Post COVID-19 condition among adults in Malaysia following the Omicron wave: A prospective cohort study

Post COVID-19 condition is an important public health problem as we emerge from the COVID-19 pandemic. In this prospective cohort study, we aimed to determine the prevalence of this condition and assess its associated factors and impact on health-related quality of life in a population setting in Malaysia. Study was conducted from April to June 2022 when the Omicron variant predominated. All individuals testing positive for SARS-CoV-2 infection (RT-PCR, RTK-Ag) were invited for participation. Study questionnaires were delivered via the MySejahtera platform (mobile application). From the total of 44,386 participants who provided responses up to 3-months interval, 1,510 participants (3.4%) fulfilled the post COVID-19 condition criteria. Majority of the affected participants (83.8%, n = 1,265) experienced either cough, fatigue or forgetfulness-the three most common symptoms. Being females, having existing comorbidities, presence of symptoms and requiring hospital admission during the acute illness were associated with higher likelihoods of developing the post COVID-19 condition at 3-months interval. Amongst the 1,510 individuals, one in five had limitations in performing their usual daily activities while at least one in three expressed that their work was affected. Understanding this condition better is essential to guide strategic and responsive plans of action, which may require coordinated multidisciplinary interventions.

Thrombocytopenia and venous thromboembolic events after BNT162b2, CoronaVac, ChAdOx1 vaccines and SARS-CoV-2 infection: a self-controlled case series study

This study assessed the association between COVID-19 vaccines, SARS-CoV-2 infection and the risk of thrombocytopenia and venous thromboembolism (VTE). This self-controlled case series study used hospital records between 1st February 2021 and 28th February 2022 linked to the national immunisation registry and COVID-19 surveillance data in Malaysia. Conditional Poisson regression was used to estimate incidence rate ratios (IRR) of events in the risk period (day 1-21 post-exposure) relative to control period with the corresponding 95% confidence interval (CI) adjusted for calendar period. We found no significant increased risk of thrombocytopenia in 1-21 days following BNT162b2, CoronaVac and ChAdOx1 vaccines while the risk was increased following SARS-CoV-2 infection (IRR 15.52, 95% CI 13.38-18.00). Similarly, vaccination with BNT162b2, CoronaVac, or ChAdOx1 was not associated with an increased risk of VTE during the 1-21 days risk period. SARS-CoV-2 infection was associated with increased risk of VTE (IRR 39.84, 95% CI 27.45-32.44). Our findings showed low event rates of thrombocytopenia and VTE following booster vaccination with comparable safety profiles between those who received homologous and heterologous booster combinations. Our findings showed the risk of thrombocytopenia and VTE was not increased after COVID-19 vaccination while the risks were substantially higher after SARS-CoV-2 infection.

Real-world nirmatrelvir-ritonavir outpatient treatment in reducing hospitalization for high-risk patients with COVID-19 during Omicron BA.4, BA.5 and XBB subvariants dominance in Malaysia: A retrospective cohort study

OBJECTIVE

To determine if nirmatrelvir-ritonavir 300mg/100mg treatment for 5 days in high-risk outpatients with mild to moderate COVID-19 symptoms was associated with a reduction in hospitalization, intensive care unit (ICU) admission, and death.

METHODS

This 1:1 propensity score matched cohort study from 647 public health clinics in Malaysia included all patients with COVID-19 with positive tests aged 18 years and older, who were eligible for nirmatrelvir-ritonavir treatment within 5 days of illness from July 14, 2022, to November 14, 2022. The exposed group was patients with COVID-19 initiated with nirmatrelvir-ritonavir treatment, whereas those not initiated with the drug served as the control group. Data was analyzed from July 14, 2022 to December 31, 2022.

RESULTS

A total of 20,966 COVID-19 high-risk outpatients (n = 10,483 for nirmatrelvir-ritonavir group and n = 10,483 for control group) were included in the study. Nirmatrelvir-ritonavir treatment was associated with a 36% reduction (adjusted hazard ratio 0.64 [95% CI 0.43, 0.94]) in hospitalization compared with those not given the drug. There was a single ICU admission for the control group and one death each was reported in the nirmatrelvir-ritonavir and control group, respectively.

CONCLUSIONS

Nirmatrelvir-ritonavir treatment was associated with reduced hospitalization in high-risk patients with COVID-19 even in highly vaccinated populations.

Myocarditis/pericarditis following vaccination with BNT162b2, CoronaVac, and ChAdOx1 among adolescent and adult in Malaysia

This study evaluates 21-day risk of myocarditis/pericarditis following COVID-19 vaccination among those aged 12 years and older in Malaysia. We used data from nationwide COVID-19 vaccine registry linked to hospital episode database to identify individuals vaccinated with BNT162b2, CoronaVac, or ChAdOx1 and hospitalised for myocarditis/pericarditis between 1 February 2021 and 28 February 2022. There were 87 myocarditis/pericarditis cases identified within 1-21 days after vaccination. Most cases were reported following BNT16262 vaccination (77.0%) with absolute risk of 0.33 cases/100,000 vaccinated persons or 1.73 per million doses administered. Highest risk was observed following second dose and in younger, male individuals. The risk of myocarditis/pericarditis following CoronaVac and ChAdOx1 were much lower compared to BNT162b2. The findings on higher risk observed among younger following mRNA vaccine were consistent with literature and important for targeted surveillance.

Time from last immunity event against infection during Omicron-dominant period in Malaysia

OBJECTIVES

To study the incidence of Omicron infections in Malaysia and the exposures that could reduce the hazard of attaining Omicron infection.

METHODS

We used a multicenter, prospective cohort to study 482 healthcare workers vaccinated with two and three doses of BNT162b2 for SARS-CoV-2 infection during the Omicron-dominant period in Malaysia.

RESULTS

Between January 31 and July 31, 2022, the cumulative incidence was 44.6% (95% CI 40.2-49.1%), and the incidence rate was 3.33 (95% CI 2.91-3.80) per 1000 person-days. Our study found that protection against Omicron infection was significantly higher for persons with previous SARS-CoV-2 infection (hazard ratio [HR] 0.41, 95% CI 0.27-0.62) and persons with a more recent immunity event (<30 days [reference] vs >90 days, HR 3.82, 95%CI 1.34-10.90) from the beginning of the Omicron period.

CONCLUSION

Pre-Omicron natural infection and a recent immunity event protect against future Omicron infections.

COVID-19 breakthrough infections and humoral immune response among BNT162b2 vaccinated healthcare workers in Malaysia

The evaluation of breakthrough infection and humoral immunity responses are important outcomes for vaccination policy for healthcare staff. This prospective cohort study collected blood samples at 5-time points; before primary vaccine doses, and at 2, 10 and 24 weeks after BNT162b2 vaccination from 551 HCWs, between March and October 2021. We investigated the association between anti-spike-1 protein receptor-binding domain (anti-S1-RBD) antibody geometric mean titre (GMT) and breakthrough infections. Two weeks post-vaccination, the GMT of anti-S1-RBD antibodies was measured at almost maximum detectable value (3115 BAU/ml [95% CI, 3051-3180]); it decreased to 1486 BAU/ml (95% CI, 1371-1610) at 10 weeks; and to 315 BAU/ml (95% CI, 283-349) at 24 weeks. Prior COVID-19 infection and age significantly affected the antibody titres. Fifty-six participants, none of whom were COVID-19 convalescents, had breakthrough infections between 10 and 24 weeks post-vaccination. Before breakthrough infections, the GMT was not different between the breakthrough and non-breakthrough individuals. After infection, the GMT was significantly higher in individuals with breakthrough infections (2038 BAU/ml [95%CI, 1547-2685]), specifically in symptomatic breakthroughs, compared to those without infection (254 BAU/ml [95%CI, 233-278]). A notable surge in breakthrough infections among healthcare workers coincided with the emergence of the Delta variant and when BNT162b2-elicited antibody responses waned in 10-24 weeks (i.e. approximately 3-6 months). Post-breakthrough, the antibody response was boosted in individuals with symptomatic presentations, but not asymptomatic individuals. The study finding supports administering booster vaccination for healthcare staff, including those who recovered from asymptomatic breakthrough infection.

Real-world effectiveness of homologous and heterologous BNT162b2, CoronaVac, and AZD1222 booster vaccination against Delta and Omicron SARS-CoV-2 infection

Given emerging evidence of immune escape in the SARS-CoV-2 Omicron viral variant, and its dominance, effectiveness of heterologous and homologous boosting schedules commonly used in low-to-middle income countries needs to be re-evaluated. We conducted a test-negative design using consolidated national administrative data in Malaysia to compare the effectiveness of homologous and heterologous BNT162b2, CoronaVac, and AZD1222 booster vaccination against SARS-CoV-2 infection in predominant-Delta and predominant-Omicron periods. Across both periods, homologous CoronaVac and AZD1222 boosting demonstrated lower effectiveness than heterologous boosting for CoronaVac and AZD1222 primary vaccination recipients and homologous BNT162b2 boosting. Broadly, marginal effectiveness was smaller by 40–50 percentage points in the Omicron period than the Delta period. Without effective and accessible second-generation vaccines, heterologous boosting using BNT162b2 for inactivated and vectored primary vaccination recipients is preferred.

Evaluation of BNT162b2 vaccine effectiveness in Malaysia: test negative case-control study

There is a notable lack of vaccine effectiveness studies using test-negative case-controlled approach in low- and middle-income countries which have different logistic, demographic and socio-economic conditions from high-income countries. We aimed to estimate the effectiveness of BNT162b2 vaccine against COVID-19 infection over time, intensive care unit admission, severe or critical disease and death due to COVID-19. This study was conducted in the resident population of Labuan aged ≥18 years who had been tested for SARS-CoV-2 by Reverse-Transcriptase Polymerase Chain Reaction between 1 March 2021 and 31 October 2021. We used a test-negative case-control design where 2644 pairs of cases and controls were matched by age, sex, testing date, nationality and testing reason. Analysis was stratified by age group to estimate age effect (<60 years and ≥60 years). Of 22217 individuals tested by Reverse-Transcriptase Polymerase Chain Reaction, 5100 were positive for SARS-CoV-2 and aged 18 years and above. Overall vaccine effectiveness ≥ 14 days after the second dose was 65.2% (95% CI: 59.8–69.9%) against COVID-19 infection, 92.5% (95% CI: 72.3–98.8%) against intensive care unit admission, and 96.5% (95% CI: 82.3–99.8%) against COVID-19 deaths. Among infected individuals, vaccine effectiveness was 79.2% (95% CI: 42.3–94.1%) in preventing severe or critical disease due to COVID-19. Vaccine effectiveness for ≥60 years was 72.3% (95% CI: 53.4–83.9%) in fully vaccinated individuals, higher than 64.8% (95% CI: 49.3–59.1%) for those <60 years. Two doses of BNT162b2 were highly effective against COVID-19 infection, severe or critical disease, intensive care unit admission and death due to COVID-19. This study addresses a gap in literature on BNT162b2 vaccine effectiveness in low- and middle-income populations and demonstrates the feasibility of such a study design in a resource limited setting while supporting evidence of waning immunity.

Clinical testing on SARS-CoV-2 swab samples using reverse-transcription loop-mediated isothermal amplification (RT-LAMP)

BACKGROUND

High cost of commercial RNA extraction kits limits the testing efficiency of SARS-CoV-2. Here, we developed a simple nucleic acid extraction method for the detection of SARS-CoV-2 directly from nasopharyngeal swab samples.

METHODS

A pH sensitive dye was used as the end point detection method. The obvious colour changes between positive and negative reactions eliminates the need of other equipment.

RESULTS

Clinical testing using 260 samples showed 92.7% sensitivity (95% CI 87.3-96.3%) and 93.6% specificity (95% CI 87.3-97.4%) of RT-LAMP.

CONCLUSIONS

The simple RNA extraction method minimizes the need for any extensive laboratory set-up. We suggest combining this simple nucleic acid extraction method and RT-LAMP technology as the point-of care diagnostic tool.

Assessment of Heterologous and Homologous Boosting With Inactivated COVID-19 Vaccine at 3 Months Compared With Homologous Boosting of BNT162b2 at 6 Months

IMPORTANCE

Evidence for the timing of booster vaccination after completion of BNT162b2 and CoronaVac primary vaccination is crucial to guide policy recommendations.

OBJECTIVE

To compare the odds of symptomatic SARS-CoV-2 infection and COVID-19-related outcomes after heterologous and homologous boosting of CoronaVac at 3-month intervals and homologous boosting of BNT162b2 at 6-month intervals, with BNT162b2 primary series (2 doses) as the reference group.

DESIGN, SETTING, AND PARTICIPANTS

This population-based retrospective cohort study used national data for Malaysia. Participants included all individuals aged 18 years and older who received a complete primary series of CoronaVac or BNT162b2 vaccine and were eligible for a booster dose between November 21, 2021, and December 28, 2021. Data were analyzed from November 21, 2021, to January 7, 2022.

EXPOSURES

Receipt of a booster vs no booster and categorized into primary series BNT162b2 (2 doses of BNT162b2), primary series CoronaVac (2 doses of CoronaVac), 3 doses of BNT162b2, primary series CoronaVac plus a BNT162b2 booster, and 3 doses of CoronaVac.

MAIN OUTCOMES AND MEASURES

The primary outcome was symptomatic SARS-CoV-2 infection. The secondary outcomes were COVID-19-related intensive care unit admission and death. All outcomes were observed from the day an individual was considered fully boosted (≥14 days after booster dose).

RESULTS

Our cohort included 13 840 240 individuals (mean [SD] age, 39.9 [15.5] years; 7 040 298 [50.9%] men; 4 451 180 individuals [32.2%] with ≥1 comorbidities), of whom 5 081 641 individuals (36.7%) had received a booster dose. Using the primary series BNT162b2 recipients as reference, the adjusted odds against symptomatic SAR-CoV-2 infection were lower for individuals who received the primary series CoronaVac plus a BNT162b2 (adjusted odds ratio [aOR], 0.06 [95% CI, 0.05-0.06]), 3 doses of CoronaVac (aOR, 0.08 [95% CI, 0.06-0.10]), or 3 doses of BNT162b2 (aOR, 0.01 [95% CI, 0.00-0.01]). Receipt of heterologous booster (primary series of CoronaVac plus a BNT162b2 booster) was associated with lower odds of SARS-CoV-2 infection (aOR, 0.17 [95% CI, 0.17-0.18]) compared with homologous booster (3 doses of CoronaVac) for individuals aged 60 years and older (aOR, 0.19 [95% CI, 0.19-0.20]).

CONCLUSIONS AND RELEVANCE

In this cohort study, for individuals who received the CoronaVac primary series and a booster dose of BNT162b2 or CoronaVac at 3 months, the observed odds of symptomatic SARS-CoV-2 infection were similar to individuals who received the BNT162b2 primary series plus a third dose of BNT162b2 at 6 months. Heterologous booster is recommended for individuals aged 60 years or older who received the CoronaVac primary series, given the lower observed odds against symptomatic SARS-CoV-2 infection among those who received a BNT1612b2 booster.

A Case-Based Monitoring Approach to Evaluate Safety of COVID-19 Vaccines in a Partially Integrated Health Information System: A Study Protocol

In response to Coronavirus disease 2019 (COVID-19) global pandemic, various COVID-19 vaccines were rapidly administered under emergency use authorization. Rare outcomes associated with COVID-19 vaccines might be less likely to be captured in clinical trials, leading to a knowledge gap in real-world vaccine safety. In contrast with high-income countries, many low-to-middle income countries have limited capacity to conduct active surveillance, owing to the absence of large and fully-integrated health information databases. This paper describes the study protocol, which aims to investigate risk of prespecified adverse events of special interests following COVID-19 vaccination in a partially integrated health information system with non-shareable electronic health records. The SAFECOVAC study is a longitudinal, observational retrospective study of active safety surveillance using case-based monitoring approach. This involves linkage of several administrative databases and hospitalization data monitoring to identify adverse events of special interests following administration of COVID-19 vaccines in Malaysia. The source population comprises of all individuals who received at least one dose of COVID-19 vaccine. Self-controlled design and vaccinated case-coverage design will be employed to assess risk of adverse events of special interests and determine the association with vaccine exposure. Data on vaccination records will be obtained from the national COVID-19 vaccination register to identify the vaccination platforms, doses and the timing of vaccinations. The outcome of this study is hospitalization for the adverse events of special interests between March 2021 and June 2022. The outcomes will be obtained through linkage with hospital admission database and national pharmacovigilance database. Findings will provide analysis of real-world data which can inform deliberations by government and public health decision makers relative to the refinement of COVID-19 vaccination recommendations.

Colorimetric detection of SARS-CoV-2 by uracil-DNA glycosylase (UDG) reverse transcription loop-mediated isothermal amplification (RT-LAMP)

OBJECTIVES

Preventing reverse transcription loop-mediated isothermal amplification (RT-LAMP) carryover contamination could be solved by adding deoxyuridine triphosphate (dUTP) and uracil-DNA glycosylase (UDG) into the reaction master mix.

METHODS

RNA was extracted from nasopharyngeal swab samples by a simple RNA extraction method.

RESULTS

Testing of 77 samples demonstrated 91.2% sensitivity (95% confidence interval [CI]: 78-98.2%) and 100% specificity (95% confidence interval: 92-100%) using UDG RT-LAMP.

CONCLUSION

This colorimetric UDG RT-LAMP is a simple-to-use, fast, and easy-to-interpret method, which could serve as an alternative for diagnosis of SARS-CoV-2 infection, especially in remote hospitals and laboratories with under-equipped medical facilities.

Risk of serious adverse events after the BNT162b2, CoronaVac, and ChAdOx1 vaccines in Malaysia: A self-controlled case series study

BACKGROUND

Rapid deployment of COVID-19 vaccines is challenging for safety surveillance, especially on adverse events of special interest (AESIs) that were not identified during the pre-licensure studies. This study evaluated the risk of hospitalisations for predefined diagnoses among the vaccinated population in Malaysia.

METHODS

Hospital admissions for selected diagnoses between 1 February 2021 and 30 September 2021 were linked to the national COVID-19 immunisation register. We conducted self-controlled case-series study by identifying individuals who received COVID-19 vaccine and diagnosis of thrombocytopenia, venous thromboembolism, myocardial infarction, myocarditis/pericarditis, arrhythmia, stroke, Bell's Palsy, and convulsion/seizure. The incidence of events was assessed in risk period of 21 days postvaccination relative to the control period. We used conditional Poisson regression to calculate the incidence rate ratio (IRR) and 95% confidence interval (CI) with adjustment for calendar period.

RESULTS

There was no increase in the risk for myocarditis/pericarditis, Bell's Palsy, stroke, and myocardial infarction in the 21 days following either dose of BNT162b2, CoronaVac, and ChAdOx1 vaccines. A small increased risk of venous thromboembolism (IRR 1.24; 95% CI 1.02, 1.49), arrhythmia (IRR 1.16, 95% CI 1.07, 1.26), and convulsion/seizure (IRR 1.26; 95% CI 1.07, 1.48) was observed among BNT162b2 recipients. No association between CoronaVac vaccine was found with all events except arrhythmia (IRR 1.15; 95% CI 1.01, 1.30). ChAdOx1 vaccine showed significant association for thrombocytopenia (IRR 2.67; 95% CI 1.21, 5.89) and venous thromboembolism (IRR 2.22; 95% CI 1.17, 4.21).

CONCLUSION

This study shows acceptable safety profiles of COVID-19 vaccines among recipients of BNT162b2, CoronaVac, and ChAdOx1 vaccines. This information can be used together with effectiveness data for risk-benefit analysis of the vaccination program. Further surveillance with more data is required to assess AESIs following COVID-19 vaccination in short- and long-term.

Real-world effectiveness of BNT162b2 vaccine against SARS-CoV-2 infection among adolescents (12 to 17-year-olds) in Malaysia

OBJECTIVES

In this study, we aimed to investigate vaccine effectiveness (VE) against SARS-CoV-2 infections among adolescents aged 12 to 17 years in Malaysia and examine potential VE differences after full vaccination.

METHODS

We consolidated data on COVID-19 testing, vaccination, and outcomes for all public school-going adolescents in Malaysia from September 1, 2021, to December 31, 2021, and estimated the VE against SARS-CoV-2 infections during this period. Cases were defined as positive tests, either by reverse transcriptase- PCR (RT-PCR) or rapid antigen (RTK-Ag) testing, while controls were negative tests. Secondarily, we restricted the analysis to all tests performed in December 2021 and compared VE by month of full vaccination.

RESULTS

A total of 175,880 eligible tests (53.4% or 93,995 RT-PCR tests) were included. After full vaccination with BNT162b2, VE against SARS-CoV-2 infections was 65.7% (95% confidence interval [CI] 64.4, 66.9) over the study period. When restricted to tests in December 2021, VEs for those fully vaccinated in September 2021, October 2021, and November 2021 were comparable (60.6% [95% CI 23.7, 81.5], 56.9% [95% CI 51.1, 62.0], and 65.7% [95% CI 59.8, 70.7] respectively).

CONCLUSIONS

Among adolescents, full vaccination with BNT162b2 offered considerable protection against SARS-CoV-2 infections over at least three months without substantial evidence of waning.

Efficacy of Ivermectin Treatment on Disease Progression Among Adults With Mild to Moderate COVID-19 and Comorbidities: The I-TECH Randomized Clinical Trial

IMPORTANCE

Ivermectin, an inexpensive and widely available antiparasitic drug, is prescribed to treat COVID-19. Evidence-based data to recommend either for or against the use of ivermectin are needed.

OBJECTIVE

To determine the efficacy of ivermectin in preventing progression to severe disease among high-risk patients with COVID-19.

DESIGN, SETTING, AND PARTICIPANTS

The Ivermectin Treatment Efficacy in COVID-19 High-Risk Patients (I-TECH) study was an open-label randomized clinical trial conducted at 20 public hospitals and a COVID-19 quarantine center in Malaysia between May 31 and October 25, 2021. Within the first week of patients' symptom onset, the study enrolled patients 50 years and older with laboratory-confirmed COVID-19, comorbidities, and mild to moderate disease.

INTERVENTIONS

Patients were randomized in a 1:1 ratio to receive either oral ivermectin, 0.4 mg/kg body weight daily for 5 days, plus standard of care (n = 241) or standard of care alone (n = 249). The standard of care consisted of symptomatic therapy and monitoring for signs of early deterioration based on clinical findings, laboratory test results, and chest imaging.

MAIN OUTCOMES AND MEASURES

The primary outcome was the proportion of patients who progressed to severe disease, defined as the hypoxic stage requiring supplemental oxygen to maintain pulse oximetry oxygen saturation of 95% or higher. Secondary outcomes of the trial included the rates of mechanical ventilation, intensive care unit admission, 28-day in-hospital mortality, and adverse events.

RESULTS

Among 490 patients included in the primary analysis (mean [SD] age, 62.5 [8.7] years; 267 women [54.5%]), 52 of 241 patients (21.6%) in the ivermectin group and 43 of 249 patients (17.3%) in the control group progressed to severe disease (relative risk [RR], 1.25; 95% CI, 0.87-1.80; P = .25). For all prespecified secondary outcomes, there were no significant differences between groups. Mechanical ventilation occurred in 4 (1.7%) vs 10 (4.0%) (RR, 0.41; 95% CI, 0.13-1.30; P = .17), intensive care unit admission in 6 (2.4%) vs 8 (3.2%) (RR, 0.78; 95% CI, 0.27-2.20; P = .79), and 28-day in-hospital death in 3 (1.2%) vs 10 (4.0%) (RR, 0.31; 95% CI, 0.09-1.11; P = .09). The most common adverse event reported was diarrhea (14 [5.8%] in the ivermectin group and 4 [1.6%] in the control group).

CONCLUSIONS AND RELEVANCE

In this randomized clinical trial of high-risk patients with mild to moderate COVID-19, ivermectin treatment during early illness did not prevent progression to severe disease. The study findings do not support the use of ivermectin for patients with COVID-19.

TRIAL REGISTRATION

ClinicalTrials.gov Identifier: NCT04920942.

Waning COVID-19 Vaccine Effectiveness for BNT162b2 and CoronaVac in Malaysia: An Observational Study

OBJECTIVES

We aimed to investigate and compare waning vaccine effectiveness (VE) against COVID-19 infection, COVID-19 related ICU admission and COVID-19 related death for BNT162b2 and CoronaVac vaccines.

METHODS

We consolidated national data on COVID-19 vaccination and outcomes, and used cases from 1 to 30 September 2021 to compare VE between the 'early' (fully vaccinated in April to June 2021) and 'late' (July to August 2021) groups. We estimated VE against COVID-19 infection with a negative binomial regression, and VE against ICU admission and death among confirmed COVID-19 cases with a logistic regression.

RESULTS

For BNT162b2, VE against COVID-19 infections declined from 90•8% (95% CI 89•4, 92•1) in the 'late' group to 79•3% (95% CI 76•1, 82•1) in the 'early' group. VE for BNT162b2 against ICU admission and death were stable. For CoronaVac, VE waned against COVID-19 infections from 74•5% (95% CI 70•6, 78•0) to 30•4% (95% CI 18•8, 40•3). Effectiveness against ICU admission waned from 56•0% (95% CI 51•2, 60•2) to 28•7% (95% CI 12•2, 42•1). CoronaVac's effectiveness against death remained stable.

CONCLUSION

VE against COVID-19 infection waned after three to five months of full vaccination for both BNT162b2 and CoronaVac vaccines in Malaysia. For CoronaVac, protection against ICU admission also declined.

RNA purification-free detection of SARS-CoV-2 using reverse transcription loop-mediated isothermal amplification (RT-LAMP)

BACKGROUND

Current diagnosis of SARS-CoV-2 infection relies on RNA purification prior to amplification. Typical extraction methods limit the processing speed and turnaround time for SARS-CoV-2 diagnostic testing.

METHODS

Here, we applied reverse transcription loop-mediated isothermal amplification directly onto human clinical swabs samples to amplify the RNA from SARS-CoV-2 swab samples after processing with chelating resin.

RESULTS

By testing our method on 64 samples, we managed to develop an RT-LAMP assay with 95.9% sensitivity (95% CI 86 to 99.5%) and 100% specificity (95% CI 78.2-100%).

CONCLUSION

The entire process including sample processing can be completed in approximately 50 min. This method has promising potential to be applied as a fast, simple and inexpensive diagnostic tool for the detection of SARS-CoV-2.

PICK-ing Malaysia's Epidemic Apart: Effectiveness of a Diverse COVID-19 Vaccine Portfolio

Malaysia rolled out a diverse portfolio of predominantly three COVID-19 vaccines (AZD1222, BNT162b2, and CoronaVac) beginning 24 February 2021. We evaluated vaccine effectiveness with two methods, covering 1 April to 15 September 2021: (1) the screening method for COVID-19 (SARS-CoV-2) infection and symptomatic COVID-19; and (2) a retrospective cohort of confirmed COVID-19 cases for COVID-19 related ICU admission and death using logistic regression. The screening method estimated partial vaccination to be 48.8% effective (95% CI: 46.8, 50.7) against COVID-19 infection and 33.5% effective (95% CI: 31.6, 35.5) against symptomatic COVID-19. Full vaccination is estimated at 87.8% effective (95% CI: 85.8, 89.7) against COVID-19 infection and 85.4% effective (95% CI: 83.4, 87.3) against symptomatic COVID-19. Among the cohort of confirmed COVID-19 cases, partial vaccination with any of the three vaccines is estimated at 31.3% effective (95% CI: 28.5, 34.1) in preventing ICU admission, and 45.1% effective (95% CI: 42.6, 47.5) in preventing death. Full vaccination with any of the three vaccines is estimated at 79.1% effective (95% CI: 77.7, 80.4) in preventing ICU admission and 86.7% effective (95% CI: 85.7, 87.6) in preventing deaths. Our findings suggest that full vaccination with any of the three predominant vaccines (AZD1222, BNT162b2, and CoronaVac) in Malaysia has been highly effective in preventing COVID-19 infection, symptomatic COVID-19, COVID-19-related ICU admission, and death.

Two extraction-free reverse transcription loop-mediated isothermal amplification assays for detection of SARS-CoV-2

BACKGROUND

Current assays for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rely on time consuming, costly and laboratory based methods for virus isolation, purification and removing inhibitors. To address this limitation, we propose a simple method for testing RNA from nasopharyngeal swab samples that bypasses the RNA purification step.

METHODS

In the current project, we have described two extraction-free reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for the detection of SARS-CoV-2 by using E gene and RdRp gene as the targets.

RESULTS

Here, results showed that reverse transcription loop-mediated isothermal amplification assays with 88.4% sensitive (95% CI: 74.9-96.1%) and 67.4% sensitive (95% CI: 51.5-80.9%) for E gene and RdRp gene, respectively.

CONCLUSION

Without the need of RNA purification, our developed RT-LAMP assays for direct detection of SARS-CoV-2 from nasopharyngeal swab samples could be turned into alternatives to qRT-PCR for rapid screening.

Sustaining effective COVID-19 control in Malaysia through large-scale vaccination

INTRODUCTION

As of 3rd June 2021, Malaysia is experiencing a resurgence of COVID-19 cases. In response, the federal government has implemented various non-pharmaceutical interventions (NPIs) under a series of Movement Control Orders and, more recently, a vaccination campaign to regain epidemic control. In this study, we assessed the potential for the vaccination campaign to control the epidemic in Malaysia and four high-burden regions of interest, under various public health response scenarios.

METHODS

A modified susceptible-exposed-infectious-recovered compartmental model was developed that included two sequential incubation and infectious periods, with stratification by clinical state. The model was further stratified by age and incorporated population mobility to capture NPIs and micro-distancing (behaviour changes not captured through population mobility). Emerging variants of concern (VoC) were included as an additional strain competing with the existing wild-type strain. Several scenarios that included different vaccination strategies (i.e. vaccines that reduce disease severity and/or prevent infection, vaccination coverage) and mobility restrictions were implemented.

RESULTS

The national model and the regional models all fit well to notification data but underestimated ICU occupancy and deaths in recent weeks, which may be attributable to increased severity of VoC or saturation of case detection. However, the true case detection proportion showed wide credible intervals, highlighting incomplete understanding of the true epidemic size. The scenario projections suggested that under current vaccination rates complete relaxation of all NPIs would trigger a major epidemic. The results emphasise the importance of micro-distancing, maintaining mobility restrictions during vaccination roll-out and accelerating the pace of vaccination for future control. Malaysia is particularly susceptible to a major COVID-19 resurgence resulting from its limited population immunity due to the country's historical success in maintaining control throughout much of 2020.

Diagnostic accuracy of fresh drooled saliva for SARS-CoV-2 in travelers

BACKGROUND

The standard for SARS-CoV-2 diagnosis is RT-PCR from nasopharyngeal or oropharyngeal swabs. Major airports require COVID-19 screening, and saliva has the potential as a substitute specimen for SARS-CoV-2 diagnosis. We investigated the utility of fresh drooled saliva against NPS for COVID-19 screening of travelers.

METHODS

We recruited 81 travelers and 15 non-travelers (including ten controls) prospectively within a mean of 3·22 days of RT-PCR confirmed COVID-19. Each study participant provided 2 mls of early morning fresh drooled whole saliva separately into a sterile plastic container and GeneFiX™ saliva collection kit. The saliva specimens were processed within 4 h and tested for SARS-CoV-2 genes (E, RdRP, and N2) and the results compared to paired NPS RT-PCR for diagnostic accuracy.

RESULTS

Majority of travellers were asymptomatic (75·0%) with a mean age of 34·26 years. 77 travelers were RT-PCR positive at the time of hospitalization whilst three travelers had positive contacts. In this group, the detection rate for SARS-CoV-2 with NPS, whole saliva, and GeneFiX™ were comparable (89·3%, 50/56; 87·8%, 43/49; 89·6%, 43/48). Both saliva collection methods were in good agreement (Kappa = 0·69). There was no statistical difference between the detection rates of saliva and NPS (p > 0·05). Detection was highest for the N2 gene whilst the E gene provided the highest viral load (mean = 27·96 to 30·10, SD = 3·14 to 3·85). Saliva specimens have high sensitivity (80·4%) and specificity (90·0%) with a high positive predictive value of 91·8% for SARS-CoV-2 diagnosis.

CONCLUSION

Saliva for SARS-CoV-2 screening is a simple accurate technique comparable with NPS RT-PCR.

Serology surveillance of SARS-CoV-2 antibodies among healthcare workers in COVID-19 designated facilities in Malaysia

Background

Asymptomatic severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections are well documented. Healthcare workers (HCW) are at increased risk of infection due to occupational exposure to infected patients. We aim to determine the prevalence of SARS-CoV-2 antibodies among HCW who did not come to medical attention.

Methods

We prospectively recruited 400 HCW from the National Public Health Laboratory and two COVID-19 designated public hospitals in Klang Valley, Malaysia between 13/4/2020 and 12/5/2020. Quota sampling was used to ensure representativeness of HCW involved in direct and indirect patient care. All participants answered a self-administered questionnaire and blood samples were taken to test for SARS-CoV-2 antibodies by surrogate virus neutralization test.

Findings

The study population comprised 154 (38.5%) nurses, 103 (25.8%) medical doctors, 47 (11.8%) laboratory technologists and others (23.9%). A majority (68.9%) reported exposure to SARS-CoV-2 in the past month within their respective workplaces. Adherence to personal protection equipment (PPE) guidelines and hand hygiene were good, ranging from 91-100% compliance. None (95% CI: 0, 0.0095) of the participants had SARS-CoV-2 antibodies detected, despite 182 (45.5%) reporting some symptoms one month prior to study recruitment. One hundred and fifteen (29%) of participants claimed to have had contact with known COVID-19 persons outside of their workplace.

Interpretation

Zero seroprevalence among HCW suggests a low incidence of undiagnosed COVID-19 infection in our healthcare setting during the first local wave of SARS-CoV-2 infection. The occupational risk of SARS-CoV-2 transmission within healthcare facilities can be prevented by adherence to infection control measures and appropriate use of PPE.

Funding

Own institutional budget and the Fundamental Research Grant Scheme.

Development of a reverse transcription recombinase polymerase amplification assay for rapid and direct visual detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

Rapid diagnosis is an important intervention in managing the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) outbreak. Real time reverse transcription polymerase chain reaction (RT-qPCR) remains the primary means for diagnosing the new virus strain but it is time consuming and costly. Recombinase polymerase amplification (RPA) is an isothermal amplification assay that does not require a PCR machine. It is an affordable, rapid, and simple assay. In this study, we developed and optimized a sensitive reverse transcription (RT)-RPA assay for the rapid detection of SARS-CoV-2 using SYBR Green I and/or lateral flow (LF) strip. The analytical sensitivity and specificity of the RT-RPA assay were tested by using 10-fold serial diluted synthetic RNA and genomic RNA of similar viruses, respectively. Clinical sensitivity and specificity of the RT-RPA assay were carried out using 78 positive and 35 negative nasopharyngeal samples. The detection limit of both RPA and RT-qPCR assays was 7.659 and 5 copies/μL RNA, respectively with no cross reactivity with other viruses. The clinical sensitivity and specificity of RT-RPA were 98% and 100%, respectively. Our study showed that RT-RPA represents a viable alternative to RT-qPCR for the detection of SARS-CoV-2, especially in areas with limited infrastructure.

Clinical characteristics and risk factors for severe COVID-19 infections in Malaysia: A nationwide observational study

BACKGROUND

COVID-19 emerged as a major public health outbreak in late 2019. Malaysia reported its first imported case on 25th January 2020, and adopted a policy of extensive contact tracing and hospitalising of all cases. We describe the clinical characteristics of COVID-19 cases nationwide and determine the risk factors associated with disease severity.

METHOD

Clinical records of all RT-PCR confirmed COVID-19 cases aged ≥12 years admitted to 18 designated hospitals in Malaysia between 1st February and 30th May 2020 with complete outcomes were retrieved. Epidemiological history, co-morbidities, clinical features, investigations, management and complications were captured using REDCap database. Variables were compared between mild and severe diseases. Univariate and multivariate regression were used to identify determinants for disease severity.

FINDINGS

The sample comprised of 5889 cases (median age 34 years, male 71.7%). Majority were mild (92%), and 3.3% required intensive care, with 80% admitted within the first five days. Older age (≥51 years), underlying chronic kidney disease and chronic pulmonary disease, fever, cough, diarrhoea, breathlessness, tachypnoea, abnormal chest radiographs and high serum CRP (≥5 mg/dL) on admission were significant determinants for severity (p<0.05). The case fatality rate was 1.2%, and the three commonest complications were liver injuries (6.7%), kidney injuries (4%), and acute respiratory distress syndrome (2.3%).

INTERPRETATIONS

Lower case fatality rate was possibly contributed by young cases with mild diseases and early hospitalisation. Abnormal chest radiographic findings in elderly with tachypnoea require close monitoring in the first five days to detect early deterioration.

A Sensitive Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Direct Visual Detection of SARS-CoV-2

A simple and rapid reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the detection of SARS-CoV-2. The RT-LAMP assay was highly specific for SARS-CoV-2 and was able to detect one copy of transcribed SARS-CoV-2 RNA within 24 minutes. Assay validation performed using 50 positive and 32 negative clinical samples showed 100% sensitivity and specificity. The RT-LAMP would be valuable for clinical diagnosis and epidemiological surveillance of SARS-CoV-2 infection in resource-limited areas as it does not require the use of sophisticated and costly equipment.

Real-time reverse transcription loop-mediated isothermal amplification for rapid detection of SARS-CoV-2

Background

Highly sensitive real-time reverse transcription polymerase chain reaction (RT-qPCR) methods have been developed for the detection of SARS-CoV-2. However, they are costly. Loop-mediated isothermal amplification (LAMP) assay has emerged as a novel alternative isothermal amplification method for the detection of nucleic acid.

Methods

A rapid, sensitive and specific real-time reverse transcription LAMP (RT-LAMP) assay was developed for SARS-CoV-2 detection.

Results

This assay detected one copy/reaction of SARS-CoV-2 RNA in 30 min. Both the clinical sensitivity and specificity of this assay were 100%. The RT-LAMP showed comparable performance with RT-qPCR. Combining simplicity and cost-effectiveness, this assay is therefore recommended for use in resource resource-limited settings.

How should front-line general practitioners use personal protective equipment (PPE)?

The COVID-19 outbreak continues to evolve with the number of cases increasing in Malaysia, placing a significant burden on general practitioners (GPs) to assess and manage suspected cases. GPs must be well equipped with knowledge to set up their clinics, use Personal Protective Equipment (PPE) appropriately, adopt standard protocols on triaging and referrals, as well as educate patients about PPE. The correct use of PPE will help GPs balance between personal safety and appropriate levels of public concern.