Can Robots Improve Testing Capacity for SARS-CoV-2?

There is currently increasing interest internationally in deploying robotic applications for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing, as these can help to reduce the risk of transmission of the virus to health care staff and patients. We provide an overview of key recent developments in this area. We argue that, although there is some potential for deploying robots to help with SARS-CoV-2 testing, the potential of patient-facing applications is likely to be limited. This is due to the high costs associated with patient-facing functionality, and risks of potentially adverse impacts on health care staff work practices and patient interactions. In contrast, back-end laboratory-based robots dealing with sample extraction and amplification, that effectively integrate with established processes, software, and interfaces to process samples, are much more likely to result in safety and efficiency gains. Consideration should therefore be given to deploying these at scale.

Hepatitis E virus mixed infection in immunocompetent patient.

We detected 2 hepatitis E virus (HEV) strains in an acutely infected immunocompetent patient. Two populations of genotype 3 virus were observed in the hypervariable regions and open reading frames 2 and 3, indicating multiple infection with hepatitis E virus. Persons with mixed infections may provide the opportunity for virus recombination.

Evolution of the hepatitis E virus hypervariable region.

The presence of a hypervariable (HVR) region within the genome of hepatitis E virus (HEV) remains unexplained. Previous studies have described the HVR as a proline-rich spacer between flanking functional domains of the ORF1 polyprotein. Others have proposed that the region has no function, that it reflects a hypermutable region of the virus genome, that it is derived from the insertion and evolution of host sequences or that it is subject to positive selection. This study attempts to differentiate between these explanations by documenting the evolutionary processes occurring within the HVR. We have measured the diversity of HVR sequences within acutely infected individuals or amongst sequences derived from epidemiologically linked samples and, surprisingly, find relative homogeneity amongst these datasets. We found no evidence of positive selection for amino acid substitution in the HVR. Through an analysis of published sequences, we conclude that the range of HVR diversity observed within virus genotypes can be explained by the accumulation of substitutions and, to a much lesser extent, through deletions or duplications of this region. All published HVR amino acid sequences display a relative overabundance of proline and serine residues that cannot be explained by a local bias towards cytosine in this part of the genome. Although all published HVRs contain one or more SH3-binding PxxP motifs, this motif does not occur more frequently than would be expected from the proportion of proline residues in these sequences. Taken together, these observations are consistent with the hypothesis that the HVR has a structural role that is dependent upon length and amino acid composition, rather than a specific sequence.

Study protocol of the Edinburgh and Lothian Virus Intervention Study in Kids: a randomised controlled trial of hypertonic saline nose drops in children with upper respiratory tract infections (ELVIS Kids).

INTRODUCTION: Edinburgh and Lothians' Viral Intervention Study Kids is a parallel, open-label, randomised controlled trial of hypertonic saline (HS) nose drops (~2.6% sodium chloride) vs standard care in children <7 years of age with symptoms of an upper respiratory tract infection (URTI). METHODS AND ANALYSIS: Children are recruited prior to URTI or within 48 hours of developing URTI symptoms by advertising in areas such as local schools/nurseries, health centres/hospitals, recreational facilities, public events, workplaces, local/social media. Willing parents/guardians, of children <7 years of age will be asked to contact the research team at their local site. Children will be randomised to either a control arm (standard symptomatic care), or intervention arm (three drops/nostril of HS, at least four times a day, until 24 hours after asymptomatic or a maximum of 28 days). All participants are requested to provide a nasal swab at the start of the study (intervention arm: before HS drops) and then daily for four more days. Parent/guardian complete a validated daily diary, an end of illness diary, a satisfaction questionnaire and a wheeze questionnaire (day 28). The parent/guardian of a child in the intervention arm is taught to prepare HS nose drops. Parent/guardian of children asymptomatic at recruitment are requested to inform the research team within 48 hours of their child developing an URTI and follow the instructions already provided. The day 28 questionnaire determines if the child experienced a wheeze following illness. Participation in the study ends on day 28. ETHICS AND DISSEMINATION: The study has been approved by the West of Scotland Research Ethics Service (18/WS/0080). It is cosponsored by Academic and Clinical Central Office for Research and Development-a partnership between the University of Edinburgh and National Health Service Lothian Health Board. The findings will be disseminated through peer-reviewed publications, conference presentations and via the study website. TRIAL REGISTRATION NUMBER: NCT03463694.

Association between viral seasonality and meteorological factors.

Numerous viruses can cause upper respiratory tract infections. They often precede serious lower respiratory tract infections. Each virus has a seasonal pattern, with peaks in activity in different seasons. We examined the effects of daily local meteorological data (temperature, relative humidity, "humidity-range" and dew point) from Edinburgh, Scotland on the seasonal variations in viral transmission. We identified the seasonality of rhinovirus, adenovirus, influenza A and B viruses, human parainfluenza viruses 1-3 (HPIV), respiratory syncytial virus (RSV) and human metapneumovirus (HMPV) from the 52060 respiratory samples tested between 2009 and 2015 and then confirmed the same by a generalised linear model. We also investigated the relationship between meteorological factors and viral seasonality. Non-enveloped viruses were present throughout the year. Following logistic regression adenovirus, influenza viruses A, B, RSV and HMPV preferred low temperatures; RSV and influenza A virus preferred a narrow "humidity-range" and HPIV type 3 preferred the season with lower humidity. A change (i.e. increase or decrease) in specific meteorological factors is associated with an increase in activity of specific viruses at certain times of the year.

A pilot, open labelled, randomised controlled trial of hypertonic saline nasal irrigation and gargling for the common cold.

There are no antivirals to treat viral upper respiratory tract infection (URTI). Since numerous viruses cause URTI, antiviral therapy is impractical. As we have evidence of chloride-ion dependent innate antiviral response in epithelial cells, we conducted a pilot, non-blinded, randomised controlled trial of hypertonic saline nasal irrigation and gargling (HSNIG) vs standard care on healthy adults within 48 hours of URTI onset to assess recruitment (primary outcome). Acceptability, symptom duration and viral shedding were secondary outcomes. Participants maintained a symptom diary until well for two days or a maximum of 14 days and collected 5 sequential mid-turbinate swabs to measure viral shedding. The intervention arm prepared hypertonic saline and performed HSNIG. We recruited 68 participants (2.6 participants/week; November 2014-March 2015). A participant declined after randomisation. Another was on antibiotics and hence removed (Intervention:32, Control:34). Follow up data was available from 61 (Intervention:30, Control:31). 87% found HSNIG acceptable, 93% thought HSNIG made a difference to their symptoms. In the intervention arm, duration of illness was lower by 1.9 days (p = 0.01), over-the-counter medications (OTCM) use by 36% (p = 0.004), transmission within household contacts by 35% (p = 0.006) and viral shedding by ≥0.5 log10/day (p = 0.04). We hence need a larger trial to confirm our findings.

Investigation of apoptotic markers among human immunodeficiency virus (HIV-1) infected individuals.

BACKGROUND & OBJECTIVES: Apoptosis causes a decline in the counts of uninfected bystander CD4+ T cells in HIV infection. The rate of disease progression of HIV infection is considered to be faster in the developing countries. The present study was carried out to investigate certain markers for apoptosis in immunopathogensis of disease in HIV infected south Indian population. METHODS: Soluble Fas (sFas) antigen and Fas ligand levels in plasma samples from 39 antiretroviral treatment naïve patients was estimated and compared with T cell subsets and HIV-1 viral load. RESULTS: The mean sFas antigen levels among controls and the CDC A, B and C clinical stages were 2.77, 3.08, 3.26 and 3.28 ng /ml respectively, higher though not significantly among HIV-1 infected individuals compared to controls. The mean sFas ligand levels in CDC A, B and C stages were 0.138, 0.125 and 0.117 ng/ml respectively were higher (P<0.001) than controls (0.073 ng/ml) and positively correlated with total lymphocyte % (r=0.43, P =0.007). sFas antigen levels were negatively correlated with total WBC count (r=-0.34, P=0.04), CD4% (r=-0.4, P=0.01) and CD4:CD8 ratio (r=-0.37, P=0.02). There was an increase in plasma levels of sFas antigen and Fas ligand over time in asymptomatics. INTERPRETATION & CONCLUSION: The high levels of sFas antigen and Fas ligand seen in HIV infected individuals suggest increased activation and apoptosis of T cells, due to constant stimulation of the immune system by inter-current infections of HIV infected individuals in south India.

Chemokine profile among human immunodeficiency virus-1 (HIV-1) infected individuals from southern India.

BACKGROUND & OBJECTIVE: Individuals infected with HIV-1 have higher levels of chemokine producing cells compared to uninfected individuals. It is important to know the changes in chemokine levels associated with rate of progression of disease. There is a paucity of information on the plasma chemokines in HIV-1 infected individuals from India. We therefore carried out this study to estimate the levels of three chemokines namely macrophage inflammatory protein alpha (MIP1alpha), MIP1beta and RANTES, in relation to disease status in HIV-1 infected individuals and compared with uninfected individuals. METHODS: RANTES and MIP1alpha were estimated using ELISA in 114 HIV-1 infected and 30 controls, whereas MIP1beta was estimated in 101 HIV infected individuals only and 30 controls. The values were compared to the T cell subsets, HIV-1 viral loads and plasma cytokines (interferon gamma and interleukin-10). RESULTS: Compared to controls the mean MIP1alpha and RANTES level among the HIV-1 infected individuals was higher while MIP1beta level was lower in HIV infected individuals except CDC C groups. There was a significant positive correlation for MIP1á with HIV-1 viral load and IFNgamma, for MIP1alpha with viral load and IL10. There was a significant negative correlation between MIP1alpha with CD4 count and CD4: CD8 ratio and MIP1beta with CD4 count and CD8 count. There was a negativecorrelation between RANTES values and CD8 per cent. INTERPRETATION & CONCLUSION: In conclusion, our study showed a significantly higher level of beta chemokines in south Indian HIV-1 infected individuals compared to controls. These beta chemokines may have the inhibitory effect on HIV-1 only during the initial period and with the progression of disease this inhibitory effect wanes as shown by the positive correlation of beta chemokines with HIV-1 viral load.

Antiviral innate immune response in non-myeloid cells is augmented by chloride ions via an increase in intracellular hypochlorous acid levels.

Phagocytes destroy ingested microbes by producing hypochlorous acid (HOCl) from chloride ions (Cl-) and hydrogen peroxide within phagolysosomes, using the enzyme myeloperoxidase. HOCl, the active ingredient in bleach, has antibacterial/antiviral properties. As myeloperoxidase is needed for HOCl production, non-myeloid cells are considered incapable of producing HOCl. Here, we show that epithelial, fibroblast and hepatic cells have enhanced antiviral activity in the presence of increasing concentrations of sodium chloride (NaCl). Replication of enveloped/non-enveloped, DNA (herpes simplex virus-1, murine gammaherpesvirus 68) and RNA (respiratory syncytial virus, influenza A virus, human coronavirus 229E, coxsackievirus B3) viruses are inhibited in a dose-dependent manner. Whilst treatment with sodium channel inhibitors did not prevent NaCl-mediated virus inhibition, a chloride channel inhibitor reversed inhibition by NaCl, suggesting intracellular chloride is required for antiviral activity. Inhibition is also reversed in the presence of 4-aminobenzoic hydrazide, a myeloperoxidase inhibitor, suggesting epithelial cells have a peroxidase to convert Cl- to HOCl. A significant increase in intracellular HOCl production is seen early in infection. These data suggest that non-myeloid cells possess an innate antiviral mechanism dependent on the availability of Cl- to produce HOCl. Antiviral activity against a broad range of viral infections can be augmented by increasing availability of NaCl.

Transmission of hepatitis B virus (genotype E) in a haemodialysis unit.

BACKGROUND: The Rosenheim report, published in 1972, was aimed at decreasing the transmission of hepatitis B virus (HBV) in the renal unit. A review in 1996, revealed the non-compliance of some centres with the guidance to vaccinate individuals against HBV. OBJECTIVES: To describe two events of acute hepatitis B virus (HBV) infection within 9 weeks in individuals attending the renal unit and the steps taken to prevent further transmission. STUDY DESIGN: Serological and molecular testing was carried out on the two individuals with acute HBV and other HBV carriers in the unit. Epidemiological information was collected along with information on HBV vaccination and HBsAg screening. RESULTS: There were 15 known HBV carriers in the unit. HBV genotype E was transmitted from a carrier to patient 1 when they were in the same ward. Transmission to patient 2 occurred when he followed patient 1 on the theatre list. Breaks in infection control were identified and steps were taken to prevent further transmission events. CONCLUSIONS: Breaks in infection control procedures were rectified. No further transmission of HBV was identified. This highlights the need for vigilance regarding infection control practices in the renal unit setting.

A pilot study on the seroprevalence of parvovirus B19 infection.

BACKGROUND & OBJECTIVES: Human parvovirus B 19 (PVB 19) causes aplastic crisis in children with congenital haemolytic anaemia, erythema infectiosum, abortion and stillbirth. Since data on PVB 19 prevalence is lacking in India, a pilot study was undertaken to estimate the prevalence of IgG antibody in children and adults. METHODS: The samples were obtained from children attending our hospital and from volunteer blood donors, majority of whom were from south India. They included 45 children aged 1-5 yr, 39 aged 6-10 yr, 42 aged 11-15 yr and 100 healthy blood donors > 15 yr of age. Sera were tested for the presence of antibody to PVB 19 using a commercial enzyme immuno assay (EIA). RESULTS: Of 226 samples tested, 113 (50%) were positive for PVB 19 IgG. The prevalence of antibody increased from 8.9 per cent at 1-5 yr to 70 per cent in those > 15 yr: the median age of infection was between 6 and 15 yr. Sex and domiciliary status did not have significant effect on the prevalence of antibody. The IgG antibody index increased significantly with age, suggesting repeated exposure to the virus. INTERPRETATION & CONCLUSION: This seroprevalence study indicates that large numbers of individuals show exposure to PVB 19 virus. The exposure as indicated by IgG positivity is seen to increase with age. The IgG negative individuals may be considered to be at risk of developing infections due to PVB 19.

Increased number of CCR5+ CD4 T cells among south Indian adults probably associated with the low frequency of X4 phenotype of HIV-1 in India.

BACKGROUND & OBJECTIVE: The shift of the human immunodeficiency virus (HIV) from nonsyncytium inducing strains (NSI/R5) to syncytium inducing strains (SI/X4) seen in subtype B infections during progression to acquired immunodeficiency syndrome (AIDS) is less frequently reported in subtype C. NSI and SI strains differ in the co-receptor they utilize to infect a T-cell. We postulated that a larger pool of CD4 T cells expressing CCR5 would be present among individuals in the Indian population. To validate this hypothesis, we estimated the percentage of CD4 cells expressing CCR5 or CXCR4 molecules among healthy south Indian adults and HIV infected individuals. METHODS: HIV-1 infected and uninfected adult volunteers, belonging to the four southern states of India with Tamil/Malayalam/Kannada or Telugu as their spoken language were prospectively recruited. A two colour flowcytometry examination of the blood sample was done using the following monoclonals; anti-CD45 (FITC)/CD14 (PE), anti IgG1 (FITC)/IgG2a (PE), anti-CD3 (FITC)/CD4 (PE), anti-CD3 (FITC)/CD8 (PE), anti-CD4 (FITC) and anti CCR5 (PE) or anti CXCR4 (PE). RESULTS: In the healthy population (n = 30) studied, 24.6 per cent of CD4 T cells expressed CCR5 and the percentage of CD4 T cells expressing CXCR4 was 80.4. Among the HIV infected individuals (n = 51) the percentage of CD4 T cells expressing CCR5 and CXCR4 was 26.8 and 78.7 per cent respectively. INTERPRETATION & CONCLUSION: The percentage of CD4 cells expressing CCR5 and CXCR4 in both the HIV uninfected and infected adults was significantly higher in the south Indian population than in the West. The larger pool of CCR5 positive CD4 cells probably allows for the R5 HIV strain to have a replication advantage over X4 HIV strains. This may explain the lack of shift in the viral phenotype during disease progression and also the perceived rapid progression of the disease in India compared to the West.

Acute viral hepatitis - should the current screening strategy be modified?

BACKGROUND: The epidemiology of viral hepatitis has changed. Since the introduction of safe and effective vaccines for hepatitis A and B in 1980s, the incidence of acute infections caused by these viruses has been declining in the UK. At the same time, hepatitis E virus (HEV) has been recognised as an increasingly important cause of acute hepatitis, but testing is not widely available. OBJECTIVES: The aim of this study was to establish the viral causes of acute hepatitis, and use that data to modify the current diagnostic algorithm. STUDY DESIGN: A Cognos search was performed to collate subjects tested for HAV, HBV, HCV, HEV, EBV and CMV between June 2010 and December 2012. Information included virological result and their ALT level if done within 5 days from virological testing. RESULTS: From 3462 subjects with suspected acute viral hepatitis, only 25% had biochemical evidence of acute hepatitis (n=854; ALT>100IU/l). The frequency of detection of acute HEV infection (25/409) was over 31-times higher than that of HAV (6/3462), and 7-times higher than that of HBV (24/3462). Most cases of acute HAV, HEV, EBV and CMV infections presented with abnormal ALT levels. Most EBV infections were associated with lymphadenopathy (23/34); in comparison most of CMV infections were not associated with lymphadenopathy (18/22). CONCLUSIONS: HEV screening should be included in the initial testing panel for acute hepatitis and screening at least for HAV and HEV might be limited to those with abnormal ALT levels.

Autochthonous hepatitis E in Scotland.

BACKGROUND: Hepatitis E virus is well recognized cause of acute hepatitis. Traditionally hepatitis E virus (HEV) infections were generally associated with travel to Asia and Africa. Autochthonous hepatitis E is recognized as a major cause acute hepatitis in England and Wales. However, autochthonous hepatitis E has never been documented in Scotland. OBJECTIVES: We attempted to determine if autochthonous HEV occurred in Scotland. STUDY DESIGN: Samples from 377 individuals in the South-East of Scotland presenting with acute hepatitis were tested over six years. Acute hepatitis E was confirmed by detecting viraemia or documenting seroconversion and ORF-2 region sequenced. Structured interviews were carried out to identify risk factors for infection. RESULTS: Sixteen individuals (4.2%) had evidence of past HEV infection. Twelve (3.2%) had acute HEV infection, 10 of whom had viraemia (genotype 1=3; genotype 3=7). Of these seven with genotype 3 infection, three had not travelled outside Scotland within the incubation period, while four had travelled to Spain (n=3) or Turkey (n=1). All three individuals with genotype 1 infection had travelled to the Indian subcontinent. CONCLUSIONS: A significant proportion of HEV genotype 3 infections was autochthonous (43%). HEV screening should hence be an integral part of acute hepatitis screening in Scotland, irrespective of the travel history.