Transmission of B.1.617.2 Delta variant between vaccinated healthcare workers
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Abstract
Breakthrough infections with SARS-CoV-2 Delta variant have been reported in doubly-vaccinated recipients and as re-infections. Studies of viral spread within hospital settings have highlighted the potential for transmission between doubly-vaccinated patients and health care workers and have highlighted the benefits of high-grade respiratory protection for health care workers. However the extent to which vaccination is preventative of viral spread in health care settings is less well studied. Here, we analysed data from 118 vaccinated health care workers (HCW) across two hospitals in India, constructing two probable transmission networks involving six HCWs in Hospital A and eight HCWs in Hospital B from epidemiological and virus genome sequence data, using a suite of computational approaches. A maximum likelihood reconstruction of transmission involving known cases of infection suggests a high probability that doubly vaccinated HCWs transmitted SARS-CoV-2 between each other and highlights potential cases of virus transmission between individuals who had received two doses of vaccine. Our findings show firstly that vaccination may reduce rates of transmission, supporting the need for ongoing infection control measures even in highly vaccinated populations, and secondly we have described a novel approach to identifying transmissions that is scalable and rapid, without the need for an infection control infrastructure.
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SciScore for 10.1101/2021.11.19.21266406: (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
Software and Algorithms Sentences Resources SNP distance, variant calling and annotation: Single-nucleotide polymorphisms (SNPs), relative to the Delta variant strain, were identified by re-alignment of groupings of sequences based on each hospital to the Delta variant consensus reference (MZ359841.1) using mafft v7.8477 with the --keeplength and --addfragments parameters. mafftsuggested: (MAFFT, RRID:SCR_011811)Multiallelic variants are broken down into biallelic variant representations and are subsequently annotated by snpEff v5.0e17 with reference to MN908947.3. snpEffsuggested: (SnpEff, RRID:SCR_005191)Results from OddPub: …
SciScore for 10.1101/2021.11.19.21266406: (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
Software and Algorithms Sentences Resources SNP distance, variant calling and annotation: Single-nucleotide polymorphisms (SNPs), relative to the Delta variant strain, were identified by re-alignment of groupings of sequences based on each hospital to the Delta variant consensus reference (MZ359841.1) using mafft v7.8477 with the --keeplength and --addfragments parameters. mafftsuggested: (MAFFT, RRID:SCR_011811)Multiallelic variants are broken down into biallelic variant representations and are subsequently annotated by snpEff v5.0e17 with reference to MN908947.3. snpEffsuggested: (SnpEff, RRID:SCR_005191)Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Our study has caveats; firstly by only considering symptomatic cases, we exclude HCWs who are asymptomatic or fail to report their infection status. Secondly, the number of valid samples is further reduced by incomplete sampling and subsequent sequence filtering, likely resulting in incomplete transmission chains. Calculations suggested that the networks inferred for hospital B are likely to be affected by missing data, though the data from hospital A was not clearly affected. Although vaccination is still highly effective for Delta in protecting against severe disease12, we have demonstrated that breakthrough infections still occur in healthcare settings in individuals within 60 days of the second dose when circulating neutralising antibody levels are at their highest13. Given the risk of onward transmission to potentially very vulnerable patients (including people in whom vaccination is less effective, such as those with compromised immune systems), our findings highlight the need for ongoing infection control measures even in highly vaccinated populations, and mask wearing in individuals who have received two doses of vaccine, in order to limit onward transmission.
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.
Results from scite Reference Check: We found no unreliable references.
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