Serial household serosurvey for COVID-19 in low and high transmission neighborhoods of urban Pakistan
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Abstract
Serial household antibody sero-surveys informs the pandemic where testing is nonuniform. Young populations with intergenerational co-residence may have different transmission dynamics. We conducted two serial cross-sectional surveys in April and June 2020 in low- and high-transmission neighborhoods of Karachi, Pakistan, using random sampling. Symptoms were assessed and blood tested for antibody using chemiluminescence. Seroprevalence was adjusted using Bayesian regression and post stratification. CRI with 95% confidence intervals was obtained. We enrolled 2004 participants from 406 households. In June 8.7% (95% CI 5.1-13.1) and 15.1% (95% CI 9.4 -21.7) were infected in low- and high-transmission-areas respectively compared with 0.2% (95% CI 0-0.7) and 0.4% (95% CI 0 - 1.3) in April. Conditional risk of infection was 0.31 (95% CI 0.16-0.47) and 0.41(95% CI 0.28-0.52) in District Malir & District East respectively with overall only 5.4% symptomatic. Rapid increase in seroprevalence from baseline is seen in Karachi, with a high probability of infection within household.
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SciScore for 10.1101/2020.07.28.20163451: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IACUC: Four sub-administrative units (union councils) of District East were selected as high-transmission areas based on the number of cases reported by the provincial government. (Supplementary Figure 1) The study was approved by the Aga Khan University Ethical Review Committee (AKU ERC).
Consent: Approval from the household and written informed consent or assent from individual participants was obtained.Randomization A detailed line-list of cases was available in District East which allowed households to be selected through systematic random sampling as follows: A case was randomly identified from the line listing that served as a reference point. Blinding not … SciScore for 10.1101/2020.07.28.20163451: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IACUC: Four sub-administrative units (union councils) of District East were selected as high-transmission areas based on the number of cases reported by the provincial government. (Supplementary Figure 1) The study was approved by the Aga Khan University Ethical Review Committee (AKU ERC).
Consent: Approval from the household and written informed consent or assent from individual participants was obtained.Randomization A detailed line-list of cases was available in District East which allowed households to be selected through systematic random sampling as follows: A case was randomly identified from the line listing that served as a reference point. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Our study had several limitations. The geographical area of the study was limited to only two neighborhoods and the sampling strategy differed, not allowing for comparisons between the areas. We also had high rates of household level refusal which can be attributable to the fact that the study was conducted in the midst of a pandemic when sentiments of fear and stigma were at their highest. Due to a limited supply chain of testing kits in Pakistan, we did not do an in-house validation on local samples, however this was compensated by modeling directly on the data reported by the manufacturer.
Results from TrialIdentifier: No clinical trial numbers were referenced.
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.
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SciScore for 10.1101/2020.07.28.20163451: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Teams sought household level approval from elders or representatives and individual participant written informed consent or assent as eligible. Randomization A reference point was identified randomly in all 4 UCs from a list of current positive cases obtained from the district health office. Blinding not detected. Power Analysis not detected. Sex as a biological variable Seropositivity rates were indistinguishable between men and women within each district. Table 2: Resources
Software and Algorithms Sentences Resources Karachi, the largest city in Pakistan has also seen most number of cases and deaths However, true extent of transmission in the community … SciScore for 10.1101/2020.07.28.20163451: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Teams sought household level approval from elders or representatives and individual participant written informed consent or assent as eligible. Randomization A reference point was identified randomly in all 4 UCs from a list of current positive cases obtained from the district health office. Blinding not detected. Power Analysis not detected. Sex as a biological variable Seropositivity rates were indistinguishable between men and women within each district. Table 2: Resources
Software and Algorithms Sentences Resources Karachi, the largest city in Pakistan has also seen most number of cases and deaths However, true extent of transmission in the community is not known as testing rates have been low resulting in under reporting of cases and omission of mildly symptomatic and asymptomatic cases Population based serosurveys can help understand true magnitude of the spread and its variation with sociodemographic and other factors We searched PubMed and its specific hub LitCovid, medRxiv and bioRxiv preprint servers up to July 25, 2020, for epidemiological studies using the terms “seroprevalence” or “seroepidemiology” and “SARS-CoV-2” for articles in English language. PubMedsuggested: (PubMed, SCR_004846)<div style="margin-bottom:8px"> <div><b>bioRxiv</b></div> <div>suggested: (bioRxiv, <a href="https://scicrunch.org/resources/Any/search?q=SCR_003933">SCR_003933</a>)</div> </div> </td></tr></table>Data from additional tools added to each annotation on a weekly basis.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.
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