bodyType

customContents

entityId

printArticlePageQuery

filter

article

body

urlAlias

articleSectionsContent

articleSeoArticle

articleSourceHeaderArticle

contentSchemaRenderContent

contentSubHeadlineContent

contentHeadlineContent

mainImagePrintArticleArticle

authorBlockPrintArticleArticle

contentSponsorTagContent

articlePianoPaywallContent

scmpYoutubeContent

hooksTrackPageViewArticle

query printArticlePageQuery(
  $entityId: String!
  $customContents: [CustomContentInput]
  $bodyType: BodyFormatTypeEnum
) {
  article(filter: {entityId: $entityId}) {
    entityId
    body(customContents: $customContents, type: $bodyType) {
      json
    }
    urlAlias
    ...articleSectionsContent
    ...articleSeoArticle_3o8td4
    ...articleSourceHeaderArticle
    ...contentSchemaRenderContent
    ...contentSubHeadlineContent
    ...contentHeadlineContent
    ...mainImagePrintArticleArticle
    ...authorBlockPrintArticleArticle
    ...contentSponsorTagContent
    ...articlePianoPaywallContent
    ...scmpYoutubeContent
    ...hooksTrackPageViewArticle
    id
  }
}

fragment articlePianoPaywallContent on Content {
  __isContent: __typename
  ...hooksPaywallPromiseContent
}

fragment articleSectionsContent on Content {
  __isContent: __typename
  sections {
    value {
      ...helpersCheckIfNewsSectionInFirstIndexSection
      ...entityLink
      name
      id
    }
  }
}

fragment articleSeoArticle_3o8td4 on Article {
  ...hooksArticleSeoArticle
  ...helpersCheckIsPostiesArticle
  ...helpersGetArticleTypeArticle
  entityId
  publishedDate
  updatedDate
  summary {
    text
  }
  subHeadline {
    text
  }
  body(customContents: $customContents, type: $bodyType) {
    text
  }
  keywords
  sections {
    value {
      name
      id
    }
  }
  topics {
    name
    entityId
    id
  }
  urlAlias
  authors {
    name
    id
  }
  images {
    style(filter: {style: "768x768"}) {
      url
    }
  }
  readingTime
}

fragment articleSourceHeaderArticle on Article {
  urlAlias
  ...entityLink
}

fragment authorBlockPrintArticleArticle on Article {
  ...defaultArticleDateContent
  ...authorNamesArticle
}

fragment authorNameAuthor on Author {
  ...entityLink
  name
  entityUuid
}

fragment authorNamesArticle on Article {
  authorLocations
  authors {
    entityId
    location
    ...authorNameAuthor
    id
  }
}

fragment blockquoteQuoteContent on Content {
  __isContent: __typename
  ...contentShareWidgetContent
}

fragment checkersCheckContentContainsStarlingImageContent on Content {
  __isContent: __typename
  topics {
    entityId
    id
  }
}

fragment contentHeadlineContent on Content {
  __isContent: __typename
  headline
  socialHeadline
  ...contentHeadlineTagContent
  ...helpersUseContentSponsorContent
}

fragment contentHeadlineTagContent on Content {
  __isContent: __typename
  ...hooksContentHeadlineTagContent
}

fragment contentNewsletterWidgetContent on Content {
  __isContent: __typename
  topics {
    relatedNewsletters {
      ...helpersMassageToNewsletterItemNewsletter
      id
    }
    id
  }
  sections {
    value {
      relatedNewsletters {
        ...helpersMassageToNewsletterItemNewsletter
        id
      }
      id
    }
  }
  ... on Article {
    relatedNewsletters {
      ...helpersMassageToNewsletterItemNewsletter
      id
    }
  }
}

fragment contentSchemaRenderContent on Content {
  __isContent: __typename
  ...blockquoteQuoteContent
  ...imageContent
  ...inlineWidgetContent
  ...photoGalleryWidgetContent
  ...scmpYoutubeContent
}

fragment contentShareWidgetContent on Content {
  __isContent: __typename
  entityId
  urlAlias
  shortUrl
  socialHeadline
  headline
}

fragment contentSponsorTagContent on Content {
  __isContent: __typename
  ...helpersUseContentSponsorContent
}

fragment contentSubHeadlineContent on Content {
  __isContent: __typename
  subHeadline {
    json
  }
  summary {
    json
  }
  ...contentSchemaRenderContent
}

fragment defaultArticleDateContent on Content {
  __isContent: __typename
  ...hooksArticleDateUtilsContent
}

fragment entityLink on BaseWithApplicationAndUrlAlias {
  __isBaseWithApplicationAndUrlAlias: __typename
  __typename
  entityId
  entityUuid
  urlAlias
  urlRedirect {
    toUrl
    id
  }
  application {
    entityId
    id
  }
  ... on Section {
    fullSectionPath {
      entityId
      id
    }
    parentSection
  }
  ...helpersAppBarVariantBase
  ...helpersApplicationBase
  ...helpersCheckIsPlusArticle
  ...helpersStyleSectionContent
}

fragment helpersAppBarVariantBase on BaseWithApplicationAndUrlAlias {
  __isBaseWithApplicationAndUrlAlias: __typename
  ...helpersCheckIsLiveArticle
  ...helpersCheckIsPlusPage
  ...helpersCheckIsPostiesArticle
  ...helpersCheckIsPostiesPage
  ...helpersCheckIsPostMagazineArticle
  ...helpersCheckIsStyleArticle
  ...helpersSectionContent
  ...helpersStyleSectionContent
}

fragment helpersApplicationBase on BaseWithApplicationAndUrlAlias {
  __isBaseWithApplicationAndUrlAlias: __typename
  ...helpersCheckIsPostiesArticle
  ...helpersCheckIsPostiesPage
  ...helpersCheckIsPlusPage
}

fragment helpersCheckIfNewsSectionInFirstIndexSection on Section {
  name
}

fragment helpersCheckIsAmpEnabledArticle on Article {
  entityId
  types {
    value {
      entityId
      id
    }
  }
  sections {
    value {
      entityId
      id
    }
  }
  disableOffPlatformContent
  sponsorType
  published
  ...helpersCheckIsPlusArticle
  ...helpersCheckIsPostiesArticle
}

fragment helpersCheckIsLiveArticle on Article {
  flattenTypeIds
  liveArticle {
    status
    id
  }
}

fragment helpersCheckIsMainTopicContent on Content {
  __isContent: __typename
  topics {
    entityId
    id
  }
}

fragment helpersCheckIsPlusArticle on Content {
  __isContent: __typename
  ... on Article {
    paywallTypes {
      entityUuid
      id
    }
  }
}

fragment helpersCheckIsPlusPage on Page {
  urlAlias
}

fragment helpersCheckIsPostMagazineArticle on Article {
  sections {
    value {
      entityId
      id
    }
  }
}

fragment helpersCheckIsPostiesArticle on Article {
  sections {
    value {
      entityId
      id
    }
  }
}

fragment helpersCheckIsPostiesPage on Page {
  urlAlias
}

fragment helpersCheckIsStyleArticle on Content {
  __isContent: __typename
  sections {
    value {
      entityId
      id
    }
  }
}

fragment helpersGetArticleTypeArticle on Content {
  __isContent: __typename
  ... on Article {
    types {
      value {
        entityId
        id
      }
    }
  }
}

fragment helpersMassageToNewsletterItemNewsletter on Newsletter {
  entityId
  name
  alternativeName
  description {
    text
  }
  summary {
    text
  }
  homepageDescription {
    text
  }
}

fragment helpersSanitizeArticleTypeEntityIdsArticle on Article {
  types {
    value {
      entityId
      id
    }
  }
}

fragment helpersSanitizeAuthorTypesArticle on Article {
  authors {
    types
    id
  }
}

fragment helpersSanitizedAuthorEntityIdsArticle on Article {
  authors {
    entityId
    id
  }
}

fragment helpersSectionContent on Section {
  fullSectionPath {
    entityId
    id
  }
}

fragment helpersStyleSectionContent on Section {
  fullSectionPath {
    entityId
    id
  }
}

fragment helpersUseContentSponsorContent on Content {
  __isContent: __typename
  topics {
    entityId
    sponsor {
      ...sponsorTagSponsor
      name
      type
      id
    }
    id
  }
  ... on Article {
    sponsorType
  }
  ...helpersCheckIsMainTopicContent
}

fragment hooksArticleDateUtilsContent on Content {
  __isContent: __typename
  createdDate
  publishedDate
  updatedDate
}

fragment hooksArticleSeoArticle on Article {
  ...helpersCheckIsPostiesArticle
  ...helpersCheckIsPostMagazineArticle
  ...helpersCheckIsStyleArticle
  ...hooksContentHeadlineTagContent
  ...helpersCheckIsAmpEnabledArticle
  entityId
  headline
  socialHeadline
  types {
    value {
      entityId
      id
    }
  }
  authors {
    entityId
    id
  }
  images {
    generic_og: style(filter: {style: "og_image_scmp_generic"}) {
      url
    }
    styles(filter: {styles: ["og_image_posties_article", "og_postmag", "og_image_style", "og_image_scmp_analysis", "og_image_scmp_explainer", "og_image_scmp_editorial", "og_image_scmp_fact_check", "og_image_scmp_debate", "og_image_scmp_live", "og_image_scmp_obituary", "og_image_scmp_opinion", "og_image_scmp_review", "og_image_scmp_series", "og_image_scmp_generic"]}) {
      url
      style
    }
    type
  }
  urlAlias
}

fragment hooksContentHeadlineTagContent on Content {
  __isContent: __typename
  __typename
  ... on Article {
    types {
      value {
        name
        entityId
        description {
          text
        }
        id
      }
    }
    ...helpersCheckIsStyleArticle
  }
  flag
  sections {
    value {
      name
      id
    }
  }
  ...hooksContentHelperContent
}

fragment hooksContentHelperContent on Content {
  __isContent: __typename
  ...helpersSanitizeArticleTypeEntityIdsArticle
  ...helpersSanitizeAuthorTypesArticle
  ...helpersSanitizedAuthorEntityIdsArticle
  flag
}

fragment hooksPaywallPromiseContent on Content {
  __isContent: __typename
  entityId
  ...helpersCheckIsPostiesArticle
}

fragment hooksTrackPageViewArticle on Article {
  entityId
  publishedDate
  headline
  sections {
    value {
      name
      id
    }
  }
  urlAlias
  authors {
    name
    id
  }
  entityUuid
}

fragment imageContent on Content {
  __isContent: __typename
  headline
  ...checkersCheckContentContainsStarlingImageContent
}

fragment inlineWidgetContent on Content {
  __isContent: __typename
  ...contentNewsletterWidgetContent
}

fragment mainImagePrintArticleArticle on Article {
  images {
    title
    url
    isSlideshow
    size_652x446: style(filter: {style: "652x446"}) {
      url
    }
  }
}

fragment photoGalleryDialogContent on Content {
  __isContent: __typename
  __typename
  ...contentShareWidgetContent
}

fragment photoGalleryWidgetContent on Content {
  __isContent: __typename
  ...photoGalleryDialogContent
}

fragment scmpYoutubeContent on Content {
  __isContent: __typename
  entityId
  urlAlias
  publishedDate
}

fragment sponsorTagSponsor on Sponsor {
  name
  type
  images {
    url
  }
}


sections

types

disableOffPlatformContent

sponsorType

published

headline

socialHeadline

authors

images

publishedDate

updatedDate

summary

subHeadline

keywords

topics

readingTime

authorLocations

entityUuid

The Conversation

New variants of SARS-CoV-2 have now evaded New Zealand’s border protections twice to spread into the community. In the most recent outbreak, which placed Auckland into an alert level 3 lockdown for three days, there were active community cases of the more infectious B.1.1.7 lineage.
While we have seen the virus mutate over the entire course of the pandemic, it was not until mid-December 2020 that variants with measurably different behaviour emerged.
There are several reasons for this, including the continued exponential rise in cases globally. Every Covid-19 case gives the virus a chance to mutate, and if the number of infections continues to rise, more new variants are likely to emerge.
Auckland lockdown ends, Japan starts coronavirus vaccine roll-out
PRESSURE TO MUTATE
The genetic code of SARS-CoV-2 is a string of RNA of about 30,000 bases, or letters. When the virus enters our cells, it hijacks them to make thousands of copies of itself, but the copying process is not perfect.
Mistakes, or mutations, happen on average once every couple of weeks in any chain of transmission. Most are changes in a single letter and do not result in a notable difference, but some will change the physical form of the virus, with possible knock-on effects to how the new variant behaves.
We know about these variants thanks to the sequencing efforts from different countries and their open sharing of this knowledge. The variants that have arisen recently – known as B.1.1.7 (first identified in the UK), B.1.351 (identified in South Africa) and P.1 (identified in Brazil) – all have a large number of mutations that have physically altered the virus.
A number of these changes are on the outside of the virus, in the spike proteins it uses to infect cells. Such changes can also undermine our immune system’s ability to detect these new versions of the virus when it has only seen the old version.
The most obvious reason new variants have been emerging recently is that the number of global cases increased massively in the last quarter of 2020. There were about 35 million cases recorded worldwide in the first nine months of 2020, but it took just two months to double that number. We are well on the way to doubling that number again soon.


EVADING RISING LEVELS OF IMMUNITY
A second reason is that the virus is responding to immunity that has started to build up in the population. Our immune system plays an important role in driving which mutations survive and are transmitted.
The immune system is constantly trying to identify and kill the virus, which can only infect new people if it escapes detection. While mutations occur randomly, ones that lead to a more transmissible variant or those that escape our immune system are preferentially selected and more likely to persist.
The mutations that characterise B.1.1.7, B.1.351 and P.1 have been shown to spread faster (especially B.1.1.7) and initial evidence points to a difference in the immune response (though not in B.1.1.7).
Another indication that immunity plays a big role is that the B.1.351 and P.1 variants came to prominence in areas with large first waves of Covid-19 where the population developed higher levels of immunity.
Explainer | Are new coronavirus strains cause for concern?
P.1 was identified in Brazil where up to 70 per cent of the population were infected during the first wave. B.1.351 quickly became the dominant strain in the Eastern Cape region of South Africa which was similarly hard hit.
The new variants could infect a greater number of people than the original wild type of the virus, which might infect only people who had never been infected before.
This is one of the reasons why historically herd immunity for a new virus has not occurred through “natural disease progression” but only through vaccination.
New coronavirus cases down 16 per cent last week, says WHO
The final part of the story is the fact that two of these variants (B.1.1.7 and P.1) differ by as many as 25 mutations from the closest known SARS-CoV-2 sequences. This is very unusual given that most viral sequences we see are within just a few mutations of others.
Such a rapid increase in diversity has been observed in chronic Covid-19 infections in immunocompromised hosts. Most people are ill for a week or two, but a few have to fight the disease for months. During that time, the virus continues to evolve, sometimes very quickly as a weakened immune system presents all sorts of challenges to the virus but fails to kill it off.
This kind of infection presents a “training ground” for the virus, as it continually adapts.


WILL WE SEE MORE NEW VARIANTS?
As long as the virus is around, it will continue to mutate. With vaccine protection and natural immunity in a growing number of people, there is greater pressure on virus variants that evade our immune defences.
The rate of new mutations varies greatly between viruses. The overall mutation rate of SARS-CoV-2 is about half that of the influenza virus and much slower than HIV. But the overall mutation rate does not tell us everything. What really matters is the rate of mutations that physically alter the virus.
There is some early evidence this rate is about the same in SARS-CoV-2 as in influenza viruses. One reason for this is that SARS-CoV-2 has only recently jumped to people and is not yet “optimised” to spread in humans.
A year after the Covid-19 pandemic began, Wuhan is a city of forgetting
Essentially the original virus was only a few mutations away from better fitness, and there may be further easy changes that could make it even better adapted to humans. Once the virus is through this initial adaptation phase, there will be fewer opportunities for easy, fitness-improving changes and new variants may appear less frequently.
The variants that have been characterised so far are likely only a small subset of those in circulation. It is no coincidence they are known from countries with comprehensive sequencing programmes (notably the UK).
Boris Johnson says world needs pandemic treaty, citing China’s Wuhan
But the new variants are not the main driver of transmission globally. Most of the world is still susceptible to any variant of SARS-CoV-2, including the original version. The protective measures used successfully in Aotearoa (New Zealand) to control the virus continue to work for any variant.
The best way to protect against all current variants and to prevent the emergence of further variants is to drive down the number of cases through ongoing control measures and vaccination.
Authored by David Welch (Senior Lecturer, University of Auckland); Jemma Geoghegan (Senior Lecturer and Associate Scientist at ESR, University of Otago); Joep de Ligt (Science Lead Genomics & Bioinformatics, ESR) and Nigel French (Professor of Food Safety and Veterinary Public Health, Massey University)

This article is republished from The Conversation under a Creative Commons licence. Read the original article.



Why more contagious Covid-19 variants are emerging

A Covid-19 particle is pictured in this image provided by the Centers for Disease Control and Prevention. Photo: CDC/TNS

This Week in Asia

Explained

Coronavirus

Explainers & FAQs

Health & Medicine


Coronavirus mutations emerged as case numbers soared worldwide and as the virus responded to immunity that started to build up in the population
The best way to protect against current variants and prevent new ones is to reduce cases through ongoing control measures and vaccination



Coronavirus mutations emerged as the number of cases soared globally and as the virus responded to immunity that started to build up in the population.


Coronavirus pandemic

Coronavirus pandemic: All stories

Disease

Coronavirus vaccine

Provide background, definition and detail of a specific topic, helping the reader understand how something works or what has happened in the past.  (Eg. What is Nafta? US and Mexico are on the verge of revising trade deal.)


Explainer

Explainer | Why more contagious Covid-19 variants are emerging

Coronavirus mutations emerged as case numbers soared worldwide and as the virus responded to immunity that started to build up in the population The best way to protect against current variants and prevent new ones is to reduce cases through ongoing control measures and vaccination

Coronavirus mutations emerged as case numbers soared worldwide and as the virus responded to immunity that started to build up in the population

The best way to protect against current variants and prevent new ones is to reduce cases through ongoing control measures and vaccination