A SARS-CoV-2 Delta Variant Containing Mutation in the Probe Binding Region Used for qRT-PCR Test in Japan Exhibited Atypical PCR Amplification and Might Induce False Negative Result (preprint)

ABSTRACT A recent pandemic of SARS-CoV-2 infection has caused severe health problems and substantially restricted social and economic activities. To cope with such an outbreak, the identification of infected individuals with high accuracy is vital. qRT-PCR plays a key role in the diagnosis of SARS-CoV-2 infection. The N protein-coding region is widely analyzed in qRT-PCR for the diagnosis of SARS-CoV-2 infection in Japan. We recently encountered two cases of SARS-CoV-2-positive specimens showing atypical amplification curves in the qRT-PCR. We performed whole-genome sequencing and found that the virus was a Delta-type variant of SARS-CoV-2 with a single nucleotide mutation in the probe-binding site. To evaluate the extent of spread of the variant in the area, we performed whole viral genome sequencing of samples collected from 61 patients infected with SARS-CoV-2 during the same time and in the same area. There were no other cases with the same mutation, indicating that the variant had not spread in the area. Furthermore, we performed phylogenetic analysis with various SARS-CoV-2 sequences deposited in the public database. Hundreds of variants were reported globally, and one in Japan were found to contain the same mutation. Phylogenetic analysis showed that the variant was very close to other Delta variants endemic in Japan but quite far from the variants containing the same mutation reported from outside Japan, suggesting that the variant would have been sporadically generated in some domestic areas. These findings propose two key points: i) mutations in the region used for SARS-CoV-2 qRT-PCR can cause abnormal amplification curves; therefore, the qRT-PCR result should not just be judged in an automated manner, but also manually checked by the examiner to prevent false-negative results, and ii) various mutations can be generated sporadically and unpredictably; therefore, efficient and robust screening systems are needed to promptly monitor the emergence of de novo variants.

Misconceptions About COVID-19 Among Older Rohingya Adults (Forcefully Displaced Myanmar Nationals) in Bangladesh: Findings from a Cross-Sectional Study (preprint)

Background: Rohingya (Forcefully Displaced Myanmar Nationals or FDMNs) in Bangladesh are at increased risk of 2019 coronavirus disease (COVID-19), especially the older population. Given low health literacy among the FDMNs and the adverse situation of their residential camps, there are possibilities of misinformation related to COVID-19 among the older FDMNs who are at greater risk. Therefore, the present research aimed to assess the level of misconceptions and the factors associated with it among the older FDMNs in Bangladesh. Methods: This cross-sectional study was conducted among 416 FDMNs, aged 60 years and above, from a Rohingya camp situated in Cox’s Bazar, a South-Eastern district of Bangladesh. We collected information on 14 different locally relevant misconceptions related to the spread, prevention, and treatment of COVID-19, scored each misconception as one, and obtained a cumulative score of the 14-items, ranging from 0 to 14, with a higher score indicating a higher level of misconceptions. With backward selection based on the Akaike information criterion, a multiple linear regression model explored the factors associated with misconceptions. Findings: The participants had an average of five misconceptions. The most prevalent misconceptions were related to the prevention of COVID-19, i.e., everyone should wear personal protective equipment when outside (86.6%), and its prevention by nutritious food (62.5%) and drinking water (59.3%). Other notable misconceptions included the spread of COVID-19 through mosquito bites (42%) and its transmissions only to the non/less-religious person (31.5%). In regression analyses, memory or concentration problems, communication frequency with social networks, pre-existing conditions, and receiving information from health workers were significantly associated with higher COVID-19 misconceptions. These misconceptions were less likely among those overwhelmed by the pandemic, having COVID-19 diagnosed friends or family members, and receiving information from friends and family. Interpretation: Overall, we found that misconceptions were prevalent among the older FDMNs in Bangladesh. The associations have important implications for programs to prevent and manage COVID-19 in these settings. Health workers need to be adequately trained to provide clear communication and counter misconceptions. Funding: No funding was received for this study.Declaration of Interests: The authors have no conflict of interest to disclose.Ethics Approval Statement: The institutional review board of the Institute of Health Economics, University of Dhaka, Bangladesh, approved the study protocol. Informed written consent was sought from the participants (thumb impressions from those who could not read and write) before administering the survey. Participation was voluntary, and participants did not receive any compensation. Written approval was also sought from the Office of the Refugee Relief and Repatriation Commissioner (RRRC) prior to accessing the camps and conducting the survey.

Global Outbreaks of SARS-nCoV-2 (COVID-19 Pandemic) and Spread out in Bangladesh

Currently, the world is concerned about the 2019 novel CoV (SARS-nCoV-2), the disease it causes has been named “coronavirus disease 2019” (COVID-19) that was initially identified in Wuhan, China on 31 December 2019. Infected patients presented with severe viral pneumonia and respiratory illness. The new SARS-CoV-2 is RNA genomes and a beta-coronavirus, like SARS-CoV and MERS-CoV. In this article, provide a brief insights into past and present outbreaks of COVID-19. At end of the April 2020, COVID-19 Pandemic spread out all over the world in 210 countries/areas and the number of confirmed cases has been mounting globally. Reported in USA alone, over one million people are infected which is one-third of world confirmed cases and deaths cases also near to one-fourth of the total estimated deaths cases so far recorded globally. In other countries of the world situation is almost same but in Europe COVID-19 positive cases so high including death cases. In Bangladesh, the number of confirmed cases and fatality rate is lower than other reported countries in the world, due to deficient testing facilities and inadequate number of samples are tested, the virus seems to be highly contagious in Bangladesh as well. Although the fatality rate of SARS-nCoV-2 is currently lower than SARS-CoV and MERS-CoV, but the virus seems to be highly contagious based on the number of infected cases to date.