How genomics will help us track Covid-19


New Zealand has found itself suddenly plunged into a dire situation: Four new cases of Covid-19 in the community with no obvious link to the border, managed isolation and quarantine facilities or overseas travel.

While contact tracing is underway to attempt to find out who infected yesterday’s four cases and search for more links to the border, it could still come up blank. Contact tracing will never be perfect and the Government is even investigating the possibility that the virus came in a cooled shipping container from overseas, rather than via a person who crossed the border on an Air New Zealand flight.

Given this, the Government has turned to a new tool in its arsenal.

“I should add that we are also doing genome sequencing on all those who have tested positive and our recent cases and current cases in managed isolation and quarantine,” Director-General of Health Ashley Bloomfield said on Wednesday.

“That will help us track where this virus may have arisen from and then gotten out into the community.”

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Why Does COVID Make Some People So Sick, Ask Their Genome

Authors: Megan Molteni i

SARS-COV-2,the pandemic coronavirus that surfaced for the first time in China last year, is an equal opportunity invader. If you’re a human, it wants in. Regardless of age, race, or sex, the virus appears to infect people at the same rate. Which makes sense, given that it’s a totally new pathogen against which approximately zero humans have preexisting immunity.

But the disease it causes, Covid-19, is more mercurial in its manifestations. Only some infected people ever get sick. Those who do experience a wide range of symptoms. Some get fever and a cough. For others it’s stomach cramps and diarrhea. Some lose their appetite. Some lose their sense of smell. Some can wait it out at home with a steady diet of fluids and The Great British Baking Show. Others drown in a sea of breathing tubes futilely forcing air into their flooded lungs. Old people, those with underlying conditions, and men make up the majority of the casualties. But not always. In the US, an alarmingly high fraction of those hospitalized with severe symptoms are adults under the age of 40. Kids, and in particular infants, aren’t invincible either.

To understand what accounts for these differences, scientists have been scouring the patchy epidemiological data coming out of hotspots like China, Italy, and the US, looking for patterns in patients’ age, race, sex, socioeconomic status, behaviors, and access to health care. And now, they’re starting to dig somewhere else for clues: your DNA.

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Authors: Seth C Inzaule, Alan Christoffels, Yenew Kebede, Tulio de Oliveira, Ahmed E Ogwell Ouma

Timely sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coupled with rapid data sharing has allowed researchers to develop counter-measures against the virus such as diagnostic tests and vaccines,1 and assess transmission and evolution dynamics as the virus spreads globally. Despite the minimal resources available in the African continent, local experts have risen to the challenge and adopted genomics-based surveillance to guide the outbreak response.2 As of June 19, 2020, a total of 568 SARS-CoV-2 genome sequences had been shared from 12 African countries and are providing insight into the ongoing epidemiology of the virus.Early findings from genome sequencing have shown that SARS-CoV-2 strains circulating in Africa are assigned to 20 imported lineages, ranging from three lineages in Nigeria to ten in Kenya.34 The majority of the SARS-CoV-2 sequences are of B.1 (65%) and B.1.1 (15%) lineages, which are thought to be predominantly of European origin (appendix). The next most predominant lineage was A (5%), which originated in China. Therefore, sequencing has revealed that multiple lineages have been introduced into the continent.

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The hallmarks of COVID-19 disease

Authors: Daolin Tang ,Paul Comish,Rui Kang 

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a novel coronavirus that has caused a worldwide pandemic of the human respiratory illness COVID-19, resulting in a severe threat to public health and safety. Analysis of the genetic tree suggests that SARS-CoV-2 belongs to the same Betacoronavirus group as severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). Although the route for viral transmission remains a mystery, SARS-CoV-2 may have originated in an animal reservoir, likely that of bat. The clinical features of COVID-19, such as fever, cough, shortness of breath, and fatigue, are similar to those of many acute respiratory infections. There is currently no specific treatment for COVID-19, but antiviral therapy combined with supportive care is the main strategy. Here, we summarize recent progress in understanding the epidemiological, virologic, and clinical characteristics of COVID-19 and discuss potential targets with existing drugs for the treatment of this emerging zoonotic disease.

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Pathophysiology of COVID-19: Mechanisms Underlying Disease Severity and Progression

Authors: Mary Kathryn BohnAlexandra HallLusia SepiashviliBenjamin JungShannon Steele, and Khosrow Adeli


The global epidemiology of coronavirus disease 2019 (COVID-19) suggests a wide spectrum of clinical severity, ranging from asymptomatic to fatal. Although the clinical and laboratory characteristics of COVID-19 patients have been well characterized, the pathophysiological mechanisms underlying disease severity and progression remain unclear. This review highlights key mechanisms that have been proposed to contribute to COVID-19 progression from viral entry to multisystem organ failure, as well as the central role of the immune response in successful viral clearance or progression to death.

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Features, Evaluation, and Treatment of Coronavirus (COVID-19)

Authors: Marco Cascella; Michael Rajnik; Abdul Aleem; Scott C. Dulebohn; Raffaela Di Napoli.

Coronavirus disease 2019 (COVID-19), the highly contagious infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has had a catastrophic effect on the world’s demographics resulting in more than 2.9 million deaths worldwide, emerging as the most consequential global health crisis since the era of the influenza pandemic of 1918.


  • Identify the etiology and epidemiology of COVID-19.
  • Describe the clinical features and radiological findings expected in patients with COVID-19.
  • Summarize the latest available treatment in the management of COVID-19, including the different vaccines available to prevent COVID-19.
  • Discuss interprofessional team strategies for improving care coordination and communication to care for patients with coronavirus and improve outcomes.

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