Widespread contamination of SARS-CoV-2 on highly touched surfaces in Brazil during the second wave of the COVID-19 pandemic

Although SARS-CoV-2 surface contamination has been investigated in health care settings, little is known about the SARS-CoV-2 surface contamination in public urban areas, particularly in tropical countries. Here, we investigated the presence of SARS-CoV-2 on high-touch surfaces in a large city in Brazil, one of the most affected countries by the COVID-19 pandemic in the world. A total of 400 surface samples were collected in February 2021 in the City of Recife, Northeastern Brazil. A total of 97 samples (24.2%) tested positive for SARS-CoV-2 by RT-qPCR using the CDC-USA protocol. All the collection sites, except one (18/19, 94.7%) had at least one environmental surface sample contaminated. SARS-CoV-2 positivity was higher in public transport terminals (47/84, 55.9%), followed by health care units (26/84, 30.9%), beach areas (4/21, 19.0%), public parks (14/105, 13.3%), supply centre (2/21, 9.5%), and public markets (4/85, 4.7%). Toilets, ATMs, handrails, playgrounds and outdoor gyms were identified as fomites with the highest rates of SARS-CoV-2 detection. Taken together, our data provide a real-world picture of SARS-CoV-2 dispersion in highly populated tropical areas and identify critical control points that need to be targeted to break SARS-CoV-2 transmission chains.     

COVID-19确诊病例居住环境病毒检测结果分析及防控探讨

新型冠状病毒肺炎(COVID-19)传播速度快、感染范围广,其感染方式主要是聚集性感染,感染途径主要是呼吸道飞沫和接触传播。了解环境中,特别是COVID-19确诊病人生活环境中的病毒存在情况,是做好环境消毒,阻断新型冠状病毒(SARS-CoV-2)传播的重要步骤,对COVID-19防控具有重要意义。本研究旨在探讨COVID-19患者生活环境中SARS-CoV-2的存在情况,从SARS-CoV-2存在的空间部位、病毒核酸含量、消毒效果等方面对SARS-CoV-2的相关特点做出初步研究,为制定有效的SARS-CoV-2防控措施提供科学依据。本研究以COVID-19病例治疗前的3个家庭居住环境和治疗出院后隔离期间的2个宾馆居住环境中采集的样本为研究材料,采用RT-PCR方法检测样本中的SARS-CoV-2核酸并进行比较分析。结果显示,首次从3个家庭环境中采样48份,RTPCR检测SARS-CoV-2核酸阳性5份(10.42%),3个家庭的环境样本中均有阳性样本检出。首次采样48h后在家庭3进行第二次采样16份,SARS-CoV-2核酸检测阳性2份(12.5%),检测Ct值比首次升高。家庭3消毒后24h采集的16份样本SARS-CoV-2核酸检测均为阴性,并且两处宾馆环境采集的24份样本SARS-CoV-2核酸检测也均为阴性。本研究提示,COVID-19病例的生活环境中可以检出SARS-CoV-2,病毒存在区域、存在物品、病毒核酸含量均有差异;对外环境进行消毒可以达到消毒目的,能够起到阻断SARS-CoV-2传播的防控效果。     

Airborne Detection and Quantification of Swine Influenza A Virus in Air Samples Collected Inside,Outside and Downwind from Swine Barns

Airborne transmission of influenza A virus (IAV) in swine is speculated to be an important route of virus dissemination, but data are scarce. This study attempted to detect and quantify airborne IAV by virus isolation and RRT-PCR in air samples collected under field conditions. This was accomplished by collecting air samples from four acutely infected pig farms and locating air samplers inside the barns, at the external exhaust fans and downwind from the farms at distances up to 2.1 km. IAV was detected in air samples collected in 3 out of 4 farms included in the study. Isolation of IAV was possible from air samples collected inside the barn at two of the farms and in one farm from the exhausted air. Between 13% and 100% of samples collected inside the barns tested RRT-PCR positive with an average viral load of 3.20E+05 IAV RNA copies/m³ of air. Percentage of exhaust positive air samples also ranged between 13% and 100% with an average viral load of 1.79E+04 RNA copies/m³ of air. Influenza virus RNA was detected in air samples collected between 1.5 and 2.1 Km away from the farms with viral levels significantly lower at 4.65E+03 RNA copies/m³. H1N1, H1N2 and H3N2 subtypes were detected in the air samples and the hemagglutinin gene sequences identified in the swine samples matched those in aerosols providing evidence that the viruses detected in the aerosols originated from the pigs in the farms under study. Overall our results indicate that pigs can be a source of IAV infectious aerosols and that these aerosols can be exhausted from pig barns and be transported downwind. The results from this study provide evidence of the risk of aerosol transmission in pigs under field conditions.     

SARS-CoV-2 Serological Survey of Cats in China before and after the Pandemic

The high percentage of seropositivity of cats in Wuhan, the epicentre of the SARS-CoV-2 epidemic, could be due to the large number of infected human cases (more than 14 folds than that in other cities) (Table 1) where cats may have been more frequently exposed to SARS-CoV-2 patients or contaminated environment. As yet, SARS-CoV-2 serological prevalence of cats in other Chinese cities remains unknown. Therefore, a serological survey including more cities with numbers of SARS-CoV-2 human cases in China will be valuable for elucidating the role of cats in transmission of the viruses and relieve public concerns. In this study, 630 cat serum samples collected before November 2019 and 423 cat serum samples collected during SARS-CoV-2 outbreak (from February 2020 to April 2020) in 20 cities in China for detecting the prevalence of SARS-CoV-2 specific antibodies.     

Biophysical analysis of SARS-CoV-2 transmission and theranostic development via N protein computational characterization

Recently, SARS-CoV-2 has been identified as the causative factor of viral infection called COVID-19 that belongs to the zoonotic beta coronavirus family known to cause respiratory disorders or viral pneumonia, followed by an extensive attack on organs that express angiotensin-converting enzyme II (ACE2). Human transmission of this virus occurs via respiratory droplets from symptomatic and asymptomatic patients, which are released into the environment after sneezing or coughing. These droplets are capable of staying in the air as aerosols or surfaces and can be transmitted to persons through inhalation or contact with contaminated surfaces. Thus, there is an urgent need for advanced theranostic solutions to control the spread of COVID-19 infection. The development of such fit-for-purpose technologies hinges on a proper understanding of the transmission, incubation, and structural characteristics of the virus in the external environment and within the host. Hence, this article describes the development of an intrinsic model to describe the incubation characteristics of the virus under varying environmental factors. It also discusses on the evaluation of SARS-CoV-2 structural nucleocapsid protein properties via computational approaches to generate high-affinity binding probes for effective diagnosis and targeted treatment applications by specific targeting of viruses. In addition, this article provides useful insights on the transmission behavior of the virus and creates new opportunities for theranostics development.     

Outbreaks of SARS-CoV-2 in naturally infected mink farms: Impact,transmission dynamics,genetic patterns,and environmental contamination

SARS-CoV-2 infection outbreaks in minks have serious implications associated with animal health and welfare, and public health. In two naturally infected mink farms (A and B) located in Greece, we investigated the outbreaks and assessed parameters associated with virus transmission, immunity, pathology, and environmental contamination. Symptoms ranged from anorexia and mild depression to respiratory signs of varying intensity. Although the farms were at different breeding stages, mortality was similarly high (8.4% and 10.0%). The viral strains belonged to lineages B.1.1.218 and B.1.1.305, possessing the mink-specific S-Y453F substitution. Lung histopathology identified necrosis of smooth muscle and connective tissue elements of vascular walls, and vasculitis as the main early key events of the acute SARS-CoV-2-induced broncho-interstitial pneumonia. Molecular investigation in two dead minks indicated a consistently higher (0.3–1.3 log₁₀ RNA copies/g) viral load in organs of the male mink compared to the female. In farm A, the infected farmers were responsible for the significant initial infection of 229 out of 1,000 handled minks, suggesting a very efficient human-to-mink transmission. Subsequent infections across the sheds wherein animals were being housed occurred due to airborne transmission. Based on a R₀ of 2.90 and a growth rate equal to 0.293, the generation time was estimated to be 3.6 days, indicative of the massive SARS-CoV-2 dispersal among minks. After the end of the outbreaks, a similar percentage of animals were immune in the two farms (93.0% and 93.3%), preventing further virus transmission whereas, viral RNA was detected in samples collected from shed surfaces and air. Consequently, strict biosecurity is imperative during the occurrence of clinical signs. Environmental viral load monitoring, in conjunction with NGS should be adopted in mink farm surveillance. The minimum proportion of minks that need to be immunized to avoid outbreaks in farms was calculated at 65.5%, which is important for future vaccination campaigns.     

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Mutational Pattern in the Fourth Pandemic Phase in Greece

The aim of this study is to investigate the circulating variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from Athens and from rural areas in Greece during July and August 2021. We also present a rapid review of literature regarding significant SARS-CoV-2 mutations and their impact on public health. A total of 2500 nasopharyngeal swab specimens were collected from suspected COVID-19 cases (definition by WHO 2021b). Viral nucleic acid extraction was implemented using an automatic extractor and the RNA recovered underwent qRT-PCR in order to characterize the specimens as positive or negative for SARS-CoV-2. The positive specimens were then used to identify specific Spike gene mutations and characterize the emerging SARS-CoV-2 variants. For this step, various kits were utilized. From the 2500 clinical specimens, 220 were tested positive for SARS-CoV-2 indicating a prevalence of 8.8% among suspected cases. The RT-PCR Ct (Cycle threshold) Value ranged from 19 to 25 which corresponds to medium to high copy numbers of the virus in the positive samples. From the 220 positive specimens 148 (67.3%) were from Athens and 72 (32.7%) from Greek rural areas. As far as the Spike mutations investigated: N501Y appeared in all the samples, D614G mutation appeared in 212 (96.4%) samples with a prevalence of 87.2% in Athens and 98.6% in the countryside, E484K had a prevalence of 10.8% and 12.5% in Athens and the rural areas, respectively. K417N was found in 18 (12.2%) samples from Athens and four (5.6%) from the countryside, P681H was present in 51 (34.5%) Athenian specimens and 14 (19.4%) specimens from rural areas, HV69-70 was carried in 32.4% and 19.4% of the samples from Athens and the countryside, respectively. P681R had a prevalence of 87.2% in Athens and 98.6% in rural areas, and none of the specimens carried the L452R mutation. 62 (28.2%) samples carried the N501Y, P681H, D614G and HV69-70 mutations simultaneously and the corresponding variant was characterized as the Alpha (UK) variant (B 1.1.7). Only six (2.7%) samples from the center of Athens had the N501Y, E484K, K417N and D614G mutations simultaneously and the virus responsible was characterized as the Beta (South African) variant (B 1.351). Our study explored the SARS-CoV-2 variants using RT-PCR in a representative cohort of samples collected from Greece in July and August 2021. The prevalent mutations identified were N501Y (100%), D614G (96.4%), P681R (90.1%) and the variants identified were the Delta (90.1%), Alpha (28.2%) and Beta (2.7%).     

Simultaneous monitoring of SARS-CoV-2 and bacterial profiles from the air of hospital environments with COVID-19-affected patients

Aerobiologia - The SARS-CoV-2 presence and the bacterial community profile in air samples collected at the Intensive Care Unit (ICU) of the Operational Unit of Infectious Diseases of Santa Caterina...     

A brief molecular insight of COVID-19: epidemiology,clinical manifestation,molecular mechanism,cellular tropism and immuno-pathogenesis

In December 2019, the emergence and expansion of novel and infectious respiratory virus SARS-CoV-2 originated from Wuhan, China caused an unprecedented threat to the public health and became a global pandemic. SARS-CoV-2 is an enveloped, positive sense and single stranded RNA virus belonging to genera betacoronavirus, of Coronaviridae family. The viral genome sequencing studies revealed 75–80% similarity with SARS-CoV. SARS-CoV-2 mainly affects the lower respiratory system and may progress to pneumonia and Acute Respiratory Distress Syndrome (ARDS). Apart from life-threatening situations and burden on the global healthcare system, the COVID-19 pandemic has imposed several challenges on the worldwide economics and livelihood. The novel pathogen is highly virulent, rapidly mutating and has a tendency to cross the species boundaries such as from bats to humans through the evolution and natural selection from intermediate host. In this review we tried to summarize the overall picture of SARS-CoV-2 including origin/ emergence, epidemiology, pathogenesis, genome organization, comparative analysis with other CoVs, infection and replication mechanism along with cellular tropism and immunopathogenesis which will provide a brief panoramic view about the virus and disease.

     

Transmission of community- and hospital-acquired SARS-CoV-2 in hospital settings in the UK: A cohort study

BackgroundNosocomial spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been widely reported, but the transmission pathways among patients and healthcare workers (HCWs) are unclear. Identifying the risk factors and drivers for these nosocomial transmissions is critical for infection prevention and control interventions. The main aim of our study was to quantify the relative importance of different transmission pathways of SARS-CoV-2 in the hospital setting.Methods and findingsThis is an observational cohort study using data from 4 teaching hospitals in Oxfordshire, United Kingdom, from January to October 2020. Associations between infectious SARS-CoV-2 individuals and infection risk were quantified using logistic, generalised additive and linear mixed models. Cases were classified as community- or hospital-acquired using likely incubation periods of 3 to 7 days. Of 66,184 patients who were hospitalised during the study period, 920 had a positive SARS-CoV-2 PCR test within the same period (1.4%). The mean age was 67.9 (±20.7) years, 49.2% were females, and 68.5% were from the white ethnic group. Out of these, 571 patients had their first positive PCR tests while hospitalised (62.1%), and 97 of these occurred at least 7 days after admission (10.5%). Among the 5,596 HCWs, 615 (11.0%) tested positive during the study period using PCR or serological tests. The mean age was 39.5 (±11.1) years, 78.9% were females, and 49.8% were nurses. For susceptible patients, 1 day in the same ward with another patient with hospital-acquired SARS-CoV-2 was associated with an additional 7.5 infections per 1,000 susceptible patients (95% credible interval (CrI) 5.5 to 9.5/1,000 susceptible patients/day) per day. Exposure to an infectious patient with community-acquired Coronavirus Disease 2019 (COVID-19) or to an infectious HCW was associated with substantially lower infection risks (2.0/1,000 susceptible patients/day, 95% CrI 1.6 to 2.2). As for HCW infections, exposure to an infectious patient with hospital-acquired SARS-CoV-2 or to an infectious HCW were both associated with an additional 0.8 infection per 1,000 susceptible HCWs per day (95% CrI 0.3 to 1.6 and 0.6 to 1.0, respectively). Exposure to an infectious patient with community-acquired SARS-CoV-2 was associated with less than half this risk (0.2/1,000 susceptible HCWs/day, 95% CrI 0.2 to 0.2). These assumptions were tested in sensitivity analysis, which showed broadly similar results. The main limitations were that the symptom onset dates and HCW absence days were not available.ConclusionsIn this study, we observed that exposure to patients with hospital-acquired SARS-CoV-2 is associated with a substantial infection risk to both HCWs and other hospitalised patients. Infection control measures to limit nosocomial transmission must be optimised to protect both staff and patients from SARS-CoV-2 infection.

In a cohort study, Mo Yin and colleagues investigate transmission of community- and hospital-acquired SARS-CoV-2 in hospital settings in the UK.     

Vaccinia virus Transmission through Experimentally Contaminated Milk Using a Murine Model

Bovine vaccinia (BV) is a zoonosis caused by Vaccinia virus (VACV), which affects dairy cattle and humans. Previous studies have detected the presence of viable virus particles in bovine milk samples naturally and experimentally contaminated with VACV. However, it is not known whether milk contaminated with VACV could be a route of viral transmission. However, anti-Orthopoxvirus antibodies were detected in humans from BV endemic areas, whom had no contact with affected cows, which suggest that other VACV transmission routes are possible, such as consumption of contaminated milk and dairy products. Therefore, it is important to study the possibility of VACV transmission by contaminated milk. This study aimed to examine VACV transmission, pathogenesis and shedding in mice orally inoculated with experimentally contaminated milk. Thirty mice were orally inoculated with milk containing 10⁷ PFU/ml of VACV, and ten mice were orally inoculated with uncontaminated milk. Clinical examinations were performed for 30 consecutive days, and fecal samples and oral swabs (OSs) were collected every other day. Mice were euthanized on predetermined days, and tissue and blood samples were collected. Nested-PCR, plaque reduction neutralization test (PRNT), viral isolation, histopathology, and immunohistochemistry (IHC) methods were performed on the collected samples. No clinical changes were observed in the animals. Viral DNA was detected in feces, blood, OSs and tissues, at least in one of the times tested. The lungs displayed moderate to severe interstitial lymphohistiocytic infiltrates, and only the heart, tonsils, tongue, and stomach did not show immunostaining at the IHC analysis. Neutralizing antibodies were detected at the 20^th and 30^th days post infection in 50% of infected mice. The results revealed that VACV contaminated milk could be a route of viral transmission in mice experimentally infected, showing systemic distribution and shedding through feces and oral mucosa, albeit without exhibiting any clinical signs.     

2020年湖北省襄阳市601份冷冻食品新冠肺炎病毒检测结果分析

自新冠疫情暴发以来,食品或其包装袋不断被检测出新型冠状病毒(SARS-CoV-2)核酸阳性,均与冷冻生鲜相关。为评估SARS-CoV-2污染冷冻食品的风险,本研究采集湖北省襄阳市各大商超、批发市场和餐饮企业的601批次冷冻食品进行新型冠状病毒核酸检测,分析国内外不同品种和不同经营场所的冷冻食品的新型冠状病毒核酸检测结果。结果显示,该601批次的冷冻食品的新型冠状病毒核酸检测结果全部为阴性。本研究提示,襄阳市的冷冻食品被SARS-CoV-2污染的风险较低,其作为SARS-CoV-2传染源的可能性较小。     

Avian influenza shedding patterns in waterfowl: implications for surveillance, environmental transmission, and disease spread

Despite the recognized importance of fecal/oral transmission of low pathogenic avian influenza (LPAI) via contaminated wetlands, little is known about the length, quantity, or route of AI virus shed by wild waterfowl. We used published laboratory challenge studies to evaluate the length and quantity of low pathogenic (LP) and highly pathogenic (HP) virus shed via oral and cloacal routes by AI-infected ducks and geese, and how these factors might influence AI epidemiology and virus detection. We used survival analysis to estimate the duration of infection (from virus inoculation to the last day virus was shed) and nonlinear models to evaluate temporal patterns in virus shedding. We found higher mean virus titer and longer median infectious period for LPAI-infected ducks (10-11.5 days in oral and cloacal swabs) than HPAI-infected ducks (5 days) and geese (7.5 days). Based on the median bird infectious dose, we found that environmental contamination is two times higher for LPAI- than HPAI-infectious ducks, which implies that susceptible birds may have a higher probability of infection during LPAI than HPAI outbreaks. Less environmental contamination during the course of infection and previously documented shorter environmental persistence for HPAI than LPAI suggest that the environment is a less favorable reservoir for HPAI. The longer infectious period, higher virus titers, and subclinical infections with LPAI viruses favor the spread of these viruses by migratory birds in comparison to HPAI. Given the lack of detection of HPAI viruses through worldwide surveillance, we suggest monitoring for AI should aim at improving our understanding of AI dynamics (in particular, the role of the environment and immunity) using long-term comprehensive live bird, serologic, and environmental sampling at targeted areas. Our findings on LPAI and HPAI shedding patterns over time provide essential information to parameterize environmental transmission and virus spread in predictive epizootiologic models of disease risks.     

From Deer-to-Deer: SARS-CoV-2 is efficiently transmitted and presents broad tissue tropism and replication sites in white-tailed deer

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) in humans, has a broad host range, and is able to infect domestic and wild animal species. Notably, white-tailed deer (WTD, Odocoileus virginianus), the most widely distributed cervid species in the Americas, were shown to be highly susceptible to SARS-CoV-2 in challenge studies and reported natural infection/exposure rates approaching 30–40% in free-ranging WTD in the U.S. Thus, understanding the infection and transmission dynamics of SARS-CoV-2 in WTD is critical to prevent future zoonotic transmission to humans, at the human-WTD interface during hunting or venison farming, and for implementation of effective disease control measures. Here, we demonstrated that following intranasal inoculation with SARS-CoV-2 B.1 lineage, WTD fawns (~8-month-old) shed infectious virus up to day 5 post-inoculation (pi), with high viral loads shed in nasal and oral secretions. This resulted in efficient deer-to-deer transmission on day 3 pi. Consistent a with lack of infectious SARS-CoV-2 shedding after day 5 pi, no transmission was observed to contact animals added on days 6 and 9 pi. We have also investigated the tropism and sites of SARS-CoV-2 replication in adult WTD (3–4 years of age). Infectious virus was detected up to day 6 pi in nasal secretions, and from various respiratory-, lymphoid-, and central nervous system tissues, indicating broad tissue tropism and multiple sites of virus replication. The study provides important insights on the infection and transmission dynamics of SARS-CoV-2 in WTD, a wild animal species that is highly susceptible to infection and with the potential to become a reservoir for the virus in the field.     

区级医院重症监护病区耐甲氧西林金黄色葡萄球菌的调查和分析

目的通过对区级医院重症监护病区耐甲氧西林金黄色葡萄球菌(MRSA)感染的流行初期进行调查和分析,以防止MRSA的暴发流行以及能够采取有效治疗措施。方法对2006年12月至2007年1月区级医院重症监护病区患者、医务人员及物体上送检标本中被MRSA感染的病例进行调查和分析。结果从重症监护病区患者、工作人员及物体上采集标本MRSA的感染阳性率分别为25%~47.6%、0%和20%。结论此次有局部暴发趋势的MRSA感染由于发现及时、措施得当被控制住。医院必须加强监督抗生素的合理用药和耐药性的检测,严格医务人员洗手及实行消毒隔离措施,切断传播途径,防止MRSA感染在医院的发生和流行。     

Plant Derived Antiviral Products for Potential Treatment of COVID-19: A Review

COVID-19 caused by SARS-CoV-2 is declared global pandemic. The virus owing high resemblance with SARS-CoV and MERS-CoV has been placed in family of beta-coronavirus. However, transmission and infectivity rate of COVID-19 is quite higher as compared to other members of family. Effective management strategy with potential drug availability will break the virus transmission chain subsequently reduce the pressure on the healthcare system. Extensive research trials are underway to develop novel efficient therapeutics against SARS-CoV-2. In this review, we have discussed the origin and family of coronavirus, structure, genome and pathogenesis of virus SARS-CoV-2 inside human host cell; comparison among SARS, MERS, SARS-CoV-2 and common flu; effective management practices; treatment with immunity boosters; available medication with ongoing clinical trials. We suggest medicinal plants could serve as potential candidates for drug development against COVID-19 infection.     

Impact of non-pharmaceutical interventions during the COVID-19 pandemic on common childhood respiratory viruses – An epidemiological study based on hospital data

Considering common childhood respiratory viruses and SARS-CoV-2 share similar transmission routes, non-pharmaceutical interventions (NPIs) to prevent SARS-CoV-2 may affect the epidemiology of respiratory viruses. Therefore, our study aimed to observe the epidemiologic characteristics of common childhood respiratory viruses in 2020 (after the pandemic) compared with 2019 (before the pandemic) in Hangzhou, China. The data were compared between 2019 and 2020 based on age and month, respectively. One or more viruses were detected in 3135/21452 (14.61%) specimens in 2019, which was significantly lower in 1110/8202 (13.53%) specimens in 2020. Respiratory syncytial virus (RSV) was the most commonly detected virus in 2019 and 2020. The positive rate of adenovirus (ADV), parainfluenza virus (PIV)1, PIV2, and PIV3 in 2020 was significantly decreased in 2019. In 2020, RSV replaced ADV as the most predominant virus in children aged 1–6 years, and the positive rate of influenza virus A (FluA), influenza virus B (FluB), PIV1, and PIV2 was not correlated to age. FluA, FluB, and PIV2 were not almost detected from February 2020. The positive rates of ADV and PIV1 were uncorrelated to the month in 2020. By strict NPIs, besides controlling the COVID-19 pandemic, incredible progress has been made to reduce the prevalence of common childhood respiratory viruses.