COVID-19 pandemic in Saint Petersburg, Russia: Combining population-based serological study and surveillance data
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Abstract
The COVID-19 pandemic in Russia has already resulted in 500,000 excess deaths, with more than 5.6 million cases registered officially by July 2021. Surveillance based on case reporting has become the core pandemic monitoring method in the country and globally. However, population-based seroprevalence studies may provide an unbiased estimate of the actual disease spread and, in combination with multiple surveillance tools, help to define the pandemic course. This study summarises results from four consecutive serological surveys conducted between May 2020 and April 2021 at St. Petersburg, Russia and combines them with other SARS-CoV-2 surveillance data.
Methods
We conducted four serological surveys of two random samples (May–June, July–August, October–December 2020, and February–April 2021) from adults residing in St. Petersburg recruited with the random digit dialing (RDD), accompanied by a telephone interview to collect information on both individuals who accepted and declined the invitation for testing and account for non-response. We have used enzyme-linked immunosorbent assay CoronaPass total antibodies test (Genetico, Moscow, Russia) to report seroprevalence. We corrected the estimates for non-response using the bivariate probit model and also accounted the test performance characteristics, obtained from independent assay evaluation. In addition, we have summarised the official registered cases statistics, the number of hospitalised patients, the number of COVID-19 deaths, excess deaths, tests performed, data from the ongoing SARS-CoV-2 variants of concern (VOC) surveillance, the vaccination uptake, and St. Petersburg search and mobility trends. The infection fatality ratios (IFR) have been calculated using the Bayesian evidence synthesis model.
Findings
After calling 113,017 random mobile phones we have reached 14,118 individuals who responded to computer-assisted telephone interviewing (CATI) and 2,413 provided blood samples at least once through the seroprevalence study. The adjusted seroprevalence in May–June, 2020 was 9.7% (95%: 7.7–11.7), 13.3% (95% 9.9–16.6) in July–August, 2020, 22.9% (95%: 20.3–25.5) in October–December, 2021 and 43.9% (95%: 39.7–48.0) in February–April, 2021. History of any symptoms, history of COVID-19 tests, and non-smoking status were significant predictors for higher seroprevalence. Most individuals remained seropositive with a maximum 10 months follow-up. 92.7% (95% CI 87.9–95.7) of participants who have reported at least one vaccine dose were seropositive. Hospitalisation and COVID-19 death statistics and search terms trends reflected the pandemic course better than the official case count, especially during the spring 2020. SARS-CoV-2 circulation showed rather low genetic SARS-CoV-2 lineages diversity that increased in the spring 2021. Local VOC (AT.1) was spreading till April 2021, but B.1.617.2 substituted all other lineages by June 2021. The IFR based on the excess deaths was equal to 1.04 (95% CI 0.80–1.31) for the adult population and 0.86% (95% CI 0.66–1.08) for the entire population.
Conclusion
Approximately one year after the COVID-19 pandemic about 45% of St. Petersburg, Russia residents contracted the SARS-CoV-2 infection. Combined with vaccination uptake of about 10% it was enough to slow the pandemic at the present level of all mitigation measures until the Delta VOC started to spread. Combination of several surveillance tools provides a comprehensive pandemic picture.
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SciScore for 10.1101/2021.07.31.21261428: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources Laboratory tests: During the four surveys, we assessed anti-SARS-CoV-2 antibodies using three different assays. anti-SARS-CoV-2suggested: NoneFinally, to report seroprevalence, we selected enzyme-linked immunosorbent assay (ELISA Coronapass) CoronaPass total antibodies test (Genetico, Moscow, Russia) that detects total antibodies (the cutoff for positivity 1.0) and is based on the recombinant SARS-CoV-2 spike protein receptor binding domain (Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA). SARS-CoV-2 spike protein receptor binding domainsuggested: NoneResults …
SciScore for 10.1101/2021.07.31.21261428: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources Laboratory tests: During the four surveys, we assessed anti-SARS-CoV-2 antibodies using three different assays. anti-SARS-CoV-2suggested: NoneFinally, to report seroprevalence, we selected enzyme-linked immunosorbent assay (ELISA Coronapass) CoronaPass total antibodies test (Genetico, Moscow, Russia) that detects total antibodies (the cutoff for positivity 1.0) and is based on the recombinant SARS-CoV-2 spike protein receptor binding domain (Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA). SARS-CoV-2 spike protein receptor binding domainsuggested: NoneResults from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Another critical limitation of the Internet search term trends lies in the spectrum of symptoms related to the disease of interest. For example, loss of smell is quite a distinct feature of SARS-CoV-2 infection. If the clinical manifestation of the infection caused by the new strains differ, surveillance strategies using search term trends should also change. More than 20,000 excess deaths have already been reported in St. Petersburg during the pandemic year [11]. The results of our seroprevalence study combined with the data on excess mortality give the IFR equal to 0.86% for the entire population, which is in line with other estimates across Europe [7, 24]. The IFR based on serological study results and excess mortality was stable for all four surveys. However, the official COVID-19 death count provided lower IFRs, which were not stable and was even lower during the pandemic waves. Thus, it seems that the number of deaths during the both waves was unprecedented for St. Petersburg to timely provide official data collection and cause of death specifications in mortality records. We continue to monitor the pandemic in St. Petersburg using all available sources and plan to run the following survey to estimate the number of individuals with antibodies to SARS-CoV-2 after the summer wave. In addition, we aim to detect the herd immunity threshold in St. Petersburg if any exists given the Delta VOC basic reproductive number and diminished vaccine effectiveness [12]. Several possibl...
Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
Identifier Status Title NCT04406038 Active, not recruiting Study of the Spread of COVID-19 in Saint Petersburg, Russia ISRCTN11060415 NA NA Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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