key: cord-0714292-4fbqc1m8
authors: Alshukairi, Abeer N; Al-Omari, Awad; Al-Tawfiq, Jaffar A; El-Kafrawy, Sherif A.; El-Daly, Mai M; Hassan, Ahmed M.; Faizo, Arwa A; Alandijany, Thamir A.; Dada, Ashraf; Saeedi, Mohammed F; Alhamlan, Fatma S.; Al Hroub, Mohammad K; Qushmaq, Ismael; Azhar, Esam I.
title: Active Viral Shedding in a Vaccinated Hospitalized Patient Infected with The Delta avariant (B.1.617.2) of SARS-CoV-2 and Challenges of De-isolation
date: 2022-04-28
journal: J Infect Public Health
DOI: 10.1016/j.jiph.2022.04.011
sha: 2b6bff7d65d885457655c33157148d2faa31490e
doc_id: 714292
cord_uid: 4fbqc1m8

In the era of SARS-CoV-2 variants and COVID-19 vaccination, the duration of infectious viral shedding and isolation in post vaccine breakthrough infections is challenging and depends on disease severity. The current study described a case of SARS-CoV-2 Delta variant pneumonia requiring hospitalization. The patient received two doses of BNT162b2 COVID-19 vaccines, and he had positive SARS-CoV-2 viral cultures 12 days post symptom onset. The time between the second dose of vaccine and the breakthrough infection was 6 months. While immunosuppression is a known risk factor for prolonged infectious viral shedding, age and time between vaccination and breakthrough infection are important risk factors that warrant further studies.

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In the pre-era of SARS-CoV-2 variants and COVID-19 vaccination, the duration of infectious viral shedding and isolation was ten days in patients with mild to moderate COVID-19 disease, twenty days in severe disease and several months in immunocompromised patients [1] . Recently, in the era of SARS-CoV-2 variants and COVID-19 vaccination, the guidelines of isolation of COVID-19 were revised by Centers for disease control and prevention and the duration of isolation of COVID-19 patients who received two doses of vaccines was limited to five days in mild disease and extended to 10 in moderate disease and 20 days in severe disease [2] . A recent study described the duration of infectious viral shedding in breakthrough SARS-CoV-2 Delta variants infections in ambulatory patients with mild disease and showed that 9 out of 10 patients (90%) had negative viral cultures within 10 days of symptoms onset [3] .There are limited studies describing the duration of infectious viral shedding of post vaccine Delta variants breakthrough infections in hospitalized patients. The current study described the viral culture results of a patient who received two doses of BNT162b2 COVID-19 vaccine and was hospitalized with Delta variant COVID-19 pneumonia, six months post second dose of vaccine, in a tertiary care center in Jeddah, Saudi

Arabia. The challenges of de-isolation for hospitalized and vaccinated patients infected with Delta variants were discussed. This research was approved by the institutional research board. The patient was consented and agreed to participate in the study.

Serial swabs were collected for SARS-CoV-2 PCR and viral cultures. Whole genome sequence was performed on one of the samples. SARS-CoV-2 PCR, whole genome sequence and viral culture were performed as previously described [4, 5] . platform. The assay detects dual targets genes RdRp and N-genes with a detection limit of 1 copy per ml. 

Collected samples were diluted at 1:10 dilution in DMEM with 10% FBS, inoculated on Vero E6 cells in 6 well plates in duplicates, and incubated for 1hrat 37°C. Inoculum was then removed and replaced with 2 mL DMEM with 2% FBS and incubated for 3 days at 37°C or until cytopathic effect (CPE) was observed in 85-90% of cells of the positive control samples.

The patient's nasopharyngeal sample was sent to the microbial genomics laboratory for SARS-CoV-2 whole-genome sequencing at the Department of Infection and Immunity, King 

In Singapore, using SARS-CoV-2 PCR Ct values as a surrogate marker of viral shedding, vaccinated hospitalized patients infected with Delta variants had a rapid decline in viral load compared to hospitalized unvaccinated patients infected with Delta variants, 6.6 days versus 9.3 days [7] . In United Kingdom, although vaccination status and Delta variants did not affect SARS-CoV-2 peak viral load, old age (more than 50 years) was associated with an increased in peak viral load. In addition, individuals with high peak viral load had a slow viral decline and clearance [8] . Sidner et al (2022) described the differences in viral clearance based on SARS-CoV-2 PCR testing and viral culture among vaccinated patients infected with Delta and non-Delta variants in the ambulatory setting [3] . Compared to individuals infected with non-Delta variants, those infected with Delta variants had longer duration of viral shedding by SARS-CoV-2 PCR (13.5 versus 4.5 days) and viral culture (7 versus 4 days). In addition, compared to individuals vaccinated less than 3 months, those vaccinated more than 3 months had a longer duration of positive SARS-CoV-2 PCR (13.5 versus 3 days) and viral culture (7 versus 3 days). Among a cohort of patients infected with Delta variants, there was no difference in the duration of viral shedding between vaccinated and partially vaccinated individuals using SARS-CoV-2 PCR testing (13 days) and viral culture (5 days) [9] . The findings from the current study of persistent positive viral cultures for more than 10 days in Omicron COVID-19 samples were higher among patients who received three mRNA vaccine compared to those who received two doses indicating a lower SAR-CoV-2 viral load among patients who had boosters compared to those who had only two vaccine doses [11] .

Determining a reliable and a rapid surrogate marker for infectious viral shedding such as rapid antigen tests requires future studies as PCR testing is associated with prolonged viral shedding and may not reflect infectious viral shedding while viral cultures are time consuming and needs special research laboratories [12] .

The current case study showed prolonged SARS-CoV-2 infectious viral shedding for 12 days post symptoms onset in a hospitalized patient with COVID-19 variant (Delta) pneumonia, who was more than 65 years old and was vaccinated 6 months prior to infection. A test-based approach may be required to end isolation. The ideal de-isolation test needs to be studied.

J o u r n a l P r e -p r o o f

SARS-CoV-2 viral shedding and transmission dynamics: implications of WHO COVID-19 discharge guidelines

Ending isolation and precautions for people with COVID-19: interim guidance

Duration of viral shedding and culture positivity with postvaccination SARS-CoV-2 delta variant infections

Re-infection with a different SARS-CoV-2 clade and prolonged viral shedding in a hematopoitic stem cell transplantation patient

Outcome of SARS-CoV-2 variant breakthrough infection in fully immunized solid organ transplant recipients

Breakthrough infections after COVID-19 vaccination: insights, perspectives and challenges

Virological and serological kinetics of SAR-CoV-2

Delta variant vaccine breakthrough infections: a multicenter cohort study. Article in press

Community transmission and viral load kinetics of the SARS-CoV-2 delta (B.1.617.2) variant in vaccinated and unvaccinated individuals in the UK: a prospective, longitudinal, cohort study

Transmission potential of vaccinated and unvaccinated persons infected with SARS-CoV-2 Delta variant in a federal prison

Waning immune humoral response to BNT162b2 COVID-19 vaccine over 6 months

Association between 3 doses of mRNA COVID-19 vaccine and symptomatic infection caused by the SARS-CoV-2 omicron and delta variants

Can testing predict SARS-CoV-2 infectivity? The potential for certain methods to be surrogates for replication-competent virus

Days post-symptoms SARS-CoV-2 PCR result

Table 1: Serial PCR and Ct values in relation to days post symptoms onset. Viral culture was available on day 12 post symptoms onset only

We would like to thank our patient who contributed to this research.The authors acknowledge the generous charitable donation from the Late Sheikh Ibraheem Ahmed Azhar in the form of reagents and supplies as a contribution to the scientific research community.

Hospital and Research Center, Jeddah, Saudi Arabia

All authors contributed equally to this research; study concept, data acquisition, data analysis, performing the experiment, writing and reviewing the manuscript.