{"doi":"10.1002/jmv.27154","title":"Reinfection with two genetically distinct SARS‐CoV‐2 viruses within 19 days","abstract":"Increasing detection of reinfections and waning neutralizing antibody (Nab) titers as early as 23 days following initial infection1 raises concerns for herd immunity and the durability of vaccine efficacy.2, 3 Since the first reported reinfection case in August 2020,4 at least 70 confirmed cases have emerged as of April 27, 2021.5 In October 2020, the US Centers for Disease Control and Prevention (CDC) published investigative criteria for suspected SARS-CoV-2 reinfections.6 These criteria included any individuals testing positive ≥90 days after their first laboratory-confirmed SARS-CoV-2 infection or symptomatic individuals testing positive 45–89 days after initial infection with paired respiratory specimens.6 Here, we describe a patient infected with two genetically distinct SARS-CoV-2 strains detected 19 days apart, indicating that reinfection can occur within a short period. Ninety-two SARS-CoV-2 positive nasopharyngeal samples (CDC 2019 Novel Coronavirus Real-Time Reverse Transcriptase-PCR Diagnostic Panel7) were collected in Columbia, Missouri from March to May 2020. Two samples, collected 19 days apart, were from the same patient. SARS-CoV-2 virus isolates were recovered from each of the two samples. The SARS-CoV-2 viruses from both clinical swabs were sequenced using Access Array microfluidic (Fluidigm Corporation) and MiSeq systems (Illumina).8 Phylogenetic analyses were performed using BEAST2 (see Supporting Information Appendix for Materials and Methods). This patient was a female in her 20 s with asthma, obesity, anxiety, and depression, who reported cough, chills, exertional dyspnea, sore throat, dizziness, rhinorrhea, and fever during her initial COVID-19 diagnosis in March 2020. She tested positive 1 day after symptom onset and was instructed to self-isolate at home. Nineteen days following her initial positive test, she returned for another COVID-19 test due to return-to-work requirements. Despite her symptoms waning to encompass only productive cough and fatigue, she tested COVID-19 positive again. She continued to experience persistent cough, fatigue, and dyspnea until 55 days after her initial positive test. Phylogenetic analyses showed that the two samples contained SARS-CoV-2 viruses from two distinct lineages (Figure 1); Sample 1 (GenBank accession No.: MW521480.1; cycle threshold [Ct] value = 17.76) belonged to the PANGOLIN A.3 lineage, whereas the Sample 2 (MW521502.1; Ct value = 20.36) belonged to the PANGOLIN B.1.1 lineage. Additionally, we compared the sequences between viral isolates and clinical samples. Results showed that sequences from each isolate were identical to the corresponding clinical sample, but those at the first sample and at the second sample were distinct. The virus sequences had 21 nucleotide substitutions relative to each other, encoding 11 nonsynonymous amino acid mutations across five genes (ORF1ab (D75E on nonstructural protein 1 (NSP1), P971L on NSP3, P4715L on NSP12, F6158L on NSP14), ORF8 (V62L, L84S), ORF7a (S81L) ORF10 (I4L), S (D614G) and N (R202K, G203R)). The average sequence depth was 3960 (Day 1 virus) and 3233 (Day 19) reads, and each of those 21-variation positions had a minimum raw read depth of 1978 reads (Table 1). No diverse polymorphisms were identified among the sequences of the viruses from each clinical sample, suggesting true reinfection rather than a coinfection. This report is limited by the unavailability of sera samples to study Nab titers and lack of information regarding the patient's potential contacts with others during the 2-week isolation period. Nevertheless, this case showed a patient who unknowingly became reinfected with two genetically distinct viruses within 19 days and may have still been infectious after the CDC-recommended 10 day isolation period.9 Additionally, the CDC has encouraged symptom-based strategies for ending isolation rather than viral retesting for asymptomatic individuals or for individuals without new symptoms during 90 days","journal":"Journal of Medical Virology","year":2021,"id":182093,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":15,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9648,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":553484,"name":"Yang Wang","orcid":"0000-0002-6527-864X","position":1,"is_corresponding":false},{"id":733878,"name":"Jane A. McElroy","orcid":"0000-0001-7518-747X","position":2,"is_corresponding":false},{"id":733879,"name":"Tao Li","orcid":"0000-0002-2548-5476","position":3,"is_corresponding":false},{"id":733880,"name":"Richard Hammer","orcid":"0000-0002-7173-9414","position":4,"is_corresponding":false},{"id":733881,"name":"Detlef Ritter","orcid":"0009-0003-5933-1621","position":5,"is_corresponding":false},{"id":734421,"name":"Grace M. Lidl","orcid":null,"position":6,"is_corresponding":false},{"id":105444,"name":"Richard J. Webby","orcid":"0000-0002-4397-7132","position":7,"is_corresponding":false},{"id":583487,"name":"Jun Hang","orcid":"0000-0002-6597-7045","position":8,"is_corresponding":false},{"id":658492,"name":"Xiu‐Feng Wan","orcid":"0000-0003-3907-5803","position":9,"is_corresponding":false},{"id":266770,"name":"Cynthia Y. Tang","orcid":"0000-0001-5272-7170","position":0,"is_corresponding":true}],"reference_count":7,"raw_metadata":null,"created_at":"2026-07-18T23:48:09.223560Z","pmid":"34170528","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}