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The designated COVID-19 testing laboratories of Virus Research Diagnostic Laboratory network (All India Institute of Medical Sciences, New Delhi; Sawai Man Singh Medical College, Jaipur; and King George's Medical University, Lucknow) referred the specimens (throat swab/nasal swab, oropharyngeal swab/sputum) to the Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, after screening for envelope (E) gene by real-time RT-PCR was done[6]. From each well of cell culture plate, on the third post-infection day (PID-3) of passage-1 (P-1), 50 μl of supernatant was taken and tested for SARS-CoV-2 using real-time RT-PCR for E and RNA-dependent RNA polymerase (RdRp) (2) genes as described earlier[7],[8]. Virus replication was confirmed using real-time RT-PCR with RNA extracted from the cell culture medium on PID-3. The number of virus copies in the isolates at P-1 in Vero CCL-81 cells ranged from 5.18×10[7] to 8.12×10[8] copy/ml and increased 1-26 fold to a range of 1.69×10[8] to 6.77×10[9] in the cell culture supernatants at P-2 [Table 1].

We have isolated the new severe acute respiratory syndrome coronavirus-2 variant of concern 202 012/01 from the positive coronavirus disease 2019 cases that travelled from the UK to India in the month of December 2020. This emphasizes the need for the strengthened surveillance system to limit the local transmission of this new variant.

Background & objectives: The global pandemic caused by SARS-CoV-2 virus has challenged public health system worldwide due to the unavailability of approved preventive and therapeutic options. Identification of neutralizing antibodies (NAb) and understanding their role is important. However, the data on kinetics of NAb response among COVID-19 patients are unclear. To understand the NAb response in COVID-19 patients, we compared the findings of microneutralization test (MNT) and plaque reduction neutralization test (PRNT) for the SARS-CoV-2. Further, the kinetics of NAb response among COVID-19 patients was assessed. Methods: A total of 343 blood samples (89 positive, 58 negative for SARS-CoV-2 and 17 cross-reactive and 179 serum from healthy individuals) were collected and tested by MNT and PRNT. SARS-CoV-2 virus was prepared by propagating the virus in Vero CCL-81 cells. The intra-class correlation was calculated to assess the correlation between MNT and PRNT. The neutralizing endpoint as the reduction in the number of plaque count by 90 per cent (PRNT90) was also calculated. Results: The analysis of MNT and PRNT quantitative results indicated that the intra-class correlation was 0.520. Of the 89 confirmed COVID-19 patients, 64 (71.9%) showed NAb response. Interpretation & conclusions: The results of MNT and PRNT were specific with no cross-reactivity. In the early stages of infection, the NAb response was observed with variable antibody kinetics. The neutralization assays can be used for titration of NAb in recovered/vaccinated or infected COVID-19 patients.

Background & objectives: Since the beginning of the year 2020, the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) impacted humankind adversely in almost all spheres of life. The virus belongs to the genus Betacoronavirus of the family Coronaviridae. SARS-CoV-2 causes the disease known as coronavirus disease 2019 (COVID-19) with mild-to-severe respiratory illness. The currently available diagnostic tools for the diagnosis of COVID-19 are mainly based on molecular assays. Real-time reverse transcription-polymerase chain reaction is the only diagnostic method currently recommended by the World Health Organization for COVID-19. With the rapid spread of SARS-CoV-2, it is necessary to utilize other tests, which would determine the burden of the disease as well as the spread of the outbreak. Considering the need for the development of such a screening test, an attempt was made to develop and evaluate an IgG-based ELISA for COVID-19. Methods: A total of 513 blood samples (131 positive, 382 negative for SARS-CoV-2) were collected and tested by microneutralization test (MNT). Antigen stock of SARS-CoV-2 was prepared by propagating the virus in Vero CCL-81 cells. An IgG capture ELISA was developed for serological detection of anti-SARS-CoV-2 IgG in serum samples. The end point cut-off values were determined by using receiver operating characteristic (ROC) curve. Inter-assay variability was determined. Results: The developed ELISA was found to be 92.37 per cent sensitive, 97.9 per cent specific, robust and reproducible. The positive and negative predictive values were 94.44 and 98.14 per cent, respectively. Interpretation & conclusions: This indigenously developed IgG ELISA was found to be sensitive and specific for the detection of anti-SARS-CoV-2 IgG in human serum samples. This assay may be used for determining seroprevalence of SARS-CoV-2 in a population exposed to the virus.

{Figure 1} Of the 107 P. giganteus bat tissue specimens (liver/spleen and kidney) tested for NiV by real-time reverse transcriptase polymerase chain reaction (RT-PCR)[12], nine bats (6 bats from Cooch Behar district of West Bengal and 3 from Dhubri district of Assam) were found to be positive for NiV RNA [Table 1]. Viral RNA from tissue samples of only one bat from Cooch Behar district of West Bengal and one bat from Dhubri district of Assam could be amplified using partial nucleocapsid gene-specific reverse transcriptase nested PCR (100 bp) as described earlier [7],[8]. Acknowledgment Authors acknowledge the support extended by the Secretary, DHR, Government of India and Director General, Indian Council of Medical Research, New Delhi, and thank the Principal Conservators of Forests of Assam and West Bengal and other concerned officials for their permission to capture bats.

The use of transgenic mice expressing the human ACE2 receptor, aged mice, knockout mice and use of mice adapted virus were found beneficial in recapitulating the clinical signs of SARS-CoV infection[4],[5],[6],[7]. Currently, there are no studies on mice regarding the susceptibility to SARS-CoV-2 except one on the transgenic mice with hACE2[12]. [...]we studied the susceptibility of rodent models such as BALB/c mice, C57BL/6 mice and golden Syrian hamsters to the SARS-CoV-2 infection. Golden Syrian hamsters showed high viral loads in the upper and lower respiratory tracts, virus shedding through the nasal cavity and mounting of humoral immune response by the first week, similar to human COVID-19 cases.

The genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), belonging to the family Coronaviridae, encodes for structural, non-structural, and accessory proteins, which are required for replication of the virus. These proteins are encoded by different genes present on the SARS-CoV-2 genome. The expression pattern of these genes in the host cells needs to be assessed. This study was undertaken to understand the transcription pattern of the SARS-CoV-2 genes in the Vero CCL-81 cells during the course of infection. Vero CCL-81 cells were infected with the SARS-CoV-2 virus inoculum having a 0.1 multiplicity of infection. The supernatants and cell pellets were harvested after centrifugation at different time points, post-infection. The 50% tissue culture infective dose (TCID )and cycle threshold (C ) values of the E and the RdRp-2 genes were calculated. Next-generation sequencing of the harvested sample was carried out to observe the expression pattern of the virus by mapping to the SARS-CoV-2 Wuhan HU-1 reference sequence. The expressions were in terms of the reads per kilobase million (RPKM) values. In the inital six hours post-infection, the copy numbers of E and RdRp-2 genes were approximately constant, which raised 10 log-fold and continued to increase till the 12 h post-infection (hpi). The TCID was observed in the supernatant after 7 hpi, indicating the release of the viral progeny. ORF8 and ORF7a, along with the nucleocapsid transcript, were found to express at higher levels. This study was a step towards understanding the growth kinetics of the SARS-CoV-2 replication cycle. The findings indicated that ORF8 and ORF7b gene transcripts were expressed in higher amounts indicating their essential role in viral replication. Future studies need to be conducted to explore their role in the SARS-CoV-2 replication.

The present manuscript deals with experimental infections of bonnet macaques ( Macaca radiata ) to study disease progression for better insights into the Kyasanur Forest Disease (KFD) pathogenesis and transmission. Experimentally, 10 monkeys were inoculated with KFD virus (KFDV) (high or low dose) and were regularly monitored and sampled for various body fluids and tissues at preset time points. We found that only 2 out of the 10 animals showed marked clinical signs becoming moribund, both in the low dose group, even though viremia, virus shedding in the secretions and excretions were evident in all inoculated monkeys. Anti-KFDV immunoglobulin (Ig)M antibody response was observed around a week after inoculation and anti-KFDV IgG antibody response after two weeks. Anaemia, leucopenia, thrombocytopenia, monocytosis, increase in average clotting time, and reduction in the serum protein levels were evident. The virus could be re-isolated from the skin during the viremic period. The persistence of viral RNA in the gastrointestinal tract and lymph nodes was seen up to 53 and 81 days respectively. Neuro-invasion was observed only in moribund macaques. Re-challenge with the virus after 21 days of initial inoculation in a monkey did not result in virus shedding or immune response boosting.