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• The Pangolin classification clustered the South Kivu sequences into seven lineages. • The Delta variant is responsible for COVID-19 outbreaks during the third wave. • D614G is the most frequent mutation observed, followed by L4715L. • There are multiple introductions of SARS-CoV-2 and subsequent circulating variants. We used whole-genome sequencing of SARS-CoV-2 to identify variants circulating in the Democratic Republic of the Congo and obtain molecular information useful for diagnosis, improving treatment, and general pandemic control strategies. A total of 74 SARS-CoV-2 isolates were sequenced using Oxford Nanopore platforms. Generated reads were processed to obtain consensus genome sequences. Sequences with more than 80% genome coverage were used for variant calling, phylogenetic analysis, and classification using Pangolin lineage annotation nomenclature. Phylogenetic analysis based on Pangolin classification clustered South Kivu sequences into seven lineages (A.23.1, B.1.1.6, B.1.214, B.1.617.2, B.1.351, C.16, and P.1). The Delta (B.1.617.2) variant was the most dominant and responsible for outbreaks during the third wave. Based on the Wuhan reference genome, 289 distinct mutations were detected, including 141 missenses, 123 synonymous, and 25 insertions/deletions when our isolates were mapped to the Wuhan reference strain. Most of these point mutations were located within the coding sequences of the SARS-CoV-2 genome that includes spike, ORF1ab, ORF3, and nucleocapsid protein genes. The most common mutation was D614G (1841A>G) observed in 61 sequences, followed by L4715L (14143 C>T) found in 60 sequences. Our findings highlight multiple introductions of SARS-CoV-2 into South Kivu through different sources and subsequent circulation of variants in the province. These results emphasize the importance of timely monitoring of genetic variation and its effect on disease severity. This work set a foundation for the use of genomic surveillance as a tool for future global pandemic management and control. [ABSTRACT FROM AUTHOR]

• SARS-CoV-2 vaccines ameliorate infection and adverse outcomes. • The booster dose induces increased humoral immune responses. • The booster dose induces an increased adaptative immune response. • The booster dose leads to early activation of the memory CD8+ T subset. Vaccines against SARS-CoV-2 ameliorate infection and adverse outcomes from SARS-CoV-2. Elicitation of high affinity and durable protective antibody responses is a hallmark of a successful humoral immune response to vaccination. To assess the relevance of serum levels of SARS-CoV-2 specific antibodies and to further characterize the immune response to SARS-CoV-2 vaccines, we report i) the levels of spike-binding and neutralizing antibodies to SARS-COV-2 in the sera of 30 healthy volunteers at nine months after the second vaccination dose of mRNA vaccine and one month after the booster dose; ii) the levels of IFN-γ production by blood T cells exposed to SARS-CoV-2 spike antigen (Wuhan, Alpha B.1.1.7, Delta B.1.617.2, and Omicron B1.1.529 variants); and iii) the specific phenotype of T cells related with exposure to SARS-CoV-2 spike antigen. We observed that the booster dose induced increased humoral and adaptive immune responses and led to early activation of the memory CD8+ T subset. [ABSTRACT FROM AUTHOR]

[Display omitted] • The mean latent/removed periods of the COVID-19 epidemic in China were 5.40/2.13 days. • There were 1.72 latent/infected persons per 10,000 Wuhan travelers up to January 20th. • Space-time R 0 estimates indicated an initial value between 2 and 3.5 in most cities. • There were 196 cities that had an estimated R 0 < 1 on February 29th. • A clear descent in temporal R 0 started one week after the outbreak and lasted for two weeks. The novel coronavirus (COVID-19) epidemic is reaching its final phase in China. The epidemic data are available for a complete assessment of epidemiological parameters in all regions and time periods. This study aims to present a spatiotemporal epidemic model based on spatially stratified heterogeneity (SSH) to simulate the epidemic spread. A susceptible-exposed/latent-infected-removed (SEIR) model was constructed for each SSH-identified stratum (each administrative city) to estimate the spatiotemporal epidemiological parameters of the outbreak. We estimated that the mean latent and removed periods were 5.40 and 2.13 days, respectively. There was an average of 1.72 latent or infected persons per 10,000 Wuhan travelers to other locations until January 20th, 2020. The space-time basic reproduction number (R 0) estimates indicate an initial value between 2 and 3.5 in most cities on this date. The mean period for R 0 estimates to decrease to 80%, and 50% of initial values in cities were an average of 14.73 and 19.62 days, respectively. Our model estimates the complete spatiotemporal epidemiological characteristics of the outbreak in a space-time domain. These findings will help enhance a comprehensive understanding of the outbreak and inform the strategies of prevention and control in other countries worldwide. [ABSTRACT FROM AUTHOR]

CORONA virus disease -19 (COVID-19) is a disease caused by SARS-CoV-2. The outbreak started from Wuhan, China in Dec'2019 and became a pandemic. Human to human transmission occurs through droplet, fomites, aerosol and contaminated surfaces.This study shows that use of portable air purifier in patient's room can actually reduce the viral load in the room air that might minimize the risk of acquiring COVID through air-borne transmission by heath care professional taking care of the COVID patients. The study was carried out in room/cabins of special ward in LN Hospital, New Delhi where recently detected (within 48 Hr of RT-PCR +Ve results) COVID-19 patient with cough were admitted for treatment.The COVID-19 patients were asked to cough on the petri dish fixed with a polyvinylidene fluoride (PVDF) membrane filter (80 mm in diameter and 3 um pore size) keeping it within 2 feet distances from his/her nose for 15 mins. Then the membrane was then removed and added to falcon tube (15ML) containing 3 ML of viral transport medium (VTM). The tube were sent to PCR lab in an ice box. Air sampler was run for 1Hr keeping it at 3 Meter distance from recently diagnosed COVID-19 patient. RT-PCR done from particulate matters collected in VTM from the air sampler.Air sampler was run similarly and RT-PCR was done from PM collected in the filter of air sampler. The primary air suction was done at two different air flow 16.7 and 27 litre per minute (LPM), after which both RDRP and E gene were positive, after the use of purifier both the genes were still positive but with increased Ct values. With continous use of the air purifier the viral load of COVID-19 present in the air of ICU with paitents is primarily reduced but not completely eliminated. [ABSTRACT FROM AUTHOR]

SARS-CoV-2 is a zoonotic pathogen able to infect humans, pets and other animal species, mustelids and felids being highly susceptible. Experimentally, it has been shown that SARS-CoV-2 replicates efficiently in cats, inducing humoral immunity and causing a variable clinical presentation. Here we report the case of two cats (G1 and G2) naturally infected with SARS-CoV-2 after contact with their COVID-19 positive owner diagnosed in September 2020. Oral swabs soaked in PBS were collected daily from 1 to 16 days after the owner tested positive for SARS-CoV-2. Urine and feces were taken several times during this period. Samples were analyzed by in-house real-time RT-PCR (based on CDC 2019-nCoV_N1). Serum samples, collected at day 30, were tested by IDVet multi-species ELISA. Vero E6 cells was used for virus isolation. Partial spike gene was sequenced by Sanger and compared with the owner sequence and the reference Wuhan 2019 (NC_045512.2). G1 showed apathy, anorexia, lack of grooming and mild respiratory symptoms (tearing and sneezing) for 5 days and then recovered gradually. G2 remained clinically asymptomatic. Viral RNA peak in oral swabs was detected in both cats at day 2 showing similar Ct value (25). SARS-CoV-2 was consistently shedding in G1 for 9 days, after sporadically detected until day 16. Viral shedding in G2 decreased quickly during the first 6 days. Faeces were positive to SARS-CoV-2 until 9 (G1) or 12 (G2) days post-viral detection. Viral RNA in urine was sporadically detected in G2 with high Ct values. Specific antibodies were detected in both cats one month after infection. Virus isolation was not successful. Cats and owner sequences of the spike protein were homologous with two mutations (A222V and D614G) that classify the virus within the 20A.EU1 clade. SARS-CoV-2 natural infection of two cats occurred after close contact with their infected owner. Both cats developed humoral immune response but they showed different clinical presentation and viral shedding pattern. Oral swabs and feces are proper samples for SARS-CoV-2 detection in cats. Variant 20A.EU1 detected in this study emerged in early summer 2020, presumably in Spain, and subsequently spread throughout Europe. [ABSTRACT FROM AUTHOR]

Severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2) causes COVID-19, which was first reported in humans in 2019, in Wuhan, China. This RNA virus has highly efficient transmission. Sporadic cases of infection in pets have been described. Human to animal transmission seems to occur, however, the epidemiologic role of pets remains unclear. This study aimed to screen dogs and cats from the North and Centre regions of Portugal for the exposure to SARS-CoV-2, during the peak of SARS-CoV-2 human infection in Portugal, which occurred between October 2020 and March 2021. A cross-sectional study was conducted in dogs and cats presented to veterinary medical centres from Portugal between October 2020 and March 2021, that required blood sampling as part of their diagnostic plan. Only surplus sera or plasma samples were used in this research. Sera or plasma were tested for the presence of specific antibodies anti-SARS-CoV-2 using a commercial ELISA adapted for multi-species detection (ID Screen SARS-CoV-2Double Antigen Multispecies®, IDVet). Laboratory results were expressed in S/P values and samples with an S/P% ≥ 60% were classified as positive. A total of 107 animals were sampled (dogs n=60; cats n=47). The canine population was composed by 25 purebred and 35 crossbreed dogs, with ages ranging from 5 months to 15 years of age. Cats were mainly of the domestic short-hair breed (n=45), with ages ranging between 6 months and 9 years old. The estimated rate of exposure was of 5.0% (95% CI: 1.71-13.7%) in dogs (n=3) and 2.13% (95% CI: 1.18-14.26%) in cats (n=1). A doubtful result (50≥S/P%<60%) was obtained in 6.7% (95% CI: 2.6-15.9%) of dogs (n=4) and in 4.26% (95% CI: 2.6-15.9%) of cats (n=3). To our best knowledge, this is the first serosurvey conducted in pets in Portugal. An exposure to the agent has been evidenced in dogs and in cats. Further studies must clarify the impact of the exposure in animal health and the role of the pets in spreading the virus. [ABSTRACT FROM AUTHOR]