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2020 Top 50 SARS-CoV-2 Articles

The 50 most downloaded Nature Communications articles* on SARS-CoV-2 published in 2020 illustrate the collaborative efforts of the international community to combat the ongoing pandemic. These papers highlight valuable research into the biology of coronavirus infection, its detection, treatment as well as into vaccine development and the epidemiology of the disease.

Browse all Top 50 subject area collections here.

* Data obtained from SN Insights (based on Digital Science's Dimensions) and has been normalised to account for articles published later in the year.

1-25

Anecdotal reports suggest potential severity and outcome differences between sexes following infection by SARS-CoV-2. Here, the authors perform meta-analyses of more than 3 million cases collected from global public data to demonstrate that male patients with COVID-19 are 3 times more likely to require intensive care, and have ~40% higher death rate.

Article | Open Access | | Nature Communications

Syndromic surveillance for COVID-19 could help to identify areas with increasing transmission. Here, the authors show that increased reports of changes in smell and taste measured at the population level are correlated with the increased COVID-19-related hospital admissions.

Article | Open Access | | Nature Communications

New Zealand implemented stringent COVID-19 control measures early after identification of its first case. Here, the authors perform whole genome sequencing of samples taken until 22 May 2020 and find high viral diversity indicative of multiple separate introductions and limited community transmission.

Article | Open Access | | Nature Communications

Vaccines and targeted therapeutics for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are currently lacking. Here, the authors report a human monoclonal antibody capable of neutralizing both authentic SARS-CoV and SARS-CoV-2 by targeting a common epitope.

Article | Open Access | | Nature Communications

Congenital infection of SARS-CoV-2 has been described, but the transmission routes remain unclear. Here, the authors report evidence of transplacental transmission of SARS-CoV-2 in a neonate born to a mother infected in the last trimester and presenting with neurological compromise.

Article | Open Access | | Nature Communications

The COVID-19 pandemic has stopped many human activities, which has had significant impact on emissions of greenhouse gases. Here, the authors present daily estimates of country-level CO2 emissions for different economic sectors and show that there has been a 8.8% decrease in global CO2 emissions in the first half of 2020.

Article | Open Access | | Nature Communications

In this study, Massachusetts Consortium for Pathogen Readiness (MassCPR) investigators assess the relationship between SARS-CoV-2 viral load and COVID-19 disease severity and report that the levels of detectable viral RNA, especially in plasma, correlates with severity of respiratory disease, inflammatory markers and predicted risk of death.

Article | Open Access | | Nature Communications

Early identification of COVID-19 patients at risk of progression may facilitate more individually aligned treatment plans. Here the authors develop an online nomogram incorporating CT severity score and clinical characteristics for early predicting the disease progression risk among COVID-19 pneumonia patients.

Article | Open Access | | Nature Communications

SARS-CoV-2 infection is widely diagnosed by RT-PCR, but RNA extraction is a bottleneck for fast and cheap diagnosis. Here, the authors develop protocols to perform RT-PCR directly on heat-inactivated subject samples or samples lysed with readily available detergents and benchmark performance against 597 clinically diagnosed patient samples.

Article | Open Access | | Nature Communications

Children with SARS-CoV-2 infection are more likely to have mild symptoms and may be asymptomatic, but underlying reasons remain unclear. Here, the authors show cellular, cytokine and antibody response to SARS-CoV-2 infection in three children who repeatedly tested negative for the virus by PCR, despite high exposure in the household.

Article | Open Access | | Nature Communications

Coronavirus main protease is essential for viral polyprotein processing and replication. Here Vuong et al. report efficient inhibition of SARS-CoV-2 replication by the dipeptide-based protease inhibitor GC376 and its parent GC373, which were originally used to treat feline coronavirus infection.

Article | Open Access | | Nature Communications

Antibody mediated immunity to SARS-CoV-2 will affect future transmission and disease severity. This systematic review on antibody response to coronaviruses, including SARS-CoV-2, SARS-CoV, MERS-CoV and endemic coronaviruses provides insights into kinetics, correlates of protection, and association with disease severity.

Article | Open Access | | Nature Communications

There is currently no licensed SARS-CoV-2 vaccine. Here, the authors generate an optimized DNA vaccine candidate encoding the SARS-CoV-2 spike antigen, demonstrating induction of specific T cells and neutralizing antibody responses in mice and guinea pigs. These initial results support further development of this vaccine candidate.

Article | Open Access | | Nature Communications

SARS-CoV-2 variants with spike (S)-protein D614G mutations currently predominate globally. Here, Zhang et al. hypothesize that D614G variant may increase infectivity by increasing S protein abundance on the virion since pseudoviruses carrying S-G614 incorporate higher amounts of S protein and enter cells more efficiently than those carrying S-D614.

Article | Open Access | | Nature Communications

Remdesivir is under evaluation for treatment of COVID-19 in clinical trials. Here, the authors report results of remdesivir treatment in a patient with COVID-19 and the genetic antibody deficiency XLA. They show a temporally correlated clinical and virological response, suggesting that remdesivir can reduce SARS-CoV-2 replication in patients.

Article | Open Access | | Nature Communications

SARS-CoV-2 can infect cats and dogs, but the extent to which pets are infected in households remains unclear. Here, Patterson et al. test 919 companion animals in northern Italy and find that some dogs and cats from COVID-19 positive households can test positive for COVID-19 neutralizing antibodies, with dogs significantly more likely to do so if they came from COVID-19 positive households.

Article | Open Access | | Nature Communications

Understanding antibody responses to Sars-CoV-2 proteins over time is complicated by many variables. Here the authors survey IgM and IgG antibodies against S protein, RBD and nucleoprotein in a large cohort of infected and recovering severe vs. moderate COVID-19 patients, comparing against clinical parameters and immunological readouts.

Article | Open Access | | Nature Communications

26-50

During SARS-CoV-2 replication subgenomic RNAs (sgRNA) are transcribed and subsequently translated into viral proteins. Here, Alexandersen et al. provide evidence that sgRNA is not necessarily an indicator for active viral replication, but can be detected up to 17 days after symptom onset in clinical samples.

Article | Open Access | | Nature Communications

Although many COVID-19 cases are mild, most information about symptoms is derived from hospitalized patients. Here, the authors link self-reported symptom surveys to primary care data to describe the longitudinal dynamics of COVID-19 in non-hospitalized individuals.

Article | Open Access | | Nature Communications

Many published studies of the current SARS-CoV-2 pandemic have analysed data from non-representative samples from populations. Here, using UK BioBank samples, Gibran Hemani and colleagues discuss the potential for such studies to suffer from collider bias, and provide suggestions for optimising study design to account for this.

Article | Open Access | | Nature Communications

Here, the authors generate a replication-competent VSV based vaccine expressing SARS-CoV-2 spike protein and show protection in the hamster model with one dose. Analysis of the antibody response in mice shows induction of neutralizing antibodies and suggests a desirable Th1-biased response to the vaccine.

Article | Open Access | | Nature Communications

Specific non-structural proteins (nsp) of SARS coronaviruses are involved in methylation of virally encoded mRNAs to mimic cellular mRNAs for protection against host innate immune restriction. Here, the authors present a high resolution structure of SARS-CoV-2 nsp16/nsp10 ternary complex in the presence of cognate RNA substrate analogue and methyl donor, S-adenosyl methionine, revealing unique ligand-binding sites that may represent alternative targets for antiviral development.

Article | Open Access | | Nature Communications

Remdesivir (RDV) is a broad-spectrum antiviral drug with activity against MERS coronavirus, but in vivo efficacy has not been evaluated. Here, the authors show that RDV has superior anti-MERS activity in vitro and in vivo compared to combination therapy with lopinavir, ritonavir and interferon beta and reduces severe lung pathology.

Article | Open Access | | Nature Communications

A high-throughput platform would greatly facilitate coronavirus disease 2019 (COVID-19) serological testing and antiviral screening. To address this, Shi and colleagues present a high-throughput nanoluciferase severe respiratory syndrome coronavirus 2 (SARS-CoV2-Nluc), and show that it has potential for large-scale vaccine evaluation and neutralizing antibody testing.

Article | Open Access | | Nature Communications

Nanopore sequencing (ONT) has been used in SARS-CoV-2 studies, however adoption of ONT for SARS-CoV-2 surveillance has been limited due to common concerns around sequencing accuracy. Here, the authors perform a comprehensive evaluation of ONT analytical performance on 157 matched SARS-CoV-2-positive patient specimens and synthetic RNA controls.

Article | Open Access | | Nature Communications

Understanding the pathology in the lungs of patients with COVID-19 might provide clues as to the susceptibility of patients and how the SARS-CoV-2 virus can be fatal. Here the authors analyze cadaveric pulmonary tissue and show one group with high viral load, early death, inflammation and inflammatory damage, and another with low viral load, longer duration of disease, and more M2-like polarization and fibrotic lung damage.

Article | Open Access | | Nature Communications

How COVID-19 pathology differs from other drivers of pneumonia is unclear. Here the authors analyze urine from patients with COVID-19 and identify an immunosuppressive protein expression pattern that is distinct from the pattern in healthy individuals or patients with non-COVID-19 pneumonia.

Article | Open Access | | Nature Communications

There is ongoing debate about the effective combination of strategies for COIVD-19 control. Here, the authors use an agent-based model to quantify and compare several intervention strategies, and identify minimal levels of social distancing compliance required to control the epidemic in Australia.

Article | Open Access | | Nature Communications

Bats are a likely reservoir of zoonotic coronaviruses (CoVs). Here, analyzing bat CoV sequences in China, the authors find that alpha-CoVs have switched hosts more frequently than betaCoVs, identify a bat family and genus that are highly involved in host-switching, and define hotspots of CoV evolutionary diversity.

Article | Open Access | | Nature Communications

The SARS-CoV-2 viral genome is encapsulated by the nucleocapsid protein (NSARS-CoV-2) that is essential for viral replication. Here, the authors show that RNA induces liquid-liquid phase separation of NSARS-CoV-2 and how NSARS-CoV-2 phosphorylation modulates RNA-binding and phase separation and that these RNA/NSARS-CoV-2-droplets recruit and concentrate the SARS-CoV-2 RNA-dependent RNA polymerase complex in vitro, which would enable high initiation and elongation rates during viral transcription.

Article | Open Access | | Nature Communications

Detailed knowledge of the characteristics of COVID-19 patients helps with public health planning. Here, the authors use routinely-collected data from seven databases in three countries to describe the characteristics of >30,000 patients admitted with COVID-19 and compare them with those admitted for influenza in previous years.

Article | Open Access | | Nature Communications

The immunopathological features of SARS-CoV-2 infection in the lungs remain unclear. Here, the authors provide a comprehensive characterization of post mortem lung tissues of COVID-19 patients and find two distinct patterns characterized by differential expression of interferon stimulated genes (ISGs), which correlate to viral loads, cytokines, lung damage and time of hospitalization, suggesting ISG profiles to mark disease progression

Article | Open Access | | Nature Communications

Here, the authors sample air and surfaces in hospital rooms of COVID-19 patients, detect SARS-CoV-2 RNA in air samples of two of three tested airborne infection isolation rooms, and find surface contamination in 66.7% of tested rooms during the first week of illness and 20% beyond the first week of illness.

Article | Open Access | | Nature Communications

Finding effective treatments for COVID-19 depends upon understanding genetic regulation of proteins involved in SARS-CoV-2 infection and host response. Here, the authors identify genetic variants linked to expression of such proteins, data which could lead to the discovery of therapeutic targets.

Article | Open Access | | Nature Communications

Large population testing is a key step to controlling the COVID-19 pandemic. Here, the authors develop a targeted mass spectrometry system for peptide-based SARS-CoV-2 detection, allowing analysis of over 500 swab samples per day and enabling virus detection even after prolonged sample storage at room temperature.

Article | Open Access | | Nature Communications

A vaccine protecting from SARS-CoV-2 infection is needed. Here the authors generate a replication-incompetent adenovirus based vaccine expressing SARS-CoV-2 spike, show protection from infection in non-human primates, and analyze the immune response after intramuscular and intranasal vaccination.

Article | Open Access | | Nature Communications

Here, the authors isolate several nanobodies from a synthetic library that bind the receptor-binding domain (RBD) of SARS-CoV-2 spike protein (S) and neutralize S pseudotyped viruses. Cryo-EM structure of Spike with one nanobody and further biophysical analysis shows competition with ACE2 binding.

Article | Open Access | | Nature Communications