Improving SARS-CoV-2 variants monitoring in the absence of genomic surveillance capabilities: a serological study in Bolivian blood donors in October 2021 and June 2022
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Curated by eLife
eLife assessment
This important study examines SARS-CoV-2 seroprevalence in Bolivia and aims to provide insights into the transmission of the virus and the effects of vaccination on population immunity. However, the evidence for the main claims is incomplete because of the uncertainties about the accuracy of the neutralization assays given the cross-neutralization present across variants, as well as the selected population of blood donors tested. These uncertainties need to be addressed to support the premise of the paper.
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Abstract
Unlike genomic data, serological data have not been previously leveraged to evaluate the SARS-CoV-2 variants circulation. In Bolivia, sustained genomic surveillance capacities were lacking especially at the beginning of the pandemic. In 2021 and 2022 we estimated the prevalence of anti-SARS-CoV-2 antibodies in Bolivian blood donors and explored the feasibility of using virus serum neutralization data for variants thought to have circulated to map their circulation across all departments over a year-long follow-up period. Anti-S1 and anti-NCP SARS-CoV-2 IgGs were studied, along with virus neutralization tests for ancestral-D614G, Gamma, Delta, and Omicron BA.1 lineages of SARS-CoV-2. Between 2021 and 2022, the overall prevalence of anti-S1 and anti-NCP antibodies increased reaching values over 90%, demonstrating that a large proportion of the Bolivian population was no longer naïve to the virus. Viral neutralization data, analyzed through multiple approaches, revealed the spread of the Gamma variant up to 2021, particularly impacting northern departments. In 2022, Gamma continued to circulate in southernmost departments of the country and the emergence of Omicron BA.1 was detected. These trends align with publicly available genomic data from neighboring countries. Our serological analyses successfully identified both new antigenic groups, such as Omicron BA.1, and individual variants related to previously circulating groups, such as Delta. The study contributes insights into overall population immunity to SARS-CoV-2 and variant-specific immunity levels across different regions of Bolivia. It also emphasizes the potency of seroprevalence studies in informing public health decisions and underscore their value in capturing the initial phases of emerging epidemics when variant diversity is limited, facilitating timely genomic surveillance setup.
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eLife assessment
This important study examines SARS-CoV-2 seroprevalence in Bolivia and aims to provide insights into the transmission of the virus and the effects of vaccination on population immunity. However, the evidence for the main claims is incomplete because of the uncertainties about the accuracy of the neutralization assays given the cross-neutralization present across variants, as well as the selected population of blood donors tested. These uncertainties need to be addressed to support the premise of the paper.
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Reviewer #1 (Public Review):
Summary:
This study provides valuable and comprehensive information about the SARS-CoV-2 seroprevalence during 2021 and 2022 in different regions of Bolivia. Moreover, data on immune responses against the SARS-CoV-2 variants based on neutralization tests denotes the presence of several virus variants circulating in the Bolivian population. Evidence for seroprevalence data provided by the authors is solid, across the study period, while data regarding variant circulation is limited to the early stages of the pandemic.
Strengths:
The major strength of this study is that it provided nationwide seroprevalence estimates from infection and/or vaccination based on antibodies against both spike and the nucleocapsid protein in a large representative sample of sera collected at two time-points from all departments of …
Reviewer #1 (Public Review):
Summary:
This study provides valuable and comprehensive information about the SARS-CoV-2 seroprevalence during 2021 and 2022 in different regions of Bolivia. Moreover, data on immune responses against the SARS-CoV-2 variants based on neutralization tests denotes the presence of several virus variants circulating in the Bolivian population. Evidence for seroprevalence data provided by the authors is solid, across the study period, while data regarding variant circulation is limited to the early stages of the pandemic.
Strengths:
The major strength of this study is that it provided nationwide seroprevalence estimates from infection and/or vaccination based on antibodies against both spike and the nucleocapsid protein in a large representative sample of sera collected at two time-points from all departments of Bolivia, gaining insight into COVID-19 epidemiology. On the other hand, data from virus neutralization assays inferred the circulation during the study period of four SARS-CoV-2 variants in the population. Overall, the study results provide an overview of the level of viral transmission and vaccination and insights into the spread across the country of SARS-CoV-2 variants.
Weaknesses:
The assessment of a Lambda variant that circulated in several neighboring countries (Peru, Chile, and Argentina), which had a significant impact on the COVID-19 pandemic in the region, may have strengthened the study to contrast Gamma spread. In addition, even though neutralizing antibodies can certainly reveal previous infections of SARSCOV2 variants in the population, it is of limited value to infer from this information some potential timing estimates of specific variant circulation, considering the heterogeneous effects that past infections, vaccinations, or a combination of both could have on the level of variant-specific neutralizing antibodies and/or their cross-neutralization capacity.
An appraisal of whether the authors achieved their aims, and whether the results support their conclusions:
The conclusions of this paper are well supported by data, particularly regarding seroprevalence that reliably reflects the epidemiology of COVID-19 in Bolivia, and seroprevalence trends in other low- and middle-income countries.
A discussion of the likely impact of the work on the field, and the utility of the methods and data to the community:
Since this is the first study that has been conducted to assess indicators of immunity against SARS-CoV-2 in the population of Bolivia at a nationwide scale, seroprevalence data provided by geographic regions at two time-points can be useful as a reference for potential retrospective global meta-analysis and further explore and compare the risk factors for infection, variant distribution, and the impact on infection and vaccination, gaining deeper insights into understanding the evolution of the COVID-19 pandemic in Bolivia and in the region.
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Reviewer #2 (Public Review):
Significance of the findings:
In this study, blood donors were assessed using serology and viral neutralization assays to determine the prevalence of SARS-CoV-2 antibodies. S1 and NCP antibodies were used to distinguish between vaccination and natural infection and virus-specific neut titers were used to determine which variants the antibodies respond to. The study reports almost universal antibody prevalence and increases in antibodies against specific variants at different points corresponding to circulating variants identified phylogenetically in neighbouring countries. The authors propose this approach for settings like Bolivia where genetic sequencing is not readily available. Unfortunately, there are significant limitations to this approach that limit its utility - serological data are available after …
Reviewer #2 (Public Review):
Significance of the findings:
In this study, blood donors were assessed using serology and viral neutralization assays to determine the prevalence of SARS-CoV-2 antibodies. S1 and NCP antibodies were used to distinguish between vaccination and natural infection and virus-specific neut titers were used to determine which variants the antibodies respond to. The study reports almost universal antibody prevalence and increases in antibodies against specific variants at different points corresponding to circulating variants identified phylogenetically in neighbouring countries. The authors propose this approach for settings like Bolivia where genetic sequencing is not readily available. Unfortunately, there are significant limitations to this approach that limit its utility - serological data are available after the fact in a fast-moving pandemic and so are a poor alternative to phylogenetic data. Rather, serological information can supplement phylogenetic data and is most useful in estimating population-level immunity.
(1) Considerations in interpreting the results:
a. Serology provides different information to phylogenetic sequencing of the viruses and so both are important. Viral sequencing provides real-time information on circulating variants and indicates the proportion of each variant in circulation at any point as there are almost always multiple variants spreading but it is the fastest spreading variant that comes to dominate. Importantly serology measures asymptomatic infections as well, providing population estimates of infection that are not available through viral gene sequencing.
b. A major concern in the interpretation of serology is that antibody titers vary markedly over time with rapid declines in the first year post-infection or post-vaccination. However, these declines vary depending on whether hybrid immunity is present. Disentangling this retrospectively is a challenge. A low antibody titer could reflect an infection that occurred a few months ago but may be below the threshold for positivity at the time of testing. There is also substantial individual variability in antibody responses.
c. Serology becomes increasingly difficult to untangle when an individual has had doses of vaccine and multiple natural infections with different variants. Due to the importance of hybrid immunity in population risk to new variants, it would be useful for estimates of hybrid immunity to be generated based on anti-S1 and anti-NCP antibodies. From a population immunity perspective, this could be important in guiding future protection and boosting strategies.
d. Since there is cross-neutralization by the antibodies stimulated by each variant, it is important to establish the sensitivity and specificity of each of the neutralization assays in a panel comprising multiple variants. An assessment of the accuracy of the neut assay for each variant is needed to be confident that it is able to distinguish between variants.
e. Blood donors are notoriously poor representations of the general population in many countries, driven partly by whether donation is financially rewarded. For example, in the USA, drug addicts are disproportionately over-represented in blood donor populations as they use it as a source of money. The authors provide no information on whether the blood donor population in Bolivia is representative of the entire population. Comparison of the prevalence of specific disease markers in the general population and in blood donors could provide a signal of their comparability.
(2) Please provide the sensitivity and specificity of each of the assays so that the reader can assess the degree of accuracy in the assay that claims that the prevalent antibodies are due to, for example, omicron.
(3) Please provide an assessment of the representativity of the blood donor population eg. Is the prevalence of hepatitis B serological markers in the blood donor population comparable with the prevalence of hepatitis B serological markers in the general population from community-based studies?
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