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COVID-19 vaccine effectiveness against severe disease from SARS-CoV-2 Omicron BA.1 and BA.2 subvariants – surveillance results from southern Sweden, December 2021 to March 2022
We compared vaccine effectiveness against severe COVID-19 between December 2021 and March 2022 when Omicron BA.1 and BA.2 were the dominating SARS-CoV-2 variants in Scania county, Sweden. Effectiveness remained above 80% after the transition from BA.1 to BA.2 among people with at least three vaccine doses but the point estimate decreased markedly to 54% among those with only two doses. Protection from prior infection was also lower after the transition to BA.2. Booster vaccination seems necessary to maintain sufficient protection.
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SARS-CoV-2 Omicron variant BA.2 neutralisation in sera of people with Comirnaty or CoronaVac vaccination, infection or breakthrough infection, Hong Kong, 2020 to 2022
Samuel MS Cheng , Chris Ka Pun Mok , Karl CK Chan , Susanna S Ng , Bosco HS Lam , Leo LH Luk , Fanny W Ko , Chunke Chen , Karen Yiu , John KC Li , Ken KP Chan , Leo CH Tsang , Leo LM Poon , David SC Hui and Malik PeirisBackgroundOmicron subvariant BA.2 circulation is rapidly increasing globally.
AimWe evaluated the neutralising antibody response from vaccination or prior SARS-CoV-2 infection against symptomatic infection by BA.2 or other variants.
MethodsUsing 50% plaque reduction neutralisation tests (PRNT50), we assessed neutralising antibody titres to BA.2, wild type (WT) SARS-CoV-2 and other variants in Comirnaty or CoronaVac vaccinees, with or without prior WT-SARS-CoV-2 infection. Titres were also measured for non-vaccinees convalescing from a WT-SARS-CoV-2 infection. Neutralising antibodies in BA.2 and BA.1 breakthrough infections and in BA.2 infections affecting non-vaccinees were additionally studied.
ResultsIn vaccinees or prior WT-SARS-CoV-2-infected people, BA.2 and BA.1 PRNT50 titres were comparable but significantly (p < 10 − 5) lower than WT. In each group of 20 vaccinees with (i) three-doses of Comirnaty, (ii) two CoronaVac followed by one Comirnaty dose, or (iii) one dose of either vaccine after a WT-SARS-CoV-2 infection, ≥ 19 individuals developed detectable (PRNT50 titre ≥ 10) antibodies to BA.2, while only 15 of 20 vaccinated with three doses of CoronaVac did. Comirnaty vaccination elicited higher titres to BA.2 than CoronaVac. In people convalescing from a WT-SARS-CoV-2 infection, a single vaccine dose induced higher BA.2 titres than three Comirnaty (p = 0.02) or CoronaVac (p = 0.00001) doses in infection-naïve individuals. BA.2 infections in previously uninfected and unvaccinated individuals elicited low (PRNT50 titre ≤ 80) responses with little cross-neutralisation of other variants. However, vaccinees with BA.1 or BA.2 breakthrough infections had broad cross-neutralising antibodies to WT viruses, and BA.1, BA.2, Beta and Delta variants.
ConclusionsExisting vaccines can be of help against the BA.2 subvariant.
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A 5-year look-back at the notification and management of vaccine supply shortages in Germany
BackgroundUnavailability of vaccines endangers the overall goal to protect individuals and whole populations against infections.
MethodsThe German notification system includes the publication of vaccine supply shortages reported by marketing authorisation holders (MAH), information on the availability of alternative vaccine products, guidance for physicians providing vaccinations and an unavailability reporting tool to monitor regional distribution issues.
AimThis study provides a retrospective analysis of supply issues and measures in the context of European and global vaccine supply constraints.
Resultsbetween October 2015 and December 2020, the 250 notifications concerned all types of vaccines (54 products). Most shortages were caused by increased demand associated with immigration in Germany in 2015 and 2016, new or extended vaccine recommendations, increased awareness, or changes in global immunisation programmes. Shortages of a duration up to 30 days were mitigated using existing storage capacities. Longer shortages, triggered by high demand on a national level, were mitigated using alternative products and re-allocation; in a few cases, vaccines were imported. However, for long lasting supply shortages associated with increased global demand, often occurring in combination with manufacturing issues, few compensatory mechanisms were available. Nevertheless, only few critical incidents were identified: (i) shortage of hexavalent vaccines endangering neonatal immunisation programmes in 2015;(ii) distribution issues with influenza vaccines in 2018; and (iii) unmet demand for pneumococcal and influenza vaccines during the coronavirus disease (COVID)-19 pandemic.
ConclusionVaccine product shortages in Germany resemble those present in neighbouring EU states and often reflect increased global demand not matched by manufacturing capacities.
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Public health considerations for transitioning beyond the acute phase of the COVID-19 pandemic in the EU/EEA
Many countries, including some within the EU/EEA, are in the process of transitioning from the acute pandemic phase. During this transition, it is crucial that countries’ strategies and activities remain guided by clear COVID-19 control objectives, which increasingly will focus on preventing and managing severe outcomes. Therefore, attention must be given to the groups that are particularly vulnerable to severe outcomes of SARS-CoV-2 infection, including individuals in congregate and healthcare settings. In this phase of pandemic management, a strong focus must remain on transitioning testing approaches and systems for targeted surveillance of COVID-19, capitalising on and strengthening existing systems for respiratory virus surveillance. Furthermore, it will be crucial to focus on lessons learned from the pandemic to enhance preparedness and to enact robust systems for the preparedness, detection, rapid investigation and assessment of new and emerging SARS-CoV-2 variants. Filling existing knowledge gaps, including behavioural insights, can help guide the response to future resurgences of SARS-CoV-2 and/or the emergence of other pandemics. Finally, ‘vaccine agility’ will be needed to respond to changes in people’s behaviours, changes in the virus, and changes in population immunity, all the while addressing issues of global health equity.
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Social conformism and confidence in systems as additional psychological antecedents of vaccination: a survey to explain intention for COVID-19 vaccination among healthcare and welfare sector workers, France, December 2020 to February 2021
BackgroundThe start of the COVID-19 vaccination campaign among French healthcare and welfare sector workers in January 2021 offered an opportunity to study psychological antecedents of vaccination in this group.
AimWe explored whether knowledge and attitude items related to social conformism and confidence in systems contributed to explaining intention for COVID-19 vaccination.
MethodsWe developed a knowledge and attitude questionnaire with 30 items related to five established and two hypothetical psychological antecedents of vaccination (KA-7C). The online questionnaire was distributed from 18 December 2020 to 1 February 2021 through chain-referral via professional networks, yielding a convenience sample. We used multivariable logistic regression to explore the associations of individual and grouped KA-7C items with COVID-19 vaccine intention.
ResultsAmong 5,234 participants, the vaccine intention model fit (pseudo R-squared values) increased slightly but significantly from 0.62 to 0.65 when adding social conformism and confidence in systems items. Intention to vaccinate was associated with the majority opinion among family and friends (OR: 11.57; 95% confidence interval (CI): 4.51–29.67) and a positive perception of employer’s encouragement to get vaccinated (vs negative; OR: 6.41; 95% CI: 3.36–12.22). The strongest association of a knowledge item was identifying the statement ‘Some stages of vaccine development (testing) have been skipped because of the epidemic emergency.’ as false (OR: 2.36; 95% CI: 1.73–3.22).
ConclusionThe results suggest that social conformism and confidence in systems are distinct antecedents of vaccination among healthcare and welfare workers, which should be taken into account in vaccine promotion.
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Genomic and epidemiological report of the recombinant XJ lineage SARS-CoV-2 variant, detected in northern Finland, January 2022
Recombinant sequences of the SARS-CoV-2 Omicron variant were detected in surveillance samples collected in north-western Finland in January 2022. We detected 191 samples with an identical genome arrangement in weeks 3 to 11, indicating sustained community transmission. The recombinant lineage has a 5’-end of BA.1, a recombination breakpoint between orf1a and orf1b (nucleotide position 13,296–15,240) and a 3’-end of BA.2 including the S gene. We describe the available genomic and epidemiological data about this currently circulating recombinant XJ lineage.
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The impact of SARS-CoV-2 on respiratory syndromic and sentinel surveillance in Israel, 2020: a new perspective on established systems
Aharona Glatman-Freedman , Lea Gur-Arie , Hanna Sefty , Zalman Kaufman , Michal Bromberg , Rita Dichtiar , Alina Rosenberg , Rakefet Pando , Ital Nemet , Limor Kliker2, , Ella Mendelson , Lital Keinan-Boker , Neta S Zuckerman , Michal Mandelboim and on behalf of The Israeli Respiratory Viruses Surveillance Network (IRVSN)BackgroundThe COVID-19 pandemic presented new challenges for the existing respiratory surveillance systems, and adaptations were implemented. Systematic assessment of the syndromic and sentinel surveillance platforms during the pandemic is essential for understanding the value of each platform in the context of an emerging pathogen with rapid global spread.
AimWe aimed to evaluate systematically the performance of various respiratory syndromic surveillance platforms and the sentinel surveillance system in Israel from 1 January to 31 December 2020.
MethodsWe compared the 2020 syndromic surveillance trends to those of the previous 3 years, using Poisson regression adjusted for overdispersion. To assess the performance of the sentinel clinic system as compared with the national SARS-CoV-2 repository, a cubic spline with 7 knots and 95% confidence intervals were applied to the sentinel network's weekly percentage of positive SARS-CoV-2 cases.
ResultsSyndromic surveillance trends changed substantially during 2020, with a statistically significant reduction in the rates of visits to physicians and emergency departments to below previous years' levels. Morbidity patterns of the syndromic surveillance platforms were inconsistent with the progress of the pandemic, while the sentinel surveillance platform was found to reflect the national circulation of SARS-CoV-2 in the population.
ConclusionOur findings reveal the robustness of the sentinel clinics platform for the surveillance of the main respiratory viruses during the pandemic and possibly beyond. The robustness of the sentinel clinics platform during 2020 supports its use in locations with insufficient resources for widespread testing of respiratory viruses.
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Vaccine-induced and naturally-acquired protection against Omicron and Delta symptomatic infection and severe COVID-19 outcomes, France, December 2021 to January 2022
More LessWe assessed the protection conferred by naturally-acquired, vaccine-induced and hybrid immunity during the concomitant Omicron and Delta epidemic waves in France on symptomatic infection and severe COVID-19. The greatest levels of protection against both variants were provided by hybrid immunity. Protection against Omicron symptomatic infections was systematically lower and waned at higher speed than against Delta in those vaccinated. In contrast, there were little differences in variant-specific protection against severe inpatient outcomes in symptomatic individuals.
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Transmission dynamics of COVID-19 in household and community settings in the United Kingdom, January to March 2020
Jamie Lopez Bernal , Nikolaos Panagiotopoulos , Chloe Byers , Tatiana Garcia Vilaplana , Nicki Boddington , Xu-Sheng Zhang , Andre Charlett , Suzanne Elgohari , Laura Coughlan , Rosie Whillock , Sophie Logan , Hikaru Bolt , Mary Sinnathamby , Louise Letley , Pauline MacDonald , Roberto Vivancos , Obaghe Edeghere , Charlotte Anderson , Karthik Paranthaman , Simon Cottrell , Jim McMenamin , Maria Zambon , Gavin Dabrera , Mary Ramsay and Vanessa SalibaBackgroundHouseholds appear to be the highest risk setting for COVID-19 transmission. Large household transmission studies in the early stages of the pandemic in Asia reported secondary attack rates ranging from 5 to 30%.
AimWe aimed to investigate the transmission dynamics of COVID-19 in household and community settings in the UK.
MethodsA prospective case-ascertained study design based on the World Health Organization FFX protocol was undertaken in the UK following the detection of the first case in late January 2020. Household contacts of cases were followed using enhanced surveillance forms to establish whether they developed symptoms of COVID-19, became confirmed cases and their outcomes. We estimated household secondary attack rates (SAR), serial intervals and individual and household basic reproduction numbers. The incubation period was estimated using known point source exposures that resulted in secondary cases.
ResultsWe included 233 households with two or more people with 472 contacts. The overall household SAR was 37% (95% CI: 31–43%) with a mean serial interval of 4.67 days, an R0 of 1.85 and a household reproduction number of 2.33. SAR were lower in larger households and highest when the primary case was younger than 18 years. We estimated a mean incubation period of around 4.5 days.
ConclusionsRates of COVID-19 household transmission were high in the UK for ages above and under 18 years, emphasising the need for preventative measures in this setting. This study highlights the importance of the FFX protocol in providing early insights on transmission dynamics.
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Immediate side effects of Comirnaty COVID-19 vaccine: A nationwide survey of vaccinated people in Israel, December 2020 to March 2021
BackgroundCOVID-19 vaccine safety is of major interest worldwide, since there is no prior experience with it. Israel was one of the first countries to widely use the Comirnaty vaccine.
AimWe aimed to assess the vaccine's short-term side effects directly from a large population and to predict influencing factors for self-reporting side effects.
MethodsIn a retrospective cohort study, we investigated self-reported systemic vaccine side-effects using electronic surveys sent to vaccinated individuals between 20 December 2020 and 11 March 2021, within 3 days following administration of the first and second dose. We determined predictors for reporting systemic side effects by logistic regression.
ResultsA total of 1,213,693 patients received at least one vaccine dose and 301,537 (24.8%) answered at least one survey. Among them, 68,162 (30.4%) and 89,854 (59.9%) individuals filled the first and the second dose surveys, respectively, and reported one or more side effects. Most common side effects were fatigue, headache and myalgia. Several respondents reported facial paraesthesia after first and second dose, respectively (n = 1,675; 0.7% and n = 1,601; 1.1%). Individuals younger than 40 years and women reported side effects more frequently than others, but pregnant women reported less. Pregnancy was a weak predictor for reporting any side effect in general and in particular fatigue, myalgia, headache, chills and fever.
ConclusionsWe found further support for minor short-term side effects, within 3 days of receiving the Comirnaty vaccine. These findings from vaccine recipients in general and pregnant women in particular can improve vaccine acceptance.
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Impact of the Omicron variant on SARS-CoV-2 reinfections in France, March 2021 to February 2022
Since the first reports in summer 2020, SARS-CoV-2 reinfections have raised concerns about the immunogenicity of the virus, which will affect SARS-CoV-2 epidemiology and possibly the burden of COVID-19 on our societies in the future. This study provides data on the frequency and characteristics of possible reinfections, using the French national COVID-19 testing database. The Omicron variant had a large impact on the frequency of possible reinfections in France, which represented 3.8% of all confirmed COVID-19 cases since December 2021.
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Risk factors associated with an outbreak of COVID-19 in a meat processing plant in southern Germany, April to June 2020
Meat processing plants have been prominent hotspots for coronavirus disease (COVID-19) outbreaks around the world. We describe infection prevention measures and risk factors for infection spread at a meat processing plant in Germany with a COVID-19 outbreak from April to June 2020. We analysed a cohort of all employees and defined cases as employees with either a PCR or ELISA positive result. Of 1,270 employees, 453 (36%) had evidence of SARS-CoV-2 infection. The highest attack rates were observed in meat processing and slaughtering areas. Multivariable analysis revealed that being a subcontracted employee (adjusted risk ratio (aRR)): 1.43, 95% CI: 1.06–1.96), working in the meat cutting area (aRR: 2.44, 95% CI: 1.45–4.48), working in the slaughtering area (aRR: 2.35, 95% CI: 1.32–4.45) and being a veterinary inspector (aRR: 4.77, 95% CI: 1.16–23.68) increased infection risk. Sharing accommodation or transportation were not identified as risk factors for infection. Our results suggest that workplace was the main risk factor for infection spread. These results highlight the importance of implementing preventive measures targeting meat processing plants. Face masks, distancing, staggering breaks, increased hygiene and regular testing for SARS-CoV2 helped limit this outbreak, as the plant remained open throughout the outbreak.
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Seroprevalence of antibodies against SARS-CoV-2 in the adult population during the pre-vaccination period, Norway, winter 2020/21
BackgroundSince March 2020, 440 million people worldwide have been diagnosed with COVID-19, but the true number of infections with SARS-CoV-2 is higher. SARS-CoV-2 antibody seroprevalence can add crucial epidemiological information about population infection dynamics.
AimTo provide a large population-based SARS-CoV-2 seroprevalence survey from Norway; we estimated SARS-CoV-2 seroprevalence before introduction of vaccines and described its distribution across demographic groups.
MethodsIn this population-based cross-sectional study, a total of 110,000 people aged 16 years or older were randomly selected during November–December 2020 and invited to complete a questionnaire and provide a dried blood spot (DBS) sample.
ResultsThe response rate was 30% (31,458/104,637); compliance rate for return of DBS samples was 88% (27,700/31,458). National weighted and adjusted seroprevalence was 0.9% (95% CI (confidence interval): 0.7–1.0). Seroprevalence was highest among those aged 16–19 years (1.9%; 95% CI: 0.9–2.9), those born outside the Nordic countries 1.4% (95% CI: 1.0–1.9), and in the counties of Oslo 1.7% (95% CI: 1.2–2.2) and Vestland 1.4% (95% CI: 0.9–1.8). The ratio of SARS-CoV-2 seroprevalence (0.9%) to cumulative incidence of virologically detected cases by mid-December 2020 (0.8%) was slightly above one. SARS-CoV-2 seroprevalence was low before introduction of vaccines in Norway and was comparable to virologically detected cases, indicating that most cases in the first 10 months of the pandemic were detected.
ConclusionFindings suggest that preventive measures including contact tracing have been effective, people complied with physical distancing recommendations, and local efforts to contain outbreaks have been essential.
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Enhancing epidemiological surveillance of the emergence of the SARS-CoV-2 Omicron variant using spike gene target failure data, England, 15 November to 31 December 2021
Paula B Blomquist , Jessica Bridgen , Neil Bray , Anne Marie O’Connell , Daniel West , Natalie Groves , Eileen Gallagher , Lara Utsi , Christopher I Jarvis , Jo L Hardstaff , Chloe Byers , Soeren Metelmann , David Simons , Asad Zaidi , Katherine A Twohig , Bethan Savagar , Alessandra Løchen , Cian Ryan , Katie Wrenn , María Saavedra-Campos , Zahidul Abedin , Isaac Florence , Paul Cleary , Richard Elson , Roberto Vivancos and Iain R LakeWhen SARS-CoV-2 Omicron emerged in 2021, S gene target failure enabled differentiation between Omicron and the dominant Delta variant. In England, where S gene target surveillance (SGTS) was already established, this led to rapid identification (within ca 3 days of sample collection) of possible Omicron cases, alongside real-time surveillance and modelling of Omicron growth. SGTS was key to public health action (including case identification and incident management), and we share applied insights on how and when to use SGTS.
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Large-scale decontamination of disposable FFP2 and FFP3 respirators by hydrogen peroxide vapour, Finland, April to June 2020
Katri Laatikainen , Markku Mesilaakso , Ilpo Kulmala , Erja Mäkelä , Petri Ruutu , Outi Lyytikäinen , Susanna Tella , Tarmo Humppi , Satu Salo , Tuuli Haataja , Kristiina Helminen , Henri Karppinen , Heli Kähkönen , Tarja Vainiola , Kirsimarja Blomqvist , Sirpa Laitinen , Kati Peltonen , Marko Laaksonen , Timo Ristimäki and Jouni KoivistoBackgroundThe shortage of FFP2 and FFP3 respirators posed a serious threat to the operation of the healthcare system at the onset of the COVID-19 pandemic.
AimOur aim was to develop and validate a large-scale facility that uses hydrogen peroxide vapour for the decontamination of used respirators.
MethodsA multidisciplinary and multisectoral ad hoc group of experts representing various organisations was assembled to implement the collection and transport of used FFP2 and FFP3 respirators from hospitals covering 86% of the Finnish population. A large-scale decontamination facility using hydrogen peroxide vapour was designed and constructed. Microbiological tests were used to confirm efficacy of hydrogen peroxide vapour decontamination together with a test to assess the effect of decontamination on the filtering efficacy and fit of respirators. Bacterial and fungal growth in stored respirators was determined by standard methods.
ResultsLarge-scale hydrogen peroxide vapour decontamination of a range of FFP2 and FFP3 respirator models effectively reduced the recovery of biological indicators: Geobacillus stearothermophilus and Bacillus atrophaeus spores, as well as model virus bacteriophage MS2. The filtering efficacy and facial fit after hydrogen peroxide vapour decontamination were not affected by the process. Microbial growth in the hydrogen peroxide vapour-treated respirators indicated appropriate microbial cleanliness.
ConclusionsLarge-scale hydrogen peroxide vapour decontamination was validated. After effective decontamination, no significant changes in the key properties of the respirators were detected. European Union regulations should incorporate a facilitated pathway to allow reuse of appropriately decontaminated respirators in a severe pandemic when unused respirators are not available.
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SARS-CoV-2 infection among educational staff in Berlin, Germany, June to December 2020
BackgroundSARS-CoV-2 infections in preschool and school settings potentially bear occupational risks to educational staff.
AimWe aimed to assess the prevalence of SARS-CoV-2 infection in teachers and preschool educators and at identifying factors associated with infection.
MethodsWe analysed cross-sectional data derived from 17,448 voluntary, PCR-based screening tests of asymptomatic educational staff in Berlin, Germany, between June and December 2020 using descriptive statistics and a logistic regression model.
ResultsParticipants were largely female (73.0%), and median age was 41 years (range: 18-78). Overall, SARS-CoV-2 infection proportion was 1.2% (95% CI: 1.0–1.4). Proportion of positive tests in educational staff largely followed community incidence until the start of the second pandemic wave, when an unsteady plateau was reached. Then, the proportion of positive tests in a (concurrent) population survey was 0.9% (95% CI: 0.6–1.4), 1.2% (95% CI: 0.8–1.8) in teachers and 2.6% (95% CI: 1.6–4.0) in preschool educators. Compared with teachers, increased odds of infection were conferred by being a preschool educator (adjusted odds ratio (aOR): 1.6; 95% CI: 1.3–2.0) and by contact with a SARS-CoV-2 infected individual outside of work (aOR: 3.0; 95% CI: 1.5–5.5). In a step-wise backward selection, the best set of associated factors with SARS-CoV-2 infection involved age, occupation, and calendar week.
ConclusionsThese results indicate that preschool educators bear increased odds of SARS-CoV-2 infection compared with teachers. At the same time, the private environment appeared to be a relevant source of SARS-CoV-2 infection for educational staff in 2020.
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Surveillance and return to work of healthcare workers following SARS-CoV-2 Omicron variant infection, Sheffield, England, 17 January to 7 February 2022
More LessThe SARS-CoV-2 Omicron variant has challenged demands to minimise workplace transmission in healthcare settings while maintaining adequate staffing. Policymakers have shortened COVID-19 isolation periods, although little real-world data have evaluated the utility. Our findings from surveillance of 240 healthcare workers from Sheffield Teaching Hospitals, England, show that 55% of affected staff could return before day 10 of isolation with over 25% eligible on day 6, pending two successive negative antigen tests. This outcome is favourable for continuity of healthcare services.
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Estimating the effect of mobility on SARS-CoV-2 transmission during the first and second wave of the COVID-19 epidemic, Switzerland, March to December 2020
More LessIntroductionHuman mobility was considerably reduced during the COVID-19 pandemic. To support disease surveillance, it is important to understand the effect of mobility on transmission.
AimWe compared the role of mobility during the first and second COVID-19 wave in Switzerland by studying the link between daily travel distances and the effective reproduction number (Rt) of SARS-CoV-2.
MethodsWe used aggregated mobile phone data from a representative panel survey of the Swiss population to measure human mobility. We estimated the effects of reductions in daily travel distance on Rt via a regression model. We compared mobility effects between the first (2 March–7 April 2020) and second wave (1 October–10 December 2020).
ResultsDaily travel distances decreased by 73% in the first and by 44% in the second wave (relative to February 2020). For a 1% reduction in average daily travel distance, Rt was estimated to decline by 0.73% (95% credible interval (CrI): 0.34–1.03) in the first wave and by 1.04% (95% CrI: 0.66–1.42) in the second wave. The estimated mobility effects were similar in both waves for all modes of transport, travel purposes and sociodemographic subgroups but differed for movement radius.
ConclusionMobility was associated with SARS-CoV-2 Rt during the first two epidemic waves in Switzerland. The relative effect of mobility was similar in both waves, but smaller mobility reductions in the second wave corresponded to smaller overall reductions in Rt. Mobility data from mobile phones have a continued potential to support real-time surveillance of COVID-19.
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Inferring transmission fitness advantage of SARS-CoV-2 variants of concern from wastewater samples using digital PCR, Switzerland, December 2020 through March 2021
BackgroundThroughout the COVID-19 pandemic, SARS-CoV-2 genetic variants of concern (VOCs) have repeatedly and independently arisen. VOCs are characterised by increased transmissibility, increased virulence or reduced neutralisation by antibodies obtained from prior infection or vaccination. Tracking the introduction and transmission of VOCs relies on sequencing, typically whole genome sequencing of clinical samples. Wastewater surveillance is increasingly used to track the introduction and spread of SARS-CoV-2 variants through sequencing approaches.
AimHere, we adapt and apply a rapid, high-throughput method for detection and quantification of the relative frequency of two deletions characteristic of the Alpha, Beta, and Gamma VOCs in wastewater.
MethodsWe developed drop-off RT-dPCR assays and an associated statistical approach implemented in the R package WWdPCR to analyse temporal dynamics of SARS-CoV-2 signature mutations (spike Δ69–70 and ORF1a Δ3675–3677) in wastewater and quantify transmission fitness advantage of the Alpha VOC.
ResultsBased on analysis of Zurich wastewater samples, the estimated transmission fitness advantage of SARS-CoV-2 Alpha based on the spike Δ69–70 was 0.34 (95% confidence interval (CI): 0.30–0.39) and based on ORF1a Δ3675–3677 was 0.53 (95% CI: 0.49–0.57), aligning with the transmission fitness advantage of Alpha estimated by clinical sample sequencing in the surrounding canton of 0.49 (95% CI: 0.38–0.61).
ConclusionDigital PCR assays targeting signature mutations in wastewater offer near real-time monitoring of SARS-CoV-2 VOCs and potentially earlier detection and inference on transmission fitness advantage than clinical sequencing.
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