A comparison of four self-controlled study designs in an analysis of COVID-19 vaccines and myocarditis using five European databases

INTRODUCTION

The aim of this study was to assess the possible extent of bias due to violation of a core assumption (event-dependent exposures) when using self-controlled designs to analyse the association between COVID-19 vaccines and myocarditis.

METHODS

We used data from five European databases (Spain: BIFAP, FISABIO VID, and SIDIAP; Italy: ARS-Tuscany; England: CPRD Aurum) converted to the ConcePTION Common Data Model. Individuals who experienced both myocarditis and were vaccinated against COVID-19 between 1 September 2020 and the end of data availability in each country were included. We compared a self-controlled risk interval study (SCRI) using a pre-vaccination control window, an SCRI using a post-vaccination control window, a standard SCCS and an extension of the SCCS designed to handle violations of the assumption of event-dependent exposures.

RESULTS

We included 1,757 cases of myocarditis. For analyses of the first dose of the Pfizer vaccine, to which all databases contributed information, we found results consistent with a null effect in both of the SCRI and extended SCCS, but some indication of a harmful effect in a standard SCCS. For the second dose, we found evidence of a harmful association for all study designs, with relatively similar effect sizes (SCRI pre = 1.99, 1.40 - 2.82; SCRI post 2.13, 95 %CI - 1.43, 3.18; standard SCCS 1.79, 95 %CI 1.31 - 2.44, extended SCCS 1.52, 95 %CI = 1.08 - 2.15). Adjustment for calendar time did not change these conclusions. Findings using all designs were also consistent with a harmful effect following a second dose of the Moderna vaccine.

CONCLUSIONS

In the context of the known association between COVID-19 vaccines and myocarditis, we have demonstrated that two forms of SCRI and two forms of SCCS led to largely comparable results, possibly because of limited violation of the assumption of event-dependent exposures.

Absence of a coding region for the helper component-proteinase in the genome of cucumber vein yellowing virus, a whitefly-transmitted member of the Potyviridae

The complete nucleotide sequence of isolates of Cucumber vein yellowing virus (CVYV) has been determined. The viral genome comprises 9734 nucleotides, excluding a 3'-terminal poly(A) sequence. The genome of CVYV has a 5'-non coding and a 3' non coding region of respectively 67 and 240 nucleotides. The RNA of CVYV encodes a single polyprotein of 3148 amino acid residues and has a deduced genome organization and motifs typical for a member of the family Potyviridae. However, CVYV is atypical because it lacks a coding sequence region for the putative helper-component as well as conserved helper-component-proteinase motifs which may account for its vector relations. All the present coding regions were compared to those from several members of the Potyviridae family. CVYV is most closely related to Sweetpotato mild mottle virus confirming its assignation to the genus Ipomovirus, despite similarities with tritimoviruses.

First Report of Southern bean mosaic virus Infecting French Bean in Morocco

Common bean (Phaseolus vulgaris L.) is grown on approximately 1,500 ha in commercial greenhouses and is of major economic importance in the Souss-Massa Region, Agadir, Morocco. Since October 2003, symptoms resembling a viral disease, consisting of pod mosaic and distortion and mild to severe mosaic in leaves, have been observed on bean plants in several greenhouses. Mechanical inoculation with symptomatic leaf extracts produced necrotic local lesions on P. vulgaris 'Pinto' and systemic symptoms similar to those observed in the naturally infected bean plants P. vulgaris 'Donna' (five plants per cultivar). Inoculated and naturally infected samples reacted positively using a double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) to Southern bean mosaic virus (SBMV) (DSMZ, Braunschweig, Germany), a member of the Sobemovirus genus that is transmitted by contact, soil, beetles, and seeds (1). Virions purified from a naturally infected 'Donna' plant contained a 30-kDa polypeptide that reacted positively using sodium dodecyl sulfate polyacrylamide gel electrophoresis and western blot analysis with SBMV antiserum (DSMZ). Reverse transcription-polymerase chain reaction amplification with SMBV primers as described by Verhoeven et al. (2) produced an expected 870-bp band. The amplicon was cloned, sequenced (GenBank Accession No. AJ748276), and compared to those isolates available in GenBank and had a nucleotide sequence identity of 87% and a derived amino acid sequence identity of 95% with an SBMV isolate from Spain (2). During a survey in different areas of the Souss-Massa Region, 20 symptomatic leaf and pod samples were randomly collected from 12 greenhouses (50 ha) where significant commercial losses were suffered because of this virus disease, and all samples were positive using DAS-ELISA for SBMV. To our knowledge, this is the first report of SBMV in Morocco. References: (1) J. H. Tremaine and R. I. Hamilton. Southern bean mosaic virus. No. 274 in: Descriptions of Plant Viruses. CMI/AAB, Kew, Surrey, England, 1983. (2) J. Th. J. Verhoeven et al. Eur. J. Plant Pathol. 109:935, 2003.

First Report of Turnip mosaic virus in Pisum sativum in Spain

During 2001 and 2002, Pisum sativum var. vulgare plants grown as commercial crops in Almeria (southeast Spain) showed vein clearing and chlorotic mottle of leaves, leaf deformation, flower abortion, necrotic mottle and deformation of pods, and stunted plant growth. Crude sap of collected plants was mechanically inoculated on healthy pea plants which reproduced symptoms observed in the field; local necrotic lesions were produced on mechanically infected Chenopodium quinoa, C. amaranticolor, and Gomphrena globosa, systemic mosaic symptoms on Brassica napus and Nicotiana benthamiana, and local lesions plus systemic mosaic symptoms on N. clevelandii, which are all characteristic of Turnip mosaic virus (TuMV) (1). A reverse transcription-polymerase chain reaction assay using general primers for the extreme 3' end of the potyvirus genome amplified products of 750 and 1,700 bp in nucleic acid extracts from naturally infected pea plants as well as from the mechanically infected test plants. The overlapping nucleotide sequences of the products (GenBank Accession No. AJ489259) had a nucleotide sequence identity of 86.5% and a derived amino acid identity of 95.0% with several published sequences of TuMV (1). This report cites the first partial nucleotide sequence of TuMV infecting pea crops, and although natural infections of this virus in pea have been reported in Morocco (1976) and in the United States (2), to our knowledge, this is the first report of TuMV in Spain. References: (1) P. Lehmann et al. Physiol. Mol. Plant Pathol. 51:195, 1997. (2) R. Provvidenti. Plant Dis. Rep. 62:482, 1978.

First Report of Cucumber leaf spot virus in Spain

Cucumber leaf spot virus (CLSV), reclassified as a species in the new genus Aureusvirus (family Tombusviridae) (1), has ≈30-nm isometric particles with a ≈4.4-kb positive-sense, single-stranded RNA. CLSV is transmitted by the chytrid fungus Olpidium bornovanus. The virus has been reported in Germany, Great Britain, Greece, Jordan, and Saudi Arabia. During the fall of 2000, abundant chlorotic spots with necrotic centers were observed on the leaves of cucumber plants grown in a commercial greenhouse in Granada (southeastern Spain). When sap from collected leaves was used to mechanically inoculate cucumber, symptoms were reproduced and were suggestive of CLSV. Based on the nucleic acid sequence of CSLV (2), the following specific primers were designed: CLSVU1440 (5'-AAGGTAGGGGAGATCTTG-3') and CLSVA2160 (5'-GCTTCGGCTGATTCTGA-3'). When used in reverse transcription-polymerase chain reactions (RT-PCR), leaves expressing symptoms yielded amplification products of the expected size (720 bp). These products were cloned into a pGEM-T vector and sequenced (GenBank Accession No. AY038365). The similarity of the nucleic acid and derived amino acid sequences with the one published for CLSV (2) was 94.5 and 99.1%, respectively. The amino acid sequence was 86% identical to that of Pothos latent virus (GenBank Accession No. AJ243370). Ten cucumber plants grown in vermiculite supplemented with rhizosphere soil (1/30, vol/wt) from infected plants developed symptoms on leaves after 1 month and were positive for CLSV when leaf and root tissues were analyzed by RT-PCR and Southern blot hybridization. Plants grown in vermiculite alone did not become infected with CLSV. Microscopic examination of root tissue revealed O. bornovanus only in infected plants. To our knowledge, this is the first record of CSLV in Spain. References: (1) G. P. Martelli et al. Arch. Virol. 143:1847, 1998. (2) J. S. Miller et al. Virus Res. 52:51, 1997.

First Report of Cucumber vein yellowing virus in Spain

In the autumn of 2000, an outbreak of a disease caused considerable losses in greenhouse cucumber crops in Almeria (Spain). Infected plants showed vein clearing followed by chlorosis in leaves and yellow/green chlorotic spots on fruits. These symptoms as well as the presence of Bemisia tabaci in the crops suggested the possible involvement of Cucumber vein yellowing virus (CVYV), a proposed member of the Potiviridae family, which was first described in 1960 in Cucumis spp. from Israel (1). B. tabaci populations and leaves from cucumber plants were collected from the greenhouses and analyzed by RT-PCR using specific primers (CV(+): 5'-AGCTAGCGCGTATGGGGTGAC-3'; CV(-): 5'-GCGCCGCAAGTGCAA-ATAAAT-3') that we designed based on the partial sequence published for CVYV (2). Total nucleic acid extracts from both B. tabaci individuals and the collected plants yielded amplification products of the expected size (449 bp), which were cloned and sequenced (Genebank accession number AJ301640). The sequence was 95.6% identical to that previously reported for CVYV. Nonviruliferous B. tabaci whiteflies were given a 24-h acquisition period on symptomatic leaves and then placed in groups of 15 insects on each of 10 healthy cucumber plants at the 4 leaf-stage for a 24-h inoculation period. Inoculated and control plants were analyzed 1 week later and the infection with CVYV was confirmed (10/10) by RT-PCR. Doublestranded RNA extractions from field-collected samples and from plants inoculated under controlled conditions suggested that no dsRNA formation was associated with the infection. This is the first report of CVYV in Spain. References: (1) S. Cohen and F. E. Nitzany. Phytopathol. Medit. 1:44, 1960. (2) H. Lecoq et al. J. Gen. Virol. 81:2289, 2000.