Seroprevalence of SARS-CoV-2 infection among frontline police personnel in Mumbai, India.

Introduction: A serosurvey was designed to ascertain the extent of infection among police personnel in Mumbai, India, during the last week of January 2021, at the end of the first wave of the COVID-19 pandemic, and just before the introduction of vaccination. Methods: The survey was carried out to screen for SARS-CoV-2 among 3232 police personnel. Of the 3176 participants willing for blood sample collection, 3077 personnel were found to be eligible for testing antibodies against the SARS-CoV-2 virus using the Roche Diagnostics' Elecsys Anti-SARS-CoV-2 assay. Results: The overall seroprevalence was 74.1% (95% CI 72.5-75.6). Males (75.1%, 73.4-76.8) had significantly higher seroprevalence than females (69.8%, 66.0-73.3), 18-39 years age group (76.4%, 74.4-78.3) than 40-59 years age group (70.6%, 67.9-73.1), non-officers (75.2%, 73.5-76.7) than officers (63.8%, 58.2-69.0), and personnel without comorbidities (75.0%, 73.3-76.6) than with comorbidities (69.7%, 65.6-73.5). Additionally, personnel with resident members positive for COVID-19 (89.6%, 84.7-93.1), personnel having reported COVID-19 earlier (95.5%, 93.8-96.7), and personnel having PCR positivity earlier (96.4%, 94.7-97.6) had significantly higher seroprevalences than others. All other variables, including diabetes and blood glucose status, lipid levels and thyroid enzymes, were not significantly associated with the seroprevalence levels. Conclusions: Almost three-fourths of frontline police personnel had evidence of past COVID-19 infection at the end of the first wave in January 2021, just before the introduction of COVID-19 vaccination. These frontline non-healthcare essential workers are an important risk group, and amenable to rapid serosurveys. These findings may help in estimating transmission status in the general community, along with disease burden, aiding prioritization of healthcare services.

Replication of SARS-CoV-2 in cell lines used in public health surveillance programmes with special emphasis on biosafety.

Background & objectives: Polio, measles, rubella, influenza and rotavirus surveillance programmes are of great public health importance globally. Virus isolation using cell culture is an integral part of such programmes. Possibility of unintended isolation of SARS-CoV-2 from clinical specimens processed in biosafety level-2 (BSL-2) laboratories during the above-mentioned surveillance programmes, cannot be ruled out. The present study was conducted to assess the susceptibility of different cell lines to SARS-CoV-2 used in these programmes. Methods: Replication of SARS-CoV-2 was studied in RD and L20B, Vero/hSLAM, MA-104 and Madin-Darby Canine Kidney (MDCK) cell lines, used for the isolation of polio, measles, rubella, rotavirus and influenza viruses, respectively. SARS-CoV-2 at 0.01 multiplicity of infection was inoculated and the viral growth was assessed by observation of cytopathic effects followed by real-time reverse transcription-polymerase chain reaction (qRT-PCR). Vero CCL-81 cell line was used as a positive control. Results: SARS-CoV-2 replicated in Vero/hSLAM, and MA-104 cells, whereas it did not replicate in L20B, RD and MDCK cells. Vero/hSLAM, and Vero CCL-81 showed rounding, degeneration and detachment of cells; MA-104 cells also showed syncytia formation. In qRT-PCR, Vero/hSLAM and MA-104 showed 106 and Vero CCL-81 showed 107 viral RNA copies per µl. The 50 per cent tissue culture infectious dose titres of Vero/hSLAM, MA-104 and Vero CCL-81 were 105.54, 105.29 and 106.45/ml, respectively. Interpretation & conclusions: Replication of SARS-CoV-2 in Vero/hSLAM and MA-104 underscores the possibility of its unintended isolation during surveillance procedures aiming to isolate measles, rubella and rotavirus. This could result in accidental exposure to high titres of SARS-CoV-2, which can result in laboratory acquired infections and community risk, highlighting the need for revisiting biosafety measures in public health laboratories.

Selection and application of biological safety cabinets in diagnostic and research laboratories with special emphasis on COVID-19.

The ongoing coronavirus disease (COVID-19) pandemic is a global public health emergency. Adherence to biosafety practices is mandatory to protect the user as well as the environment, while handling infectious agents. A biological safety cabinet (BSC) is the most important equipment used in diagnostic and research laboratories in order to safeguard the product, the person, and the environment. The World Health Organization has emphasized the use of validated BSCs in order to ensure quality of the results. There are different classes of BSCs that are used in various work environments based on the need. It is imperative to use appropriate levels of biosafety and types of BSCs in laboratories based on the risk assessment of the pathogen used. During the development of COVID-19 laboratories and training of laboratory staff, we came across several queries about the functions and selection of BSCs and realized that the knowledge about the detailed information on selections and applications of BSCs is scanty. There are several guidelines regarding the biosafety aspects for diagnostic and research laboratories handling infectious pathogens from national and international agencies. However, there is no detailed information on the use of appropriate types of BSCs and their functions in the context of Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2). In view of this, the present paper describes in detail the selection and applications of BSCs, which could be useful for laboratories handling or planning to handle SARS-CoV-2 and suspected samples.

Phylogenetic classification of the whole-genome sequences of SARS-CoV-2 from India & evolutionary trends.

BACKGROUND & OBJECTIVES: Several phylogenetic classification systems have been devised to trace the viral lineages of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, inconsistency in the nomenclature limits uniformity in its epidemiological understanding. This study provides an integration of existing classifications and describes evolutionary trends of the SARS-CoV-2 strains circulating in India. METHODS: The whole genomes of 330 SARS-CoV-2 samples were sequenced using next-generation sequencing (NGS). Phylogenetic and sequence analysis of a total of 3014 Indian SARS-CoV-2 sequences from 20 different States/Union Territories (January to September 2020) from the Global Initiative on Sharing All Influenza Data (GISAID) database was performed to observe the clustering of Nextstrain and Phylogenetic Assignment of Named Global Outbreak LINeages (Pangolin) lineages with the GISAID clades. The identification of mutational sites under selection pressure was performed using Mixed Effects Model of Evolution and Single-Likelihood Ancestor Counting methods available in the Datamonkey server. RESULTS: Temporal data of the Indian SARS-CoV-2 genomes revealed that except for Uttarakhand, West Bengal and Haryana that showed the circulation of GISAID clade O even after July 2020, the rest of the States showed a complete switch to GR/GH clades. Pangolin lineages B.1.1.8 and B.1.113 identified within GR and GH clades, respectively, were noted to be indigenous evolutions. Sites identified to be under positive selection pressure within these clades were found to occur majorly in the non-structural proteins coded by ORF1a and ORF1b. INTERPRETATION & CONCLUSIONS: This study interpreted the geographical and temporal dominance of SARS-CoV-2 strains in India over a period of nine months based on the GISAID classification. An integration of the GISAID, Nextstrain and Pangolin classifications is also provided. The emergence of new lineages B.1.1.8 and B.1.113 was indicative of host-specific evolution of the SARS-CoV-2 strains in India. The hotspot mutations such as those driven by positive selection need to be further characterized.

Steps, implementation and importance of quality management in diagnostic laboratories with special emphasis on coronavirus disease-2019.

A well-established and functional quality management system is an integral part of any diagnostic laboratory. It assures the reliability and standards of the laboratory function. A pandemic situation such as that caused by the influenza H1N1 2009 virus or the recent severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) increases the demands on the public health system, and the need to build, upgrade and expand the number of diagnostic laboratories. The Coronavirus disease-19 (COVID-19) pandemic caused by the SARS-CoV-2 unleashed a public health emergency of an unprecedented scale. The need has been highlighted for the accreditation of tests relating to COVID-19 by the National Accreditation Board for Testing and Calibration Laboratories (NABL) or any agencies approved by the World Health Organization (WHO) or Indian Council of Medical Research. The implementation of quality system in diagnostic laboratories would ensure accurate, reliable and efficient test results at par with the international standards. The functional aspects of a laboratory such as a well-defined organogram, standard operating procedures, good laboratory practices, quality controls, human resources, equipment management, reagents, inventory of records, proper communication need to be addressed to assure quality. Biosafety considerations should include the guidelines laid out by the WHO, the Institutional Biosafety Committee and the Department of Biotechnology, Government of India for carrying out diagnostic work in the laboratory. Currently, there are 1922 laboratories, operational for COVID-19 diagnosis in India. Considering the urgency of testing, the NABL has expedited the process of accreditation and issued accreditation to 818 laboratories. The adherence to the practicable aspects of quality described in this article would help in establishing quality in COVID-19 testing laboratories.