche, Diasorin, Abbott and microneutralisation assays respectively. Given the low prevalence in this community, two-step algorithms on initial positive results saw an increase in the positive predictive value (PPV) of positive samples (39 %-65 % to ≥98 %) for all combinations. Similarly accuracy increased from a range of 98.5 %-99.4 % to ≥99.8 % assuming a 1 % seroprevalence. Negative predictive value (NPV) was high (≥99.8 %) regardless of which assay was used initially.


Subject(s)
Antibodies, Viral/blood , COVID-19 Serological Testing/methods , COVID-19/diagnosis , Reagent Kits, Diagnostic , Adolescent , Adult , Aged , Aged, 80 and over , Australia/epidemiology , COVID-19/epidemiology , Child , Coronavirus Nucleocapsid Proteins/immunology , Female , Humans , Immunoglobulin Isotypes/blood , Male , Middle Aged , Phosphoproteins/immunology , Prevalence , Sensitivity and Specificity , Seroepidemiologic Studies , Spike Glycoprotein, Coronavirus/immunology , Young Adult
11.
Pathology ; 52(7): 783-789, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-1043870

ABSTRACT

The aim of this study was to assess the analytic and clinical performance of four rapid lateral flow point-of-care tests (POCTs) for identifying SARS-CoV-2-specific antibodies. A retrospective study was conducted between 22 January and 30 March 2020 on 132 serum samples for SARS-CoV-2-specific antibody detection referred to a tertiary referral hospital laboratory in New South Wales. Multiple sera were tested from 20 confirmed or suspected COVID-19 patients with SARS-CoV-2-specific antibodies detected by immunofluorescence (IFA) or neutralisation, and 71 SARS-CoV-2 uninfected individuals. We measured the sensitivity and specificity for detection of SARS-CoV-2 IgM and IgG antibodies for each POCT in comparison to positive SARS-CoV-2-specific IFA and viral neutralisation, our current laboratory benchmark tests. All POCTs were found to have a low analytic sensitivity for SARS-CoV-2 antibodies, ranging from 27.3% to 58.2%, with a specificity between 88.3% and 100%, and a low clinical sensitivity from 45% to 65%, with a clinical specificity between 87.3% and 100%. All POCTs had an increased sensitivity when specimens were collected more than 14 days from onset of symptoms. The detection using point-of-care testing of SARS-CoV-2-specific antibodies after disease onset lagged behind IFA by a range of 0-9 days. POCTs promise the benefit of providing quick easy testing for SARS-CoV-2-specific antibodies. However, their poor sensitivity and delayed antibody detection make them unsuitable as a diagnostic or screening tool alone.


Subject(s)
Antibodies, Viral/blood , COVID-19 Serological Testing/methods , COVID-19/diagnosis , Point-of-Care Testing , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/blood , Child , Child, Preschool , Female , Humans , Male , Middle Aged , Retrospective Studies , SARS-CoV-2 , Sensitivity and Specificity , Young Adult
12.
Intern Med J ; 51(1): 42-51, 2021 01.
Article in English | MEDLINE | ID: covidwho-944728

ABSTRACT

BACKGROUND: On 31 December 2019, the World Health Organization recognised clusters of pneumonia-like cases due to a novel coronavirus disease (COVID-19). COVID-19 became a pandemic 71 days later. AIM: To report the clinical and epidemiological features, laboratory data and outcomes of the first group of 11 returned travellers with COVID-19 in Australia. METHODS: This is a retrospective, multi-centre case series. All patients with confirmed COVID-19 infection were admitted to tertiary referral hospitals in New South Wales, Queensland, Victoria and South Australia. RESULTS: The median age of the patient cohort was 42 years (interquartile range (IQR), 24-53 years) with six men and five women. Eight (72.7%) patients had returned from Wuhan, one from Shenzhen, one from Japan and one from Europe. Possible human-to-human transmission from close family contacts in gatherings overseas occurred in two cases. Symptoms on admission were fever, cough and sore throat (n = 9, 81.8%). Co-morbidities included hypertension (n = 3, 27.3%) and hypercholesterolaemia (n = 2, 18.2%). No patients developed severe acute respiratory distress nor required intensive care unit admission or mechanical ventilation. After a median hospital stay of 14.5 days (IQR, 6.75-21), all patients were discharged. CONCLUSIONS: This is a historical record of the first COVID-19 cases in Australia during the early biocontainment phase of the national response. These findings were invaluable for establishing early inpatient and outpatient COVID-19 models of care and informing the management of COVID-19 over time as the outbreak evolved. Future research should extend this Australian case series to examine global epidemiological variation of this novel infection.


Subject(s)
COVID-19/epidemiology , Adult , Australia/epidemiology , COVID-19/therapy , Female , Humans , Male , Middle Aged , Patient Discharge , Retrospective Studies , Tertiary Care Centers , Young Adult
13.
SSRN; 2020.
Preprint | SSRN | ID: ppcovidwho-1894

ABSTRACT

Background: School closures have occurred globally during the COVID-19 pandemic despite limited data on transmission among children and in educational setting

14.
Am J Infect Control ; 48(12): 1445-1450, 2020 12.
Article in English | MEDLINE | ID: covidwho-739727

ABSTRACT

BACKGROUND: Isolation and quarantine are key measures in outbreak management and disease control. They are, however, associated with negative patient experiences and outcomes, including an adverse impact on mental health and lower quality of care due to limited interaction with healthcare workers. In this study, we explore the lived experience and perceptions of patients in isolation with COVID-19 in an Australian healthcare setting. METHODS: Using a phenomenological approach from a Heideggerian hermeneutical perspective, we conducted individual semistructured interviews with the first 11 COVID-19 patients admitted to a designated COVID-19 facility in Australia. Interviews were audiorecorded, transcribed verbatim, and imported into NVivo 12 for coding and analysis. RESULTS: Participants' lived experience and perceptions of COVID-19 were represented by 5 themes: "Knowing about COVID-19," "Planning for, and responding to, COVID-19," "Being infected," "Life in isolation and the room," and "Post-discharge life." Within these, participants conveyed both positive and negative lived experiences of infection, isolation, and illness. The contextual aspects of their social and physical environment together with their individual resources contributed to the framing of their planning for, and response to, the outbreak, and were important mediators in their experience. CONCLUSIONS: Findings from this study provide a valuable insight into the lived experiences of patients with COVID-19, which reflect those of patients with other infectious diseases who require isolation.


Subject(s)
COVID-19/psychology , Patient Acceptance of Health Care/psychology , Patient Isolation/psychology , SARS-CoV-2 , Adult , Aged , Australia , Female , Humans , Male , Middle Aged , Perception , Qualitative Research
15.
Lancet Child Adolesc Health ; 4(11): 807-816, 2020 11.
Article in English | MEDLINE | ID: covidwho-692308

ABSTRACT

BACKGROUND: School closures have occurred globally during the COVID-19 pandemic. However, empiric data on transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among children and in educational settings are scarce. In Australia, most schools have remained open during the first epidemic wave, albeit with reduced student physical attendance at the epidemic peak. We examined SARS-CoV-2 transmission among children and staff in schools and early childhood education and care (ECEC) settings in the Australian state of New South Wales (NSW). METHODS: Laboratory-confirmed paediatric (aged ≤18 years) and adult COVID-19 cases who attended a school or ECEC setting while considered infectious (defined as 24 h before symptom onset based on national guidelines during the study period) in NSW from Jan 25 to April 10, 2020, were investigated for onward transmission. All identified school and ECEC settings close contacts were required to home quarantine for 14 days, and were monitored and offered SARS-CoV-2 nucleic acid testing if symptomatic. Enhanced investigations in selected educational settings included nucleic acid testing and SARS-CoV-2 antibody testing in symptomatic and asymptomatic contacts. Secondary attack rates were calculated and compared with state-wide COVID-19 rates. FINDINGS: 15 schools and ten ECEC settings had children (n=12) or adults (n=15) attend while infectious, with 1448 contacts monitored. Of these, 633 (43·7%) of 1448 had nucleic acid testing, or antibody testing, or both, with 18 secondary cases identified (attack rate 1·2%). Five secondary cases (three children; two adults) were identified (attack rate 0·5%; 5/914) in three schools. No secondary transmission occurred in nine of ten ECEC settings among 497 contacts. However, one outbreak in an ECEC setting involved transmission to six adults and seven children (attack rate 35·1%; 13/37). Across all settings, five (28·0%) of 18 secondary infections were asymptomatic (three infants [all aged 1 year], one adolescent [age 15 years], and one adult). INTERPRETATION: SARS-CoV-2 transmission rates were low in NSW educational settings during the first COVID-19 epidemic wave, consistent with mild infrequent disease in the 1·8 million child population. With effective case-contact testing and epidemic management strategies and associated small numbers of attendances while infected, children and teachers did not contribute significantly to COVID-19 transmission via attendance in educational settings. These findings could be used to inform modelling and public health policy regarding school closures during the COVID-19 pandemic. FUNDING: NSW Government Department of Health.


Subject(s)
Clinical Laboratory Techniques , Communicable Disease Control , Coronavirus Infections , Disease Transmission, Infectious , Pandemics , Pneumonia, Viral , Quarantine , School Health Services , Adolescent , Australia/epidemiology , Betacoronavirus/isolation & purification , COVID-19 , COVID-19 Testing , Child , Clinical Laboratory Techniques/methods , Clinical Laboratory Techniques/statistics & numerical data , Communicable Disease Control/methods , Communicable Disease Control/organization & administration , Coronavirus Infections/diagnosis , Coronavirus Infections/epidemiology , Coronavirus Infections/prevention & control , Disease Transmission, Infectious/prevention & control , Disease Transmission, Infectious/statistics & numerical data , Education, Distance/methods , Female , Humans , Male , Pandemics/prevention & control , Pneumonia, Viral/epidemiology , Pneumonia, Viral/prevention & control , Population , Quarantine/organization & administration , Quarantine/statistics & numerical data , SARS-CoV-2 , School Health Services/organization & administration , School Health Services/statistics & numerical data
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