Hydrodynamics of spike proteins dictate a transport-affinity competition for SARS-CoV-2 and other enveloped viruses

Many viruses, such as SARS-CoV-2 or Influenza, possess spike-decorated envelopes. Depending on the virus type, a large variability is present in spikes number, morphology and reactivity, which remains generally unexplained. Since viruses' transmissibility depend on features beyond their genetic sequence, new tools are required to discern the effects of spikes functionality, interaction, and morphology. Here, we postulate the relevance of hydrodynamic interactions in the viral infectivity of enveloped viruses and propose micro-rheological characterization as a platform for viruses differentiation. To understand how the spikes affect virion mobility and infectivity, we investigate the diffusivity of spike-decorate structures using mesoscopic-hydrodynamic simulations. Furthermore, we explored the interplay between affinity and passive viral transport. Our results revealed that the diffusional mechanism of SARS-CoV-2 is strongly influenced by the size and distribution of its spikes. We propose and validate a universal mechanism to explain the link between optimal virion structure and maximal infectivity for many virus families.

DETECTION OF SARS-COV-2 FROM SURFACE OF PATIENTS’ LEFTOVER FOOD PACKAGES AT A COVID-19 QUARANTINE CENTRE

In healthcare facilities, food waste and its packaging are mostly managed as non-infectious general waste. However, waste from SARS-CoV-2 positive patients, are treated as medical waste as they may be contaminated by the virus. We investigated the possibility of SARS-CoV-2 contamination from positive COVID-19 patients to their leftover food packages at a quarantine centre. Food packages surface was swabbed using prewetted cellular foam, placed into viral transport media and analysed using real time reverse transcription polymerase chain reaction. SARS-CoV-2 RNA was detected in two samples (4.5%) from asymptomatic patients who were at day-2 positive SARS-CoV-2 with cycle threshold (Ct) value (RdRp/E), 34.96/35.72 and 37.1/36.48 respectively. Detection of SARS-CoV-2 supports that there is contamination to the waste. These poses risk of exposure as SAR-COV-2 survive on the surfaces, thus, safe handling and disposal of food waste should be maintained. However, further study involving viral culture should be explored to determine the viability of the SARS-CoV-2 from leftover food packages

Ecological surveillance of bat coronaviruses in Sarawak, Malaysian Borneo

Objective Coronaviruses (CoVs) are natural commensals of bats. Two subgenera, namely Sarbecoviruses and Merbecoviruses have a high zoonotic potential and have been associated with three separate spillover events in the past 2 decades, making surveillance of bat-CoVs crucial for the prevention of the next epidemic. The study was aimed to elucidate the presence of coronavirus in fresh bat guano sampled from Wind Cave Nature Reserve (WCNR) in Sarawak, Malaysian Borneo. Samples collected were placed into viral transport medium, transported on ice within the collection day, and preserved at − 80 °C. Nucleic acid was extracted using the column method and screened using consensus PCR primers targeting the RNA-dependent RNA polymerase (RdRp) gene. Amplicons were sequenced bidirectionally using the Sanger method. Phylogenetic tree with maximum-likelihood bootstrap and Bayesian posterior probability were constructed. Results CoV-RNA was detected in ten specimens (47.6%, n = 21). Six alphacoronavirus and four betacoronaviruses were identified. The bat-CoVs can be phylogenetically grouped into four novel clades which are closely related to Decacovirus-1 and Decacovirus-2, Sarbecovirus, and an unclassified CoV. CoVs lineages unique to the Island of Borneo were discovered in Sarawak, Malaysia, with one of them closely related to Sarbecovirus. All of them are distant from currently known human coronaviruses.

A Retrospective Study of COVID-19 Cases Based on Age and Gender in Patient’s Visiting Tertiary Care Centre, Tezpur Medical College and Hospital, Tezpur, Assam

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which is also called COVID-19 has affected millions of people globally and has led to unprecedented disruptions to health systems, as well as affected individuals social, economic and psychological lives very badly. The present study was an attempt to address the association between age and gender among positive COVID-19 cases and also to discuss the possible reasons for the variation among age categories and gender. This was a retrospective based study. Samples were collected in Viral Transport Media and sent to the testing laboratory for confirmation by nucleic acid–based reverse transcription polymerase chain reaction (RT-PCR). Data regarding patients’ details were collected in the hospital facility. A total of 1,11,379 (Assam - 1,08,836 and Arunachal Pradesh-2543) samples were collected from patient’s and tested for COVID-19 (April to December 2020). During this period a total of 2,600 positive cases were detected at the laboratory from Assam (n= 2,480, 95.38%) and Arunachal Pradesh (n= 120, 4.62%) respectively. Males (n=2106, 81%) was affected more than females (n= 494, 19%). In both male & female the age group which was affected the most was between 20-29 yrs and 30-39 yrs. Month wise distribution of the positive COVID-19 cases showed maximum spike in the month of August (n=902). Early diagnosis by real time PCR has helped in the identification of the pathogen in individuals at an early stage, which has facilitated the containment of positive cases.

Sample collection and transport strategies to enhance yield, accessibility, and biosafety of COVID-19 RT-PCR testing

Introduction. Non-invasive sample collection and viral sterilizing buffers have independently enabled workflows for more widespread COVID-19 testing by reverse-transcriptase polymerase chain reaction (RT-PCR). Gap statement. The combined use of sterilizing buffers across non-invasive sample types to optimize sensitive, accessible, and biosafe sampling methods has not been directly and systematically compared. Aim. We aimed to evaluate diagnostic yield across different non-invasive samples with standard viral transport media (VTM) versus a sterilizing buffer eNAT- (Copan diagnostics Murrieta, CA) in a point-of-care diagnostic assay system. Methods. We prospectively collected 84 sets of nasal swabs, oral swabs, and saliva, from 52 COVID-19 RT-PCR-confirmed patients, and nasopharyngeal (NP) swabs from 37 patients. Nasal swabs, oral swabs, and saliva were placed in either VTM or eNAT, prior to testing with the Xpert Xpress SARS-CoV-2 (Xpert). The sensitivity of each sampling strategy was compared using a composite positive standard. Results. Swab specimens collected in eNAT showed an overall superior sensitivity compared to swabs in VTM (70 % vs 57 %, P=0.0022). Direct saliva 90.5 %, (95 % CI: 82 %, 95 %), followed by NP swabs in VTM and saliva in eNAT, was significantly more sensitive than nasal swabs in VTM (50 %, P<0.001) or eNAT (67.8 %, P=0.0012) and oral swabs in VTM (50 %, P<0.0001) or eNAT (58 %, P<0.0001). Saliva and use of eNAT buffer each increased detection of SARS-CoV-2 with the Xpert; however, no single sample matrix identified all positive cases. Conclusion. Saliva and eNAT sterilizing buffer can enhance safe and sensitive detection of COVID-19 using point-of-care GeneXpert instruments.

Study of vertical transmission of COVID-19 infection in COVID-19 positive obstetrical patients by comparing amniotic fluid and immediate neonatal COVID-19 RT-PCR

Background: The objective of this study was to estimate the incidence of vertical transmission COVID-19 by RT-PCR.Methods: In this hospital based prospective study, all COVID-19 positive pregnant women admitted in COVID ward in Muzaffarnagar medical college and hospital from April 2020 to January 2021 were included. A detailed history and examination was done and all routine investigations were done as per protocol. Samples were taken from amniotic fluid during vaginal delivery or caesarean section and collected in viral transport medium. Sample were also collected as nasal and oropharyngeal swab from neonate immediately after birth and sent for COVID 19 RT-PCR.Results: Out of total 50 cases; 43 (86%) neonates were delivered via LSCS and 7 (14%) by normal delivery, out of these 41 (82%) neonates were normal; 4 (8%) were IUGR, 2 (4%) were IUD, 2 (4%) were pre-term and 1 (2%) neonatal death. All 50 amniotic fluid as well as nasal and oropharyngeal samples of all neonates were negative by RT-PCR.Conclusions: Low vertical transmission may be due to the fact that antibodies are produced by mother that crosses the placenta and saves the fetus or there are highly specific immunological mediators in the placenta that do not allow the infection to pass to the fetus.

SARS COV-2 PANDEMIC: EXPERIENCE AT REFERENCE VIROLOGY LABORATORY SHORT RUNNING TITLE: SARS COV-2 PANDEMIC EXPERIENCE

Objective: To share our large scale SARS CoV-2 PCR test experience in Northern Pakistan. Study Design: Prospective observational study. Place and Duration of Study: Virology Department, Armed Forces Institute of Pathology, Rawalpindi, from Feb to Dec 2020. Methodology: All the patients reporting to COVID-19 desk both indoor and outdoor were included in study. Nasopharyngeal swab specimen was taken from the patients arriving at reception. For hospitalized patient’s samples were received at reception placed in viral transport medium maintaining cold chain. Results: Among 193656 samples tested for SARS CoV-2 RNA by RT-PCR, 24338 (12.6%) were found positive and 169318 (87.4%) were negative. Mean age of patients was 38.25 ± 16.73 (1-110 years). 138781 (71.7%) were males and 54875 (28.3%) were females. 109765 (56.7%) samples were received from in patient department and 83891 (43.3%) samples were received from outpatient department. Highest number of cases (n=6224) seen during month of June followed by 5813 cases during May and 4786 cases during November (p-value <0.001). Most of the positive cases were in age group 21-40 years; 11122 (6%), followed by age group 41-60 years; 8133 (4.2%). More positive samples 14890 (7.7%) were received from in patient department and males 17928 (9.3%) were affected more than females. Conclusion: The two peaks of COVID-19 pandemic in Pakistan were observed during the months of May to July and again during October to December. Most positive patients in our setup were males in age group 21-40 years as this age group is more exposed to external environment.

Harmony COVID-19: a ready-to-use kit, low-cost detector, and smartphone app for point-of-care SARS-CoV-2 RNA detection

RNA amplification tests sensitively detect SARS-CoV-2 infection, but their complexity and cost are prohibitive for expanding COVID-19 testing. We developed Harmony COVID-19, a point-of-care test using inexpensive consumables, ready-to-use reagents, and a simple device accommodating up to 4 samples simultaneously. Our ready-to-use, 4-plex reverse-transcription, loop-mediated isothermal amplification (RT-LAMP) can detect down to 0.38 SARS-CoV-2 RNA copies/μL and can report in 17 min for high viral load samples (5,000 copies/μL). Harmony detected 97% or 83% of contrived samples with ≥0.5 viral particles/μL in nasal matrix or saliva, respectively. Evaluation in clinical nasal specimens in viral transport media (VTM, n=101) showed 100% detection of RNA extracted from specimens with ≥0.5 SARS-CoV-2 RNA copies/μL, with 100% specificity in specimens positive for other respiratory pathogens. VTM is non-ideal for Harmony system, yet extraction-free analysis of VTM specimens (n=29) had 95% success in specimens with ≥1 RNA copies/μL. Usability testing performed first-time by healthcare workers showed 95% accuracy

Viral Transport Media (VTM) Pooling To Scale-Up COVID-19 Diagnostics: Resource Optimization at Population Level Screening

Background: The threat of coronavirus disease 2019 (COVID-19) is still looming large on humankind. Pooled-testing can serve as a method of choice for current and future mass surveillance. The aim is to economically benefit in the face of resource-paucity in overburdened public health systems. Methods: This study assesses the viability of pooled-testing with viral transport media (VTM) for COVID-19 diagnosis. For this, we designed high-dilution pools using samples with wide-ranging viral loads. The testing employs common TaqMan-based RT-PCR assay considering biological as well as technical replicates. Results: We successfully detected a single positive sample in a pool (up to 1/32 dilutions) without loss of sensitivity. The results from biological and technical replicates were found to be satisfactory and reproducible for the objective. We have also discussed multiple variables that can influence the final outcome of pooled testing strategy. Conclusions: We show that pooling approach can be efficiently applied for the detection of SARS-CoV-2. We report improved pooling success compared to published studies, even with very low input volume of media, in very high pool-sizes using low-viral load samples. We consider these features to be unique to this study. The study outcomes are encouraging and can be implemented in public health settings to conserve precious resources.