Background
Methods
Eligibility
Search strategy and article selection
Data extraction
Risk of bias
Sampling method and grouping
RT-PCR test result conversion to binary results
Data analysis
Results
Included studies
Ref | Author year | Country | Location | Setting | Date recruited | No. of participants in study | No. of IPD participants | Study design | Inclusion criteria: reference test |
---|---|---|---|---|---|---|---|---|---|
[9] | Cai 2020a | China | Wenzhou | Community | 18 December 2019–12 February 2020 | 35 | 34 | Contact tracing, all patients visited a shopping mall (confirmed COVID-19 cases that had contact with each other) | Positive RT-PCR test |
[16] | Chang 2020 | China | PLA General Hospital, Beijing | Hospital | 28 January 2020 to 9 February 2020 | 16 | 16 | Confirmed COVID-19 patients released from the Treatment Center of PLA General Hospital | Positive RT-PCR test from throat swabs |
[10] | Chen 2020a | China | Beijing Ditan Hospital, Capital Medical University | Hospital | 20 January to 27 February | 133 | 22 | Retrospectively identified a convenience sample of patients admitted to hospital | At least 2 positive RT-PCR test pharyngeal swabs |
[12] | Chen 2020b | China | Shanghai, Shanghai Public Health Clinical Center. | Public Health Clinical Center | 20 January 2020 to 6 February 2020 | 249 | 248 | Retrospective cohort of laboratory confirmed cases | Positive RT-PCR test according to WHO interim guidelines |
[29] | He 2020 | China | Guangzhou Eighth People’s Hospital, Guangzhou, China | Hospital | 21 January 2020 to 14 February 2020 | 94 | 19 | All admitted COVID confirmed cases admitted to hospital | At least one positive RT-PCR test throat sample |
[24] | Hu 2020a | China | Qingdao, Shandong | Hospital | 29 January 2020 to 12 March 2020 | 59 | 59 | Retrospective cohort of confirmed hospital cases | Positive RT-PCR test |
[30] | Hu 2020b | China | Second Hospital of Nanjing, China | Hospital | 28 January 2020 to 9 February 2020 | 24 | 23 | Initial asymptomatic patients | Positive RT-PCR test and/or positive CT |
[28] | Cai 2020b | China | Shanghai, China | Hospital | 19 January 2020 to 3 February 2020 | 10 | 10 | 10 children admitted to hospital | Positive RT-PCR test nasopharyngeal or throat swab |
[31] | Kujawski 2020 | USA | Multiple sites, USA | Community | 20 January 2020 to 5 February 2020 | 12 | 12 | First 12 patients confirmed SARS-CoV-2 positive in the USA | Positive RT-PCR test in ≥ 1 specimen from a patient. Confirmed by CDC |
[39] | Lavezzo 2020 | Italy | Padua, Veneto region, Italy | Community | 21 February 2020 to 7 March 2020 | 2812 | 80 | Epidemiological study of entire population of Vo’, Italy, during complete closure of population movement | Positive RT-PCR test on nasopharyngeal swab |
[27] | Lescure 2020 | France | Paris, Bordeaux | Hospital | 24 January 2020 to 29 January 2020 | 5 | 5 | First 5 patients in France, exposed to COVID-19 in Hubei Province, China, prior to travel to France | Positive RT-PCR test |
[34] | Li 2020 | China | Xuzhou | Community | 13 January 2020 to 17 February 2020 | 7 | 7 | Asymptomatic contact tracing | Positive RT-PCR test |
[14] | Liu 2020a | China | Hospital of Nanchang University | Hospital | 21 January 2020 to 4 February 2020 | 76 | 25 | Patients admitted to the hospital | Positive RT-PCR test from nasal swabs |
[32] | Liu 2020b | China | Xixi Hospital of Hangzhou | Hospital | 22 January 2020 to 11 February 2020 | 10 | 10 | Hospital admission | Two consecutive positive RT-PCR tests |
[18] | Lo 2020 | China | Centro Hospitalar Conde de Sao Januario, Macau SAR, China | Hospital | 21 January 2020 to 16 February 2020 | 10 | 10 | Retrospective study of first 10 COVID-confirmed patients in Macau | Positive RT-PCR test |
[20] | Lu 2020 | China | Nantong, Nantong Third Hospital | Hospital | 23 January 2020 to 6 March 2020 | 36 | 35 | Retrospective analysis of clinical patients with fever, coughing, or lung inflammation | Positive RT-PCR test |
[19] | Song 2020 | China | Wuhan No. 1 Hospital, Nanjing Medical University | Hospital | 31 January to 14 March 2020 | 13 | 13 | Confirmed by CT images | Positive RT-PCR test |
[13] | To 2020 | China (Hong Kong) | Public Health Lab services branch in Hong Kong | Public Health Lab | Not reported | 12 | 12 | 12 patients who presented with fever and acute respiratory distress, or pneumonia, and travel to Wuhan 14 days before onset of symptoms | Positive RT-PCR test from nasopharyngeal or sputum sample |
[17] | Wolfel 2020 | Germany | Munich, Germany | Hospital | Not reported | 9 | 9 | Patients that acquired infections upon known close contact to an index case (part of a larger cluster of epidemiologically linked cases that occurred after 23 January 2020 in Munich, Germany) | Positive RT-PCR test from oro- or nasopharyngeal swab |
[37] | Wu 2020 | China | Zhuhai, Guangdong | Hospital | 16 January 2020 to 15 March 2020 | 74 | 41 | Retrospective study of hospitalised patients | Positive RT-PCR test in two sequential respiratory tract samples |
[40] | Wyllie 2020 | USA | New Haven, CT | Community (healthcare workers) | Not reported to 5 April 2020 | 98 (44 inpatients) | 19 | Study of inpatients (44) and healthcare workers (98) | Positive RT-PCR test by nasopharyngeal swab or saliva |
[21] | Xia 2020 | China | Zhejiang | Hospital | 26 January 2020 to 9 February 2020 | 30 | 30 | A prospective interventional case series study of confirmed novel coronavirus pneumonia (NCP) patients at hospital | Positive RT-PCR test |
[23] | Xiao 2020 | China | Tongji Hospital, Huazhong, Wuhan | Hospital | 21 January 2020 to 12 February 2020 | 56 | 56 | 30 confirmed novel coronavirus pneumonia (NCP) patients were selected | Positive RT-PCR test |
[33] | Xu 2020a | China | Changzhou | Hospital | 23 January 2020 to 27 February 2020 | 51 | 48 | Hospital admission including 12 family clusters | Confirmed COVID-19 by Chinese diagnosis and treatment guideline |
[36] | Xu 2020b | China | Guangzhou, Guangzhou Women and Children’s Medical Center | Hospital but from community surveillance | 22 January 2020 to 20 February 2020 | 10 | 10 | “Highly suspected” children with contact with confirmed COVID-19 person, or member of infected family group who was placed in quarantine | Positive RT-PCR test from nasopharyngeal or rectal swabs |
[11] | Yang 2020 | China | Shenzhen Third People’s | Hospital | 11 January and 3 February 2020 | 213 | 13 | COVID-19 positive hospitalised patients | Positive RT-PCR test |
[26] | Young 2020 | Singapore | 4 hospitals in Singapore | Hospital | 23 January 2020 to 3 February 2020 | 18 | 18 | Contact tracing. First hospitalised patients in Singapore | Positive RT-PCR test |
[22] | Yuan 2020 | China | Fifth Affiliated Hospital, Zhuhai, Guangdong Province, China | Hospital | Late January | 6 | 6 | Case series | Positive RT-PCR test |
[25] | Zhang 2020a | China | Wuhan Pulmonary Hospital, CAS Key Laboratory of Special Pathogens | Hospital | Not reported | Unclear | 16 | Prospective cohort patients | Positive RT-PCR test from oral swab |
[35] | Zhang 2020b | China | Guangdong | Hospital | 30 January 2020 to 5 February 2020 | 7 | 7 | Prior hospitalisation for COVID-19, discharged under quarantine and subsequently positive by RT-PCR again | Positive RT-PCR test |
[38] | Zheng 2020 | China | Zheijang, China | Hospital | 19 January 2020 to 15 February 2020 | 96 | 96 | Retrospective cohort of 96 consecutively confirmed hospital cases | Positive RT-PCR test |
[15] | Zou 2020 | China | Zhuhai, Guangdong | Community and hospital | 7 January to 26 January 2020 | 18 | 17 | 2 family clusters of patients infected by SARS-CoV | Positive RT-PCR test. Assay from Chinese CDC |
Ref | Author year | How were IPD participants selected? | Percentage of male | Age median (years) | Age mean (years) | Age range (years) | Sample site | PCR test type; name of equipment if reported | Genomic targets; primers reported/referenced/ included |
---|---|---|---|---|---|---|---|---|---|
[9] | Cai 2020 | IPD of almost all patients in study | NR | NR | NR | NR | Not reported | qRT-PCR; not reported | ORF1ab, N-gene; not reported |
[16] | Chang 2020 | IPD of all patients in study | 69 | 36 | Not reported | IQR 24–43 | Throat | qRT-PCR; not reported | Not reported; not reported |
[10] | Chen 2020a | Initial or follow-up positive sputum or faecal samples paired with a follow-up negative pharyngeal sample | 64 | 37 | 37 | IQR 30–49 | Faeces, sputum, URT (pharyngeal) | qRT-PCR; not reported | ORF1ab, N-gene; not reported |
[12] | Chen 2020b | IPD of all patients in study | 51 | 51 | IQR 36–64 | URT | qRT-PCR; not reported | ORF1ab, N-gene; not reported | |
[29] | He 2020 | IPD for all 94 patients presented, but could only extract 19 IPD from overlapping graphs | 50 | 47 | Throat | qRT-PCR; not reported | N-gene; not reported | ||
[24] | Hu 2020a | IPD of all patients in study | 48 | 46 | NR | NR | Nasopharyngeal | qRT-PCR; not reported | ORF1ab, N-gene; not reported |
[30] | Hu 2020b | IPD of almost all patients in study | 33 | 33 | 38 | 5–95 | Throat | qRT-PCR; BGI Genomics | ORF1ab; primers included |
[28] | Jiehao 2020 | IPD of all patients in study | 40 | 7 | 6 | 3 months–11 years | URT | qRT-PCR; not reported | ORF1ab, N-gene; not reported |
[31] | Kujawski 2020 | IPD of all patients in study | 67 | 53 | 21–68 | Throat, nasopharyngeal, sputum, urine, faeces | qRT-PCR; not reported | N-gene; not reported | |
[39] | Lavezzo 2020 | All residents identified with infection | 50 | NR | NR | NR | Nasopharyngeal | qRT-PCR; One Step Real Time kit (Thermo Fisher Scientific, USA) | E-gene, RdRp; primers referenced |
[27] | Lescure 2020 | IPD of all patients in study | 60 | 46 | 47 | 30–80 | Nasopharyngeal, faeces, conjunctiva, urine, blood, LRT (pleural) | qRT-PCR; not reported | E-gene, RdRp; primers included |
[34] | Li 2020 | IPD of all patients in study | 57 | 42 | 43 | 21–62 | Throat | qRT-PCR; not reported | Not reported; not reported |
[14] | Liu 2020a | 25 participants with serial samples tested for PCR | NR | NA | NA | NA | Nasopharyngeal | qRT-PCR; not reported | Not reported; not reported |
[32] | Liu 2020b | IPD of all patients in study | 40 | 42 | 34–50 | Mixed URT (nasal, throat) | qRT-PCR; not reported | E-gene, RdRp, N-gene; not reported | |
[18] | Lo 2020 | IPD of all patients in study | 30 | 54 | NR | NR | Faeces, nasopharyngeal, urine | qRT-PCR; BioGerm | ORF1ab, N-gene; not reported |
[20] | Lu 2020 | IPD of all patients in study | NR | NR | NR | NR | Sputum, URT (pharyngeal), faeces, blood | qRT-PCR; not reported | ORF1ab, N-gene; primers included |
[19] | Song 2020 | IPD of all patients in study | 100 | NR | NR | 22–67 | URT (pharyngeal) | qRT-PCR; Huirui biotechnology | Not reported; not reported |
[13] | To 2020 | IPD of all patients in study | 58 | 63 | 37 to 75 | Saliva | qRT-PCR; QuantiNova SYBR Green RT-PCR kit (Qiagen) | S-gene; not reported | |
[17] | Wolfel 2020 | IPD of all patients in study | NR | Not reported | Not reported | Not reported | Sputum, faeces, URT (pharyngeal) | qRT-PCR; Tib-Molbiol, Germany | E-gene, RdRp; not reported |
[37] | Wu 2020 | Retrospective 41 patients with positive faecal samples only | 53 | NR | NR | NR | Throat, faeces | qRT-PCR; 2019-nCOV Real Time RT-PCR kit (LifeRiver Ltd) | E-gene, RdRp, N-gene |
[40] | Wyllie 2020 | Patients with multiple nasopharyngeal swabs or multiple saliva swabs | Inpatients (52), healthcare workers (16) | NR | 61 | 23–92 | Nasopharyngeal, saliva | qRT-PCR; US CDC RT-PCR primer/probe sets | N-gene; primers referenced |
[21] | Xia 2020 | IPD of all patients in study | 70 | 51 | 55 | 13–83 | Sputum, conjunctiva | qRT-PCR; BioGerm | Not reported; not reported |
[23] | Xiao 2020 | IPD of all patients in study | 61 | 55 | 55 | 25–83 | URT (pharyngeal) | qRT-PCR; Shanghai Huirui Biotechnology Co. | ORF1ab, N-gene; not reported |
[33] | Xu 2020a | IPD of almost all patients in study | 49 | 3 groups: imported 35 [29–51], secondary 37 [24–47.5], tertiary 53 [35–65] | 24–65 | Throat | qRT-PCR; BioGerm | ORF1ab, N-gene; not reported | |
[36] | Xu 2020b | IPD of all patients in study | 60 | 7 | 8 | 2 months–16 years | Nasopharyngeal, faeces | qRT-PCR; BioGerm | ORF1ab, N-gene; primers included |
[11] | Yang 2020 | Not reported how 13 patients for serial sampling IPD data chosen | 51 | 52 | 2–86 | Mixed URT (nasal swabs, throat swabs) and mixed LRT (sputum and bronchoalveolar lavage fluid (BALF)) | qRT-PCR; GeneoDX Co. | Not reported; not reported | |
[26] | Young 2020 | IPD of all patients in study | 50 | 47 | 31–73 | Nasopharyngeal, faeces, urine, blood | qRT-PCR; not reported | ORF1ab, N-gene, S-gene; primers included | |
[22] | Yuan 2020 | IPD of all patients in study | 33 | 64 | 59 | 36–71 | Nasopharyngeal, faeces | qRT-PCR; not reported | E-gene, RdRp, N-gene; not reported |
[25] | Zhang 2020a | Not reported | NR | NR | NR | NR | URT (oral), faeces | qRT-PCR; HiScript®II One Step qRT-PCR SYBR®Green Kit (Vazyme Biotech Co.) | S-gene; primer included |
[35] | Zhang 2020b | IPD of all patients in study | 86 | 26 | 22 | 10 months–35 years | Throat, faeces, blood | qRT-PCR; not reported | Not reported; not reported |
[38] | Zheng 2020 | IPD of all patients in study | 60 | 55 | NR | NR | Sputum, faeces, blood | qRT-PCR; SARS-CoV-2 detection kit (BoJie Shanghai) | ORF1ab; not reported |
[15] | Zou 2020 | IPD of almost all patients in study | 50 | 59 | 26–76 | Throat, URT (nasal) | qRT-PCR; not reported | ORF1ab, N-gene; not reported |
Sampling site reporting
Sampling site positivity over time
Upper and lower respiratory tract sampling
Faecal vs. respiratory tract sampling
Intermittent false negative results
Risk of bias
Discussion
Key findings
Domain | Details of bias and applicability issues | Impact on interpretation of study data |
---|---|---|
Participants (source of bias) | In these studies, the reference test usually incorporates RT-PCR (index test). • RT-PCR testing is usually a key component of identifying people with SARS-CoV-2 infection. • Participants will not be detected or included in these studies when SARS-CoV-2 is not present at easily sampled sites and at the time that participants were available for testing. | Unclear how many and what severity of participants with SARS-CoV-2 are not included in studies. People who do not have a positive RT-PCR test at some point are excluded. This could lead to overestimation of positivity. |
Rates of positivity will be inflated as only people with virus accessible for sampling for RT-PCR tests will be included in studies. | ||
Participants (source of bias) | Most participants are identified or present based on respiratory tract symptoms such as cough or respiratory distress. | Unclear how many and what severity of participants with SARS-CoV-2 are not included in studies. |
• Participants will not be detected or included in these studies when less common symptoms or asymptomatic. | ||
• Participants included will be biased to over-represent people with detectable virus in respiratory tract sampling sites and at times frequently used for testing (post symptom onset or at admission to hospital). | Studies will inflate positivity for sampling sites that overlap with sampling sites used in RT-PCR reference testing. • For example, we identified 30% of participants with RT positivity but with negative results from faecal sampling. However, if participants had only faecal virus, would they have been included in the studies? | |
Index test: RT-PCR (applicability) | • Studies included are likely to use more invasive sampling methods than acceptable in widespread population testing. For example, nasopharyngeal testing is likely in many current studies to be based on long swabs and self test kits. | Percentage of people with detectable virus may be overestimated when testing is applied in real-world clinical use and in population testing. |
• Studies will use experienced staff to obtain samples, handle, process, and conduct tests. | ||
• Studies are mostly sampling participants in hospital settings or in specialised research community testing research where sample handling, transport, and storage have been standardised. | ||
• Variation in RT-PCR kits is minimised as studies are based in few hospitals or limited to a research setting | ||
Index test: RT-PCR (applicability) | Sample RNA extraction methods are designed predominantly for respiratory samples. • RT-PCR sample preparation kits used are mostly designed for extraction of virus from respiratory samples, not from faecal samples. It is unclear how efficiently these kits extract virus RNA from stool samples. | Percentage of people with virus present in faecal samples and duration of shedding in faecal samples may be underestimated. |
Index test: RT-PCR (applicability) | RT-PCR tests detect both infectious and inactive (inactive due to immune system or dead) virus. | Percentage of people with clinically important detectable virus may be overestimated. |
• Few studies link RT-PCR testing to cell assays to test for infectious virus. | ||
Index test: RT-PCR (applicability) | Rate of virus aggregation or clearance by immune system may affect the sampling efficiency at some sampling sites. • Both the innate and adaptive immune system will aggregate and clear virus particles from bodily fluids. It is not clear what the time scale of clearance or how this influences detection of virus at different sites and at which time points. | Percentage of people with detectable virus may be underestimated. |
Index test: RT-PCR (applicability) | Reporting of sampling sites and methods is poor. • Poor reporting may have led to less ideal grouping of sampling in analysis. • Some studies are likely to use a variety of nasopharyngeal sampling methods depending on the individual participants, but the type of sampling is typically reported at a study level for a particular sampling site. | Percentage of people with detectable virus may be over- or underestimated. |
Flow and timing | Uncertainty and inconsistencies in time of sampling | Percentage of people with detectable virus may be over- or underestimated at particular times. |
• Time of symptom onset can be subjective unless based on fever, but some participants do not have fever. • Time of symptom onset may be different if asked of participants in ICU setting. • Time of hospitalisation and discharge may be affected by function hospitalisation serves in containment of disease spread. In some studies, the hospitals were also quarantine centres, so participants were hospitalised immediately at onset of mild symptoms rather than restricted to patients needing oxygen. | ||
Flow and timing | Clinical cohort within studies changes across time points. | Percentage of people with detectable virus may be overestimated at particular later time points as these correspond to participants who were severely ill. |
• Participants who have recovered from COVID-19 in most studies are typically not tested after 2 negative tests 24 h apart. • Many studies only test inpatients at the hospital, so the participants sampled between 0 and 14 days typically have less severe disease than those tested longer | ||
Flow and timing (selective outcome reporting) | Some studies only publish IPD data for a selection of people. | Available IPD data may not represent a typical spectrum of participants in the different settings (community setting, hospital, ICU, nursing home, prison). |
Publication bias | Published data is likely to be biased towards publication of research active groups which may not represent typical real world. | Percentage of people with detectable virus may be overestimated. |
Putting the findings into context of literature
Strengths of study
Limitations of study
Implications for policy/practice/future research
Study characteristic | Detail | Reference |
---|---|---|
Study design: representative recruitment | Representative participants • Community infection • Contact tracing including asymptomatic • Hospitalised patients | Population surveillance of Italian town, with PCR testing across [39] Retrospective cohort of 96 hospitalised patients [38] |
Study design: planned testing and follow-up | Informative sampling • Multiple sampling sites per participant • Planned schedule of sampling • Sampling continues after negative test results • Sampling continues after hospital discharge | Three samples per patient, multiple testing including prolonged testing even after multiple negative results [10] Population surveillance of Italian town over 18 days [39] |
Study design: sampling | Reporting of sampling methods (sample site, staff conducting test, sample volumes, and methods) | Most studies had very sparse reporting of sample collection methods. Example of fuller reporting [40] |
Individual participant data reporting for sharing | Examples of plots and tables that facilitated sharing of individual participant data | Retrospective cohort of 96 patients all tested with sputum, faeces, and blood. Plot shows time span of positive test results, hospitalisation timing, and disease severity for individual patients [38] Data showing RT-PCR test results by patient and time point [10] Viral load over time [15] |