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Community SARS-CoV-2 (COVID-19) transmission was eliminated in New Zealand by May 2020 following a stringent nationwide lockdown.[[1]] Other than two discrete community clusters (179 cases in August 2020 and 15 cases in February 2021) there has been no evidence of ongoing community transmission in New Zealand despite extensive surveillance testing.[[2]] Here we report a case of prolonged viral shedding in an individual infected in the August 2020 cluster, who tested positive again 150 days later.

Case report

A fit and well 34-year-old man with mild COVID-19 symptoms tested positive on 14 August 2020 (nasopharyngeal swab [NPS], in-house E-gene RT-PCR assay,[[3]] cycle threshold [Ct] value 17.6) (Figure 1). The patient was linked to the August 2020 cluster epidemiologically (likely infected via his church congregation) and genomically (identical lineage with signature T15867G single nucleotide polymorphism). He re-presented 150 days later on 11 January 2021 with acute breathlessness and tested positive again for SARS-CoV-2 on two different highly specific commercial RT-PCR assays, effectively ruling out a false-positive result due to non-specific reactions or laboratory contamination (NPS, BioFire Respiratory 2.1plus Panel and Xpert Xpress SARS-CoV-2 [E/N2 Ct values 36.9/38.4]). He denied infective symptoms and could not be linked contemporaneously to any imported COVID-19 cases or high-risk exposures. The aetiology of his breathlessness was mediastinal lymphadenopathy causing bronchial obstruction, and he was later diagnosed with sarcoidosis. Re-infection was considered unlikely, and since there was an alternative diagnosis for his clinical presentation, the “weak” positive (high Ct value) result from 11 January 2021 was attributed to prolonged viral shedding from the upper respiratory tract and he was discharged without further isolation. Whole genome sequencing was attempted but failed to yield any analysable sequence, likely due to the low viral load in the sample (reflected by the high Ct value). He had tested negative twice on pooled tests in the interim since his initial positive result, and repeat testing the following day was negative.

Figure 1: Summary of the patient’s SARS-CoV-2 PCR test results.

Discussion

New Zealand is one of the few countries to have eliminated COVID-19, and this post-elimination setting presents a relatively unique opportunity to observe patterns of SARS-CoV-2 viral shedding in the absence of re-infection or re-exposure. Viral shedding duration (presence of detectable viral nucleic acid) should be distinguished from duration of infectivity (presence of viable virus). Infectivity generally ends 10 days  after symptom onset in adults with mild–moderate COVID-19, with replication-competent virus rarely isolated after this time.[[4–6]] In contrast, upper respiratory tract viral shedding lasts for a mean of 17 days and can persist for months after recovery.[[4,7]] Prolonged viral shedding in no longer infectious individuals can result in unnecessary isolation, inappropriate use of PPE and limited isolation rooms, delays in medical care, discharge and return to work and separation from social support.[[4]] Laboratory testing alone cannot reliably establish a case as being “historical”: RT-PCR Ct values should not be used to exclude infectivity,[[8]] and due to considerable variation in serological assay performance and individual patient seroconversion rates and timings, serology should not be used to exclude acute SARS-CoV-2 infection.[[9]] Classification of any newly detected case as non-infectious should be made cautiously with expert consultation.[[4]]

This case is important for illustrating that, in individuals previously infected with SARS-CoV-2, sporadic positive RT-PCR results may be obtained many months after initial infection, even with multiple negative results in the interim. At 150 days, this case represents one of the longest shedding durations reported to date.[[7]] It has important public health implications for the interpretation of SARS-CoV-2 RT-PCR results in previously infected individuals and for studies characterising the SARS-CoV-2 shedding duration, which may otherwise fail to accurately capture the maximum shedding duration and thus underestimate the mean duration of viral shedding.

Summary

Abstract

Aim

Method

Results

Conclusion

Author Information

Andrew Fox-Lewis: Clinical Microbiology Registrar, Microbiology Department, Middlemore Hospital, Auckland, New Zealand. Shivani Fox-Lewis, Clinical Virology Registrar, Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand. Sandra Hotu: Respiratory Physician, Respiratory Department, Auckland City Hospital, Auckland, New Zealand. Sally Roberts: Clinical Microbiologist, Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand. Gary McAuliffe: Clinical Virologist, Virology-Immunology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand . Mary De Almeida: Clinical Microbiologist, Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand.

Acknowledgements

Andrew Fox-Lewis and Shivani Fox-Lewis contributed equally to this work. The authors would like to thank the patient for their co-operation and consent in writing up their clinical case.

Correspondence

Dr Andrew Fox-Lewis, Microbiology Department, LabPLUS, Building 31, Auckland City Hospital, Gate 4 off Grafton Rd, Grafton, Auckland, New Zealand, +64224586511

Correspondence Email

afoxlewis@gmail.com

Competing Interests

Nil.

1) Baker MG, Wilson N, Anglemyer A. Successful Elimination of Covid-19 Transmission in New Zealand. N Engl J Med. 2020 Aug 20;383(8):e56.

2) Ministry of Health New Zealand. COVID-19: Source of cases [Available from: https://www.health.govt.nz/our-work/diseases-and-conditions/covid-19-novel-coronavirus/covid-19-data-and-statistics/covid-19-source-cases#clusters-news, accessed 10/06/2021].

3) Corman VM, Landt O, Kaiser M, Molenkamp R, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 2020;25(3):2000045. doi:10.2807/1560-7917.ES.2020.25.3.2000045

4) Rhee C, Kanjilal S, Baker M, Klompas M. Duration of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infectivity: When Is It Safe to Discontinue Isolation? Clin Infect Dis. 2021 Apr 26;72(8):1467-1474. doi: 10.1093/cid/ciaa1249.

5) Centers for Disease Control and Prevention. Duration of Isolation and Precautions for Adults with COVID-19 [Available from: https://www.cdc.gov/coronavirus/2019-ncov/hcp/duration-isolation.html, accessed 10/06/2021].

6) World Health Organization. Criteria for releasing COVID-19 patients from isolation [Available from: https://www.who.int/news-room/commentaries/detail/criteria-for-releasing-covid-19-patients-from-isolation, accessed 10/06/2021].

7) Cevik M, Tate M, Lloyd O, Maraolo AE, et al. SARS-CoV-2, SARS-CoV, and MERS-CoV viral load dynamics, duration of viral shedding, and infectiousness: a systematic review and meta-analysis. Lancet Microbe. 2021 Jan;2(1):e13-e22. doi: 10.1016/S2666-5247(20)30172-5. Epub 2020 Nov 19.

8) Fox-Lewis A, Fox-Lewis S, Beaumont J, Drinković D, et al. SARS-CoV-2 viral load dynamics and real-time RT-PCR cycle threshold interpretation in symptomatic non-hospitalised individuals in New Zealand: a multicentre cross sectional observational study. Pathology. 2021 Jun;53(4):530-535. doi: 10.1016/j.pathol.2021.01.007. Epub 2021 Mar 20.

9) Centers for Disease Control and Prevention. Interim Guidelines for COVID-19 Antibody Testing [Available from: https://www.cdc.gov/coronavirus/2019-ncov/lab/resources/antibody-tests-guidelines.html, accessed 10/06/2021].

For the PDF of this article,
contact nzmj@nzma.org.nz

View Article PDF

Community SARS-CoV-2 (COVID-19) transmission was eliminated in New Zealand by May 2020 following a stringent nationwide lockdown.[[1]] Other than two discrete community clusters (179 cases in August 2020 and 15 cases in February 2021) there has been no evidence of ongoing community transmission in New Zealand despite extensive surveillance testing.[[2]] Here we report a case of prolonged viral shedding in an individual infected in the August 2020 cluster, who tested positive again 150 days later.

Case report

A fit and well 34-year-old man with mild COVID-19 symptoms tested positive on 14 August 2020 (nasopharyngeal swab [NPS], in-house E-gene RT-PCR assay,[[3]] cycle threshold [Ct] value 17.6) (Figure 1). The patient was linked to the August 2020 cluster epidemiologically (likely infected via his church congregation) and genomically (identical lineage with signature T15867G single nucleotide polymorphism). He re-presented 150 days later on 11 January 2021 with acute breathlessness and tested positive again for SARS-CoV-2 on two different highly specific commercial RT-PCR assays, effectively ruling out a false-positive result due to non-specific reactions or laboratory contamination (NPS, BioFire Respiratory 2.1plus Panel and Xpert Xpress SARS-CoV-2 [E/N2 Ct values 36.9/38.4]). He denied infective symptoms and could not be linked contemporaneously to any imported COVID-19 cases or high-risk exposures. The aetiology of his breathlessness was mediastinal lymphadenopathy causing bronchial obstruction, and he was later diagnosed with sarcoidosis. Re-infection was considered unlikely, and since there was an alternative diagnosis for his clinical presentation, the “weak” positive (high Ct value) result from 11 January 2021 was attributed to prolonged viral shedding from the upper respiratory tract and he was discharged without further isolation. Whole genome sequencing was attempted but failed to yield any analysable sequence, likely due to the low viral load in the sample (reflected by the high Ct value). He had tested negative twice on pooled tests in the interim since his initial positive result, and repeat testing the following day was negative.

Figure 1: Summary of the patient’s SARS-CoV-2 PCR test results.

Discussion

New Zealand is one of the few countries to have eliminated COVID-19, and this post-elimination setting presents a relatively unique opportunity to observe patterns of SARS-CoV-2 viral shedding in the absence of re-infection or re-exposure. Viral shedding duration (presence of detectable viral nucleic acid) should be distinguished from duration of infectivity (presence of viable virus). Infectivity generally ends 10 days  after symptom onset in adults with mild–moderate COVID-19, with replication-competent virus rarely isolated after this time.[[4–6]] In contrast, upper respiratory tract viral shedding lasts for a mean of 17 days and can persist for months after recovery.[[4,7]] Prolonged viral shedding in no longer infectious individuals can result in unnecessary isolation, inappropriate use of PPE and limited isolation rooms, delays in medical care, discharge and return to work and separation from social support.[[4]] Laboratory testing alone cannot reliably establish a case as being “historical”: RT-PCR Ct values should not be used to exclude infectivity,[[8]] and due to considerable variation in serological assay performance and individual patient seroconversion rates and timings, serology should not be used to exclude acute SARS-CoV-2 infection.[[9]] Classification of any newly detected case as non-infectious should be made cautiously with expert consultation.[[4]]

This case is important for illustrating that, in individuals previously infected with SARS-CoV-2, sporadic positive RT-PCR results may be obtained many months after initial infection, even with multiple negative results in the interim. At 150 days, this case represents one of the longest shedding durations reported to date.[[7]] It has important public health implications for the interpretation of SARS-CoV-2 RT-PCR results in previously infected individuals and for studies characterising the SARS-CoV-2 shedding duration, which may otherwise fail to accurately capture the maximum shedding duration and thus underestimate the mean duration of viral shedding.

Summary

Abstract

Aim

Method

Results

Conclusion

Author Information

Andrew Fox-Lewis: Clinical Microbiology Registrar, Microbiology Department, Middlemore Hospital, Auckland, New Zealand. Shivani Fox-Lewis, Clinical Virology Registrar, Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand. Sandra Hotu: Respiratory Physician, Respiratory Department, Auckland City Hospital, Auckland, New Zealand. Sally Roberts: Clinical Microbiologist, Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand. Gary McAuliffe: Clinical Virologist, Virology-Immunology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand . Mary De Almeida: Clinical Microbiologist, Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand.

Acknowledgements

Andrew Fox-Lewis and Shivani Fox-Lewis contributed equally to this work. The authors would like to thank the patient for their co-operation and consent in writing up their clinical case.

Correspondence

Dr Andrew Fox-Lewis, Microbiology Department, LabPLUS, Building 31, Auckland City Hospital, Gate 4 off Grafton Rd, Grafton, Auckland, New Zealand, +64224586511

Correspondence Email

afoxlewis@gmail.com

Competing Interests

Nil.

1) Baker MG, Wilson N, Anglemyer A. Successful Elimination of Covid-19 Transmission in New Zealand. N Engl J Med. 2020 Aug 20;383(8):e56.

2) Ministry of Health New Zealand. COVID-19: Source of cases [Available from: https://www.health.govt.nz/our-work/diseases-and-conditions/covid-19-novel-coronavirus/covid-19-data-and-statistics/covid-19-source-cases#clusters-news, accessed 10/06/2021].

3) Corman VM, Landt O, Kaiser M, Molenkamp R, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 2020;25(3):2000045. doi:10.2807/1560-7917.ES.2020.25.3.2000045

4) Rhee C, Kanjilal S, Baker M, Klompas M. Duration of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infectivity: When Is It Safe to Discontinue Isolation? Clin Infect Dis. 2021 Apr 26;72(8):1467-1474. doi: 10.1093/cid/ciaa1249.

5) Centers for Disease Control and Prevention. Duration of Isolation and Precautions for Adults with COVID-19 [Available from: https://www.cdc.gov/coronavirus/2019-ncov/hcp/duration-isolation.html, accessed 10/06/2021].

6) World Health Organization. Criteria for releasing COVID-19 patients from isolation [Available from: https://www.who.int/news-room/commentaries/detail/criteria-for-releasing-covid-19-patients-from-isolation, accessed 10/06/2021].

7) Cevik M, Tate M, Lloyd O, Maraolo AE, et al. SARS-CoV-2, SARS-CoV, and MERS-CoV viral load dynamics, duration of viral shedding, and infectiousness: a systematic review and meta-analysis. Lancet Microbe. 2021 Jan;2(1):e13-e22. doi: 10.1016/S2666-5247(20)30172-5. Epub 2020 Nov 19.

8) Fox-Lewis A, Fox-Lewis S, Beaumont J, Drinković D, et al. SARS-CoV-2 viral load dynamics and real-time RT-PCR cycle threshold interpretation in symptomatic non-hospitalised individuals in New Zealand: a multicentre cross sectional observational study. Pathology. 2021 Jun;53(4):530-535. doi: 10.1016/j.pathol.2021.01.007. Epub 2021 Mar 20.

9) Centers for Disease Control and Prevention. Interim Guidelines for COVID-19 Antibody Testing [Available from: https://www.cdc.gov/coronavirus/2019-ncov/lab/resources/antibody-tests-guidelines.html, accessed 10/06/2021].

For the PDF of this article,
contact nzmj@nzma.org.nz

View Article PDF

Community SARS-CoV-2 (COVID-19) transmission was eliminated in New Zealand by May 2020 following a stringent nationwide lockdown.[[1]] Other than two discrete community clusters (179 cases in August 2020 and 15 cases in February 2021) there has been no evidence of ongoing community transmission in New Zealand despite extensive surveillance testing.[[2]] Here we report a case of prolonged viral shedding in an individual infected in the August 2020 cluster, who tested positive again 150 days later.

Case report

A fit and well 34-year-old man with mild COVID-19 symptoms tested positive on 14 August 2020 (nasopharyngeal swab [NPS], in-house E-gene RT-PCR assay,[[3]] cycle threshold [Ct] value 17.6) (Figure 1). The patient was linked to the August 2020 cluster epidemiologically (likely infected via his church congregation) and genomically (identical lineage with signature T15867G single nucleotide polymorphism). He re-presented 150 days later on 11 January 2021 with acute breathlessness and tested positive again for SARS-CoV-2 on two different highly specific commercial RT-PCR assays, effectively ruling out a false-positive result due to non-specific reactions or laboratory contamination (NPS, BioFire Respiratory 2.1plus Panel and Xpert Xpress SARS-CoV-2 [E/N2 Ct values 36.9/38.4]). He denied infective symptoms and could not be linked contemporaneously to any imported COVID-19 cases or high-risk exposures. The aetiology of his breathlessness was mediastinal lymphadenopathy causing bronchial obstruction, and he was later diagnosed with sarcoidosis. Re-infection was considered unlikely, and since there was an alternative diagnosis for his clinical presentation, the “weak” positive (high Ct value) result from 11 January 2021 was attributed to prolonged viral shedding from the upper respiratory tract and he was discharged without further isolation. Whole genome sequencing was attempted but failed to yield any analysable sequence, likely due to the low viral load in the sample (reflected by the high Ct value). He had tested negative twice on pooled tests in the interim since his initial positive result, and repeat testing the following day was negative.

Figure 1: Summary of the patient’s SARS-CoV-2 PCR test results.

Discussion

New Zealand is one of the few countries to have eliminated COVID-19, and this post-elimination setting presents a relatively unique opportunity to observe patterns of SARS-CoV-2 viral shedding in the absence of re-infection or re-exposure. Viral shedding duration (presence of detectable viral nucleic acid) should be distinguished from duration of infectivity (presence of viable virus). Infectivity generally ends 10 days  after symptom onset in adults with mild–moderate COVID-19, with replication-competent virus rarely isolated after this time.[[4–6]] In contrast, upper respiratory tract viral shedding lasts for a mean of 17 days and can persist for months after recovery.[[4,7]] Prolonged viral shedding in no longer infectious individuals can result in unnecessary isolation, inappropriate use of PPE and limited isolation rooms, delays in medical care, discharge and return to work and separation from social support.[[4]] Laboratory testing alone cannot reliably establish a case as being “historical”: RT-PCR Ct values should not be used to exclude infectivity,[[8]] and due to considerable variation in serological assay performance and individual patient seroconversion rates and timings, serology should not be used to exclude acute SARS-CoV-2 infection.[[9]] Classification of any newly detected case as non-infectious should be made cautiously with expert consultation.[[4]]

This case is important for illustrating that, in individuals previously infected with SARS-CoV-2, sporadic positive RT-PCR results may be obtained many months after initial infection, even with multiple negative results in the interim. At 150 days, this case represents one of the longest shedding durations reported to date.[[7]] It has important public health implications for the interpretation of SARS-CoV-2 RT-PCR results in previously infected individuals and for studies characterising the SARS-CoV-2 shedding duration, which may otherwise fail to accurately capture the maximum shedding duration and thus underestimate the mean duration of viral shedding.

Summary

Abstract

Aim

Method

Results

Conclusion

Author Information

Andrew Fox-Lewis: Clinical Microbiology Registrar, Microbiology Department, Middlemore Hospital, Auckland, New Zealand. Shivani Fox-Lewis, Clinical Virology Registrar, Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand. Sandra Hotu: Respiratory Physician, Respiratory Department, Auckland City Hospital, Auckland, New Zealand. Sally Roberts: Clinical Microbiologist, Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand. Gary McAuliffe: Clinical Virologist, Virology-Immunology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand . Mary De Almeida: Clinical Microbiologist, Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand.

Acknowledgements

Andrew Fox-Lewis and Shivani Fox-Lewis contributed equally to this work. The authors would like to thank the patient for their co-operation and consent in writing up their clinical case.

Correspondence

Dr Andrew Fox-Lewis, Microbiology Department, LabPLUS, Building 31, Auckland City Hospital, Gate 4 off Grafton Rd, Grafton, Auckland, New Zealand, +64224586511

Correspondence Email

afoxlewis@gmail.com

Competing Interests

Nil.

1) Baker MG, Wilson N, Anglemyer A. Successful Elimination of Covid-19 Transmission in New Zealand. N Engl J Med. 2020 Aug 20;383(8):e56.

2) Ministry of Health New Zealand. COVID-19: Source of cases [Available from: https://www.health.govt.nz/our-work/diseases-and-conditions/covid-19-novel-coronavirus/covid-19-data-and-statistics/covid-19-source-cases#clusters-news, accessed 10/06/2021].

3) Corman VM, Landt O, Kaiser M, Molenkamp R, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 2020;25(3):2000045. doi:10.2807/1560-7917.ES.2020.25.3.2000045

4) Rhee C, Kanjilal S, Baker M, Klompas M. Duration of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infectivity: When Is It Safe to Discontinue Isolation? Clin Infect Dis. 2021 Apr 26;72(8):1467-1474. doi: 10.1093/cid/ciaa1249.

5) Centers for Disease Control and Prevention. Duration of Isolation and Precautions for Adults with COVID-19 [Available from: https://www.cdc.gov/coronavirus/2019-ncov/hcp/duration-isolation.html, accessed 10/06/2021].

6) World Health Organization. Criteria for releasing COVID-19 patients from isolation [Available from: https://www.who.int/news-room/commentaries/detail/criteria-for-releasing-covid-19-patients-from-isolation, accessed 10/06/2021].

7) Cevik M, Tate M, Lloyd O, Maraolo AE, et al. SARS-CoV-2, SARS-CoV, and MERS-CoV viral load dynamics, duration of viral shedding, and infectiousness: a systematic review and meta-analysis. Lancet Microbe. 2021 Jan;2(1):e13-e22. doi: 10.1016/S2666-5247(20)30172-5. Epub 2020 Nov 19.

8) Fox-Lewis A, Fox-Lewis S, Beaumont J, Drinković D, et al. SARS-CoV-2 viral load dynamics and real-time RT-PCR cycle threshold interpretation in symptomatic non-hospitalised individuals in New Zealand: a multicentre cross sectional observational study. Pathology. 2021 Jun;53(4):530-535. doi: 10.1016/j.pathol.2021.01.007. Epub 2021 Mar 20.

9) Centers for Disease Control and Prevention. Interim Guidelines for COVID-19 Antibody Testing [Available from: https://www.cdc.gov/coronavirus/2019-ncov/lab/resources/antibody-tests-guidelines.html, accessed 10/06/2021].

Contact diana@nzma.org.nz
for the PDF of this article

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