Sex: F
Vaccine: COVID19
Symptoms: COVID-19, Computerised tomogram, Drug ineffective, Polymerase chain reaction
Clinical narrative: symptomatic infection despite having completed vaccination with the PfizerBioNTech mRNA vaccine, including a booster approximately 6 weeks prior to symptom onset; Covid-19; This is a literature report for the following literature source(s): "Rapid detection and characterization of SARS-CoV-2 omicron variant in a returning traveler", Clinical Infectious Diseases, 2022; pgs:1-12, DOI:10.1093/cid/ciac032/6509065.  An adult female patient received bnt162b2 (BNT162B2), administration date Oct2021 (Batch/Lot number: unknown) as dose 3 (booster), single, administration date Feb2021 (Batch/Lot number: unknown) as dose 2, single and administration date Feb2021 (Batch/Lot number: unknown) as dose 1, single for covid-19 immunisation. The patient's relevant medical history and concomitant medications were not reported. The following information was reported: DRUG INEFFECTIVE (medically significant) with onset Nov2021, outcome "unknown", described as "symptomatic infection despite having completed vaccination with the PfizerBioNTech mRNA vaccine, including a booster approximately 6 weeks prior to symptom onset"; COVID-19 (medically significant) with onset Nov2021, outcome "recovered", described as "Covid-19". The patient underwent the following laboratory tests and procedures: computerised tomogram: 22.2, notes: VALUE; polymerase chain reaction: negative, notes: prior to departing to home; negative, notes: 48 hours prior to return travel; positive, notes: on day 3 after symptom onset; sars-cov-2 omicron variant, notes: SNP PCR; spike snp results, notes: variant sequence at amino acid position 417; spike snp results, notes: mutation conferring N501Y; l452r/l452q, notes: NOT DETECTED; e484k, notes: NOT DETECTED; f4905, notes: NOT DETECTED; negative, notes: T478K AFTER 72 HOURS. Therapeutic measures were not taken as a result of covid-19. Clinical course: Authors identified a previously-healthy woman in her 30s who presented with upper respiratory symptoms following a trip to country and was diagnosed with COVID-19 upon return to home in November 2021, four days after identification of omicron as a VOC. She was fully-vaccinated with the Pfizer-BioNTech BNT162b2 mRNA vaccine as of February 2021 and had received a booster of the same vaccine in early October 2021. She had a negative PCR test prior to departing the country and wore a medical-grade procedure mask and glasses on all flights. She stayed in a hotel in town for six days and attended an indoor, unmasked event with nine family members and friends, four of whom subsequently also tested positive for SARS-CoV-2. She had a negative PCR test 48 hours prior to return travel while asymptomatic, but then developed mild congestion on her last day in town, followed by a sore throat during travel home the next day. After arrival in (private), she also began experiencing nausea, fatigue, cough, and myalgias. She therefore had nasopharyngeal PCR testing performed at a community testing site on day 3 after symptom onset, which was positive. This sample was unable to be located during a contact tracing investigation. She never developed fevers, shortness of breath, or chest discomfort, and did not require medical attention. All symptoms had resolved by day 9, with the exception of ongoing myalgias and significant fatigue.   The patient was enrolled in a research study for emerging pathogens (Review Board STUDY00022371). A mid-turbinate nasal swab was obtained on day 4 after symptom onset. Nucleic acids were extracted from 400uL of swab sample and tested by rRT-PCR for the SARS-CoV-2 N2 target as previously described, yielding a Ct value of 22.2. The sample was also tested for specific single nucleotide polymorphisms (SNPs) in the spike receptor binding motif using the multiplex rRT-PCR Spike SNP assay. Briefly, the Spike SNP assay uses a single primer pair to amplify a 348bp region and tiled hydrolysis probes to differentiate mutations that are associated with VOC and variants of interest (VOI). Within 24 hours after sample collection, Spike SNP results from this sample detected a variant sequence at amino acid position 417 and the mutation conferring N501Y. It did not detect the mutations conferring L452R/L452Q, E484K, or F490S. This pattern of SNPs is consistent with the sequence expected for the omicron variant and different from results observed with prior VOCs/VOIs. Interestingly, the T478K mutation was not detected in this sample, though 90% of omicron sequences bear this mutation.   Within 72 hours after sample collection, the SARS-CoV-2 lineage from this sample's sequence was classified as B.1.1.529, and the variant as omicron, using cov-lineages.org. The sequence of the spike protein confirmed results from the multiplex spike SNP PCR assay, and additionally detected both T478K and the adjacent mutation S477N. The negative result for T478K by the Spike SNP assay is most likely because the mutation conferring S477N is located within the probe for T478K, preventing its binding. Overall, the spike sequence from this sample contained all mutations originally described for the omicron variant, including: amino acid substitutions at 30 positions; deletions at positions 69-70, 143-145, and 212; and insertion EPE after residue R214. Across the entire SARS-CoV-2 genome, the sequence from this sample did not harbor any unique mutations compared to available omicron reference genomes (N=538, downloaded from GISAID 2021-12-05).   Virus from the patient's nasal swab was successfully isolated in Vero-TMPSS2 cells. Its neutralization susceptibility was tested to serum collected from the patient on day 12, as well as sera from seven individuals who had undergone a similar vaccination regimen as the patient, with two doses plus a booster of the Pfizer-BioNTech BNT162b2 mRNA vaccine. The patient's post-infection serum was able to neutralize autologous virus with a FRNT50 GMT of 687, substantially higher than neutralization of this virus by sera from the other seven individuals.  Author summarized that they we rapidly detected the SARS-CoV-2 omicron variant in a patient with compatible epidemiological exposure using a combination of multiplex SARS-CoV-2 spike SNP PCR and viral genome sequencing. This was the first case detected by SARS-CoV-2 genomic surveillance in the state. Identifying this case required eliciting an appropriate travel history and being able to identify and perform sequencing for COVID patients in the community, since the patient had mild symptoms and did not seek clinical care. This underscores the importance of strong public health surveillance systems across a variety of settings. Thew patient had symptomatic infection despite having completed vaccination with Pfizer BioNTech mRNA vaccine, including a booster approximately 6 weeks prior to symptom onset. She experienced only mild illness, consistent with reports that the SARS-CoV-2 omicron variant is associated with fewer presentations to care and hospital admissions. Authors reassured, that this patient mounted a robust antibody response against autologous virus, and her post-infection serum was also able to neutralize other VOCs.  Follow-up (09Feb2022): This is a literature report for the following literature source entitled Rapid detection and characterization of SARS-CoV-2 omicron variant in a returning traveler, Clinical Infectious Diseases, 2022 , DOI: 10.1093/cid/ciac032/6509065. This is a follow-up report based on the receipt of the publication; the case has been updated to include additional information identified in the publication. Updated information: LOE classification updated, invalid classification removed, Reporter and Literature information updated. Lab data, products details (Name, dose number), Biological product, events tab updated (Events DRUG INEFFECTIVE and COVID-19) and case seriousness.  No follow-up attempts are possible. No further information is expected.; Sender's Comments: The vaccine efficacy varies from one patient to another and can be affected by different factors; however, a contributory role of the suspect vaccine BNT162B2 to the drug ineffective (LOE) cannot be ruled out.