Prolonged positive RT-PCR result in

COVID-19 patients:
should we end their isolation and
discharge them?

Titik Nuryastuti
Microbiology Dept, FK-KMK UGM
Prolonged positive RT PCR

Does it match with clinical

manifestation?
Positive RT PCR for > 14 days
after the first result Is it still infectious ?

PCR kinetic: Cycle

threshold/ Ct value?
How to manage these
cases?
 Real time RT-PCR SARS-CoV-2
rapid and accurate
detection: early diagnosis of COVID-
control the sources of 19: critical for prevention
infection and help patients and control of this
to prevent the illness pandemic
progression

clinical characteristics
cannot alone define the
Able to detect in all stage diagnosis of COVID-19,
of infection especially for patients
presenting early-onset of
symptoms
Tahamtan,2020
Limitation, false negative

variation of viral RNA

sequences

Genetic diversity and

• mutations in the primer and probe target
rapid evolution of this
regions in the SARS-CoV-2 genome
novel coronavirus

mismatches between the • multiple target gene amplification

primers and probes and
• several types of SARSCoV-2 real-time RT-PCR kit
the target sequences
Limitation, false negative

viral load kinetics in different anatomic 93% for broncho-alveolar lavage, 72% for
sites of the patients, sampling sputum, 63% for nasal swabs, and only 32%
procedures largely contribute for throat swabs

vary depending on stage of disease and degree of viral multiplication or

clearance

samples should be obtained by dacron or polyester flocked swabs

BMJ 2020;369:m1808 doi: 10.1136/bmj.m1808
 Limitation, false positive
• A positive result indicates the detection of nucleic acid from
SARS-CoV-2.
• Include negative template control (NTC) sample
• Include internal control : identify the specimens containing substances that
may interfere with the extraction of nucleic acid and PCR amplification

• Nucleic acid may persist even after the virus is no longer

viable WHO,2019
Ct value for interpretation of viral load
• Ct values were inversely related
to viral RNA copy numbers
• Ct value <= 40 being
considered positive
• Higher viral loads were
detected soon after symptom
onset, with higher viral loads
detected in the nose than in the
throat

Zou et al., 2020, Tianmin Xu, 2020

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Patient with prolonged pos RT PCR (69)

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Ex. Case report
• Tn K, 59 th, Laki-laki
• Riw. CHF e.c IHD, HT (sejak th 2016)
• Tanggal Masuk : 18/3/2020, sudah dirawat selama 75 hari
• Awal masuk sd 2 minggu onset: foto thorax pneumonia,
trombositopenia, leukopenia
• Perjalanan penyakit : Minggu ke-3: Klinis membaik, Foto thorax,
parameter lab membaik
• RT PCR swab OP/NP: masih positif
Evaluasi PCR

MRS PCR 2 PCR 4 PCR 6

18/3 2-3/4 30-1/5 26-27/5

Positif positif positif

positif positif positip

Demam PCR 3 PCR 5
4 hari PCR 1
26-27/3 15-16/4 14-15/5

Dilakukan di 2 lab : BBTKL dan Lab FK-KMK

 Follow up pasien:
• KU membaik: tidak ada keluhan pernafasan, tidak demam
• Foto Thorax: pneumonia membaik
• Parameter lab darah rutin normal
• Pasien gelisah, stres dan tidak bisa tidur (perlu tx alprazolam dan
valisanbe) karena terlalu lama diisolasi
• Ct value rRT PCR: cenderung mendekati 40
 Ct value observation
Ct value ORF1ab gene
Ct value N gene 45

45
40 40 40 40 40 40 40 40
39 39 39.22
39
38 38 38 38
40 40 39.5 39 39.54 38.98 39.9
40 40 37
36.62 37.24 37
37.9 38.11
37.79 38.81 38.8
38.5 38.8 35
36.15
37 37.06
36.1 36
34.8
35 35.7
34.88
33.16 33.3
32 30 29.73
30 29.59 28.19
29
28.64 28 29
27.2 26.6 25
25

20 20

15 15

10 10

5 5

0
0
0 1 2 3 4 5 6 7 1 2 3 4 5 6 7 8

Km-ORF1ab Nb-ORF1ab Ep- ORF1ab

Km-N Nb-N Ep-N Yt-N KS-N IH-N
Yt-ORF1ab KS-ORF1ab IH-ORF1ab
 Association of CT, Symptom to
test, and SARS-CoV-2 Infectivity

No positive viral cultures with a Ct greater

than 24 or STT greater than 8 days

Bullard et al.,2020, CID, https://doi.org/10.1093/cid/ciaa638

Microbiologic Data for Period of Infectivity and Viral RNA Shedding

30% are PCR-negative by day 15 Infectious period of SARS-CoV-2 in

symptomatic:
Data from NCID 68% by day 21
Singapore, May
2020: 88% by day 28
95% negative by day 33
• 2 days before the symptoms onset,
and persists for about 7 - 10 days
after
duration of viral
shedding by PCR viral RNA detection by PCR does not • “presymptomatic” period: can be
may extend to a
month and equate to infectiousness or viable contagious, from 1–3 days before
sometimes
longer
virus. symptom onset
• persistent RNA detection represent
non-viable virus and such patients
A surrogate multicenter cohort of 73 COVID-19 patients: are non-infectious
marker of ‘viral Ct value was 30 or higher, no viable virus
load’ with PCR is
the cycle found
threshold value virus could not be cultured after day 11 of NCID Singapore, May 2020,
(Ct). https://apps.who.int/iris/bitstream/handle
illness.
Prolonged positive RT-PCR, meaning?
The qualitative report of SARS-CoV-2 RT-PCR
as positive or negative is sufficient for
diagnosis
RT-PCR detects RNA, not infectious virus, thus its ability to
determine duration of infectivity of patients is limited.
Infectivity is a critical determinant in informing public health
guidelines/interventions.

If supplemented by Ct, and time of symptom onset, will be benefit to guide infection control,
public health and occupational health decisions.

demonstration of in vitro infectiousness on

cell lines is a more informative surrogate of labour-intensive, need BSL-3 facilities
viral transmission.

other viruses viral RNA can persist beyond infectivity

persistence of SARS-CoV-2 RNA within
• SARS-CoV, MERS-CoV, influenza virus, Ebola virus, Zika virus,
different body sites Measles, Dengue

(Bullard et al.2020)
 China, Korea reported some
patients have recurrent positive
PCRs after initial negatives
• Persistent carrier state’ or
‘recurrent infections’
• asymptomatic
• stable radiographic findings
• no-onward transmission
• nor isolation of live virus by
viral cultures
Korean CDC concluded that
these were due to detection of
non-viable RNA from dead virus
• WHO May 2020:
• patients can remain
consistently PCR positive for
many weeks, or even test PCR
positive after days/weeks of a
negative test
(Lan L, Xu D, Ye G, et al. J Am Med Assoc 2020,
Kim B,The Korea Herald, 29 Apr 2020, Who 2020
 NCID Singapore, May 2020

• revised discharge criteria based on the data on

the time course of infectiousness rather than the
These findings are absence of RNA detection by PCR testing
supported by • taking into consideration both the clinical and
public health perspectives, including the
epidemiologic, individual patient’s physical and mental well-
microbiologic and being.
clinical data • focus on testing persons with acute respiratory
symptoms and suspectedCOVID-19 in early
presentation

WHO,
https://apps.who.int/iris/bitstream/
• Repeated PCR for confirmed
positive patient can be done, but
are no longer indicated for release
from COVID- 19 precautions.
Discontinue transmission-based
precautions (including isolation) and
release from the COVID-19 care
pathway as follows:
• For symptomatic patients: 10 days
after symptom onset, plus at least
3 days without symptoms (without
fever and respiratory symptoms).
• For asymptomatic patients: 10 days
after test positive
 Take home message: Manajemen of prolonged pos RTPCR
• Discontinue transmission
precautions Note onset of symptom: > 10 days
• Discharge and release from
hospital isolation
• Monitor at designated COVID-19 Clinical manifestation : no
health facility, community facility
or at home (self-isolation)
• Patient cohorting Comorbid factor: Controlled
• Self Toilet facilities: shedding virus in
feces still unknown ?
• PPE level 1 Ct value: > 30 ?
Terimakasih