39 On 31 st December 2019, the World Health Organization was informed of a cluster of cases of 40 pneumonia of unknown etiology in Wuhan, China. Subsequent investigations identified a novel 41 coronavirus, now named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 42 from the affected patients. Highly sensitive and specific laboratory diagnostics are important for 43 controlling the rapidly evolving SARS-CoV-2-associated Coronavirus Disease 2019 (COVID-44 19) epidemic. In this study, we developed and compared the performance of three novel real-time 45 RT-PCR assays targeting the RNA-dependent RNA polymerase (RdRp)/helicase (Hel), spike (S), 46 and nucleocapsid (N) genes of SARS-CoV-2 with that of the reported RdRp-P2 assay which is 47 used in >30 European laboratories. Among the three novel assays, the COVID-19-RdRp/Hel 48 assay had the lowest limit of detection in vitro (1.8 TCID 50 /ml with genomic RNA and 11.2 RNA 49 copies/reaction with in vitro RNA transcripts). Among 273 specimens from 15 patients with 50 laboratory-confirmed COVID-19 in Hong Kong, 77 (28.2%) were positive by both the COVID-51 19-RdRp/Hel and RdRp-P2 assays. The COVID-19-RdRp/Hel assay was positive for an 52 additional 42 RdRd-P2-negative specimens [119/273 (43.6%) vs 77/273 (28.2%), P<0.001], 53including 29/120 (24.2%) respiratory tract specimens and 13/153 (8.5%) non-respiratory tract 54 specimens. The mean viral load of these specimens was 3.21×10 4 RNA copies/ml (range, 55 2.21×10 2 to 4.71×10 5 RNA copies/ml). The COVID-19-RdRp/Hel assay did not cross-react with 56 other human-pathogenic coronaviruses and respiratory pathogens in cell culture and clinical 57 specimens, whereas the RdRp-P2 assay cross-reacted with SARS-CoV in cell culture. The highly 58 sensitive and specific COVID-19-RdRp/Hel assay may help to improve the laboratory diagnosis 59 of COVID-19. 60 61 on March 16, 2020 by guest http://jcm.asm.org/ Downloaded from 4

All hepatitis E virus (HEV) variants reported to infect humans belong to the species Orthohepevirus A (HEV-A). The zoonotic potential of the species Orthohepevirus C (HEV-C), which circulates in rats and is highly divergent from HEV-A, is unknown. We report a liver transplant recipient with hepatitis caused by HEV-C infection. We detected HEV-C RNA in multiple clinical samples and HEV-C antigen in the liver. The complete genome of the HEV-C isolate had 93.7% nt similarity to an HEV-C strain from Vietnam. The patient had preexisting HEV antibodies, which were not protective against HEV-C infection. Ribavirin was an effective treatment, resulting in resolution of hepatitis and clearance of HEV-C viremia. Testing for this zoonotic virus should be performed for immunocompromised and immunocompetent patients with unexplained hepatitis because routine hepatitis E diagnostic tests may miss HEV-C infection. HEV-C is also a potential threat to the blood product supply.

Background and Aims Hepatitis E virus (HEV) variants causing human infection predominantly belong to HEV species A (HEV‐A). HEV species C genotype 1 (HEV‐C1) circulates in rats and is highly divergent from HEV‐A. It was previously considered unable to infect humans, but the first case of human HEV‐C1 infection was recently discovered in Hong Kong. The aim of this study is to further describe the features of this zoonosis in Hong Kong. Approach and Results We conducted a territory‐wide prospective screening study for HEV‐C1 infection over a 31‐month period. Blood samples from 2,860 patients with abnormal liver function (n = 2,201) or immunosuppressive conditions (n = 659) were screened for HEV‐C1 RNA. In addition, 186 captured commensal rats were screened for HEV‐C1 RNA. Sequences of human‐derived and rat‐derived HEV‐C1 isolates were compared. Epidemiological and clinical features of HEV‐C1 infection were analyzed. HEV‐C1 RNA was detected in 6/2,201 (0.27%) patients with hepatitis and 1/659 (0.15%) immunocompromised persons. Including the previously reported case, eight HEV‐C1 infections were identified, including five in patients who were immunosuppressed. Three patients had acute hepatitis, four had persistent hepatitis, and one had subclinical infection without hepatitis. One patient died of meningoencephalitis, and HEV‐C1 was detected in cerebrospinal fluid. HEV‐C1 hepatitis was generally milder than HEV‐A hepatitis. HEV‐C1 RNA was detected in 7/186 (3.76%) rats. One HEV‐C1 isolate obtained from a rat captured near the residences of patients was closely related to the major outbreak strain. Conclusions HEV‐C1 is a cause of hepatitis E in humans in Hong Kong. Immunosuppressed individuals are susceptible to persistent HEV‐C1 infection and extrahepatic manifestations. Subclinical HEV‐C1 infection threatens blood safety. Tests for HEV‐C1 are required in clinical laboratories.

Background Access to rapid diagnosis is key to the control and management of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Laboratory RT-PCR testing is the current standard of care but usually requires a centralised laboratory and significant infrastructure. We describe our diagnostic accuracy assessment of a novel, rapid point-of-care real time RT-PCR CovidNudge test, which requires no laboratory handling or sample pre-processing. Methods Between April and May, 2020, we obtained two nasopharyngeal swab samples from individuals in three hospitals in London and Oxford (UK). Samples were collected from three groups: self-referred health-care workers with suspected COVID-19; patients attending emergency departments with suspected COVID-19; and hospital inpatient admissions with or without suspected COVID-19. For the CovidNudge test, nasopharyngeal swabs were inserted directly into a cartridge which contains all reagents and components required for RT-PCR reactions, including multiple technical replicates of seven SARS-CoV-2 gene targets (rdrp1, rdrp2, e-gene, n-gene, n1, n2 and n3) and human ribonuclease P (RNaseP) as sample adequacy control. Swab samples were tested in parallel using the CovidNudge platform, and with standard laboratory RT-PCR using swabs in viral transport medium for processing in a central laboratory. The primary analysis was to compare the sensitivity and specificity of the point-of-care CovidNudge test with laboratory-based testing. Findings We obtained 386 paired samples: 280 (73%) from self-referred health-care workers, 15 (4%) from patients in the emergency department, and 91 (23%) hospital inpatient admissions. Of the 386 paired samples, 67 tested positive on the CovidNudge point-of-care platform and 71 with standard laboratory RT-PCR. The overall sensitivity of the point-of-care test compared with laboratory-based testing was 94% (95% CI 86-98) with an overall specificity of 100% (99-100). The sensitivity of the test varied by group (self-referred healthcare workers 93% [95% CI 84-98]; patients in the emergency department 100% [48-100]; and hospital inpatient admissions 100% [29-100]). Specificity was consistent between groups (self-referred health-care workers 100% [95% CI 98-100%]; patients in the emergency department 100% [69-100]; and hospital inpatient admissions 100% [96-100]). Point of care testing performance was similar during a period of high background prevalence of laboratory positive tests (25% [95% 20-31] in April, 2020) and low prevalence (3% [95% 1-9] in inpatient screening). Amplification of viral nucleocapsid (n1, n2, and n3) and envelope protein gene (e-gene) were most sensitive for detection of spiked SARS-CoV-2 RNA. Interpretation The CovidNudge platform was a sensitive, specific, and rapid point of care test for the presence of SARS-CoV-2 without laboratory handling or sample pre-processing. The device, which has been implemented in UK hospitals since May, 2020, could enable rapid decisions for clinical care and testing programmes.